A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

A_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
The "A" chromosome of a pair, sometimes of three.
A_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
abbreviation - Variable in class org.concord.util.CCUnit
 
aboutToQuit() - Method in class org.concord.collisions.ui.GUIElementsFrame
 
aboutToQuit() - Method in class org.concord.collisions.ui.GUITestIngrid
 
aboutToQuit() - Method in class org.concord.collisions.ui.IngridProblem
 
abs(double) - Method in class org.concord.flash.player.builtin.FMath
 
accept(File) - Method in class org.concord.biologica.ui.WorldFileFilter
 
accept(File) - Method in class org.concord.biologica.ui.XMLFileFilter
 
accept(File) - Method in class org.concord.biologica.ui.SpeciesFileFilter
 
accept(File) - Method in class org.concord.biologica.ui.GifFileFilter
 
acos(double) - Method in class org.concord.flash.player.builtin.FMath
 
ACTION - Static variable in class org.concord.util.LogProcess
 
actionPerformed(ActionEvent) - Method in class org.concord.util.PathDialog
 
actionPerformed(ActionEvent) - Method in class org.concord.util.Editor
 
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.PedigreeView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.DNAView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.AllInOneView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.ToolView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.biologica.ui.SexView
React to actions
actionPerformed(ActionEvent) - Method in class org.concord.collisions.engine.JPartWorld
called by CCTimer
actionPerformed(ActionEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
actionPerformed(ActionEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
actionPerformed(ActionEvent) - Method in class org.concord.collisions.ui.IngridProblem
 
actionPerformed(ActionEvent) - Method in class org.concord.collisions.ui.DataCrossPanel
 
actionPerformed(ActionEvent) - Method in class org.concord.collisions.ui.GUIPanel
Deprecated.  
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.CustomTableQuestion
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.HTMLViewCustomizer
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.LoginPanel
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.TableInputView
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.VariableDialog
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.LogView
 
actionPerformed(ActionEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
actions - Variable in class org.concord.flash.player.FMovieBuilder.ActionsBuilder
 
activate() - Method in class org.concord.collisions.engine.JDaemon
 
activate() - Method in class org.concord.collisions.engine.CCImpulseForce
 
activate() - Method in class org.concord.pedagogica.engine.ActivityArc
 
activateFrame(JInternalFrame) - Method in class org.concord.util.Editor.EditorDesktopManager
 
activationSteps - Variable in class org.concord.collisions.engine.JDaemon
 
ACTIVE_TOOL - Static variable in class org.concord.biologica.ui.UIProp
The active tool in a view has changed.
activeColor - Variable in class org.concord.collisions.engine.JDaemon
 
activity - Variable in class org.concord.util.LogProcess
 
activity - Variable in class org.concord.pedagogica.engine.Logging
 
activity - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
activity - Variable in class org.concord.pedagogica.ui.ActivityView
 
Activity - class org.concord.pedagogica.engine.Activity.
header - edit "Data/yourJavaHeader" to customize contents - edit "EventHandlers/Java file/onCreate" to customize
ACTIVITY - Static variable in class org.concord.util.LogProcess
 
Activity() - Constructor for class org.concord.pedagogica.engine.Activity
 
Activity(Activity) - Constructor for class org.concord.pedagogica.engine.Activity
 
Activity(NodeAccess, String) - Constructor for class org.concord.pedagogica.engine.Activity
 
ActivityAccess - interface org.concord.pedagogica.engine.ActivityAccess.
 
activityAlias - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
ActivityArc - class org.concord.pedagogica.engine.ActivityArc.
 
ActivityArc(Activity) - Constructor for class org.concord.pedagogica.engine.ActivityArc
Primary constructor for arc object in Activity state machine.
ActivityArc(Activity, ActivityNode, ActivityNode) - Constructor for class org.concord.pedagogica.engine.ActivityArc
 
ActivityArcItem - class org.concord.pedagogica.ui.ActivityArcItem.
 
ActivityArcItem(ActivityNodeItem) - Constructor for class org.concord.pedagogica.ui.ActivityArcItem
 
activityColor - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
ActivityErrorHandler - interface org.concord.pedagogica.engine.ActivityErrorHandler.
 
activityItem - Variable in class org.concord.pedagogica.PedAgogica
 
activityItem - Variable in class org.concord.pedagogica.ui.ActivitySearchResult
 
ActivityItem - interface org.concord.pedagogica.ui.ActivityItem.
 
ActivityItemErrorHandler - interface org.concord.pedagogica.ui.ActivityItemErrorHandler.
 
ActivityItemEvent - class org.concord.pedagogica.ui.event.ActivityItemEvent.
 
ActivityItemEvent(Object) - Constructor for class org.concord.pedagogica.ui.event.ActivityItemEvent
 
ActivityItemListener - interface org.concord.pedagogica.ui.event.ActivityItemListener.
 
activityName - Variable in class org.concord.pedagogica.engine.Logging
 
activityNameField - Variable in class org.concord.pedagogica.ui.ActivityView
 
activityNameLabel - Variable in class org.concord.pedagogica.ui.ActivityView
 
activityNode - Variable in class org.concord.pedagogica.ui.ActivityView
 
ActivityNode - class org.concord.pedagogica.engine.ActivityNode.
The ActivityNode is the state object of the state machine controlled by the Activity object.
ActivityNode() - Constructor for class org.concord.pedagogica.engine.ActivityNode
 
ActivityNode(Activity) - Constructor for class org.concord.pedagogica.engine.ActivityNode
 
ActivityNodeItem - class org.concord.pedagogica.ui.ActivityNodeItem.
 
ActivityNodeItem(ActivityNodeItem, NodeViewEditor, String) - Constructor for class org.concord.pedagogica.ui.ActivityNodeItem
 
ActivityRenderer - class org.concord.pedagogica.ui.ActivityRenderer.
 
ActivityRenderer() - Constructor for class org.concord.pedagogica.ui.ActivityRenderer
 
ActivityScript - class org.concord.pedagogica.engine.ActivityScript.
 
activityScroll - Variable in class org.concord.pedagogica.PedAgogica
 
ActivitySearch - class org.concord.pedagogica.ui.ActivitySearch.
 
ActivitySearch(JFrame) - Constructor for class org.concord.pedagogica.ui.ActivitySearch
 
ActivitySearchResult - class org.concord.pedagogica.ui.ActivitySearchResult.
 
ActivitySearchResult(String, ActivityItem, int) - Constructor for class org.concord.pedagogica.ui.ActivitySearchResult
 
activityView - Variable in class org.concord.pedagogica.PedAgogica
 
ActivityView - class org.concord.pedagogica.ui.ActivityView.
 
ActivityView() - Constructor for class org.concord.pedagogica.ui.ActivityView
 
actuals - Variable in class org.concord.util.script.InvocationExpression
 
actuals - Variable in class org.concord.util.script.IndexExpression
 
acx - Variable in class org.concord.collisions.engine.JWorldElement
 
acy - Variable in class org.concord.collisions.engine.JWorldElement
 
add(Component) - Method in class org.concord.biologica.ui.BioToolBar
Add a component to the toolbar.
add(int) - Method in class org.concord.molecular.engine.IndexList
 
addActionListener(ActionListener) - Method in class org.concord.biologica.ui.DNAView
 
addActionListener(ActionListener) - Method in class org.concord.flash.player.FButton
 
addActionListener(ActionListener) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
addActionListener(ActionListener) - Method in class org.concord.pedagogica.ui.TableInputView
 
addActivationStep(DaemonActivationStep) - Method in class org.concord.collisions.engine.JDaemon
Add an activation step to the daemon This method checks if the step is valid according to the list of steps the daemon already has
addActivationStep(float) - Method in class org.concord.collisions.engine.JDaemon
 
addActivationStep(float, float) - Method in class org.concord.collisions.engine.JDaemon
Add an activation step to the daemon This method checks if the step is valid according to the list of steps the daemon already has
addActivityItemListener(ActivityItemListener) - Method in class org.concord.pedagogica.ui.ActivityView
 
addActual(Object) - Method in class org.concord.util.script.InvocationExpression
 
addActual(Object) - Method in class org.concord.util.script.IndexExpression
 
addApplet(Applet, String) - Method in class org.concord.pedagogica.ui.ViewerContext
 
addArcItem(ActivityArcItem) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
addAreaListener(AreaListener, int, int, int, int) - Method in class org.concord.collisions.engine.JWorldElement
 
addAreaListener(AreaListener, PassiveElement) - Method in class org.concord.collisions.engine.JWorldElement
 
addAreaToListen(AreaListener, int, int, int, int) - Method in class org.concord.collisions.engine.JWorldElement
 
addAreaToListen(AreaListener, PassiveElement) - Method in class org.concord.collisions.engine.JWorldElement
 
addAtom() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
addAtom(int, int, int) - Method in class org.concord.molecular.ui.MolecularView
Short concise description.
addAtomicDataListener(AtomicDataListener) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
addAtomicValue(ConditionValue) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
The AtomicValue object represents a specific model calculation.
addAvailableButton(AbstractButton) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
addAvailableField(JTextField) - Method in class org.concord.pedagogica.ui.BlankFill
 
addAvailableText(JTextField) - Method in class org.concord.pedagogica.ui.BlankFill
 
addBorder(boolean, int) - Method in class org.concord.collisions.engine.BedSpringWorld
 
addBorder(boolean, int, boolean) - Method in class org.concord.collisions.engine.BedSpringWorld
 
addButton - Variable in class org.concord.util.PathDialog
 
addButton - Variable in class org.concord.pedagogica.ui.VariableDialog
 
addCaretListener(CaretListener) - Method in class org.concord.util.EditorInternalFrame
 
addCCGraphReadyListener(CCGraphReadyListener) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addChangeListener(ChangeListener) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
addCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Adds a characteristic to the column.
addCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageRow
Adds a characteristic to the row.
addChild(Organism) - Method in class org.concord.biologica.engine.Family
Adds a child organism to this fammmily.
addChildren(int, boolean) - Method in class org.concord.biologica.engine.Family
 
addChildren(int, int, boolean) - Method in class org.concord.biologica.engine.Family
 
addChildren(Vector, PedigreeOrganismView) - Method in class org.concord.biologica.ui.PedigreeFamily
Add the given children to the family.
addClass(String) - Method in class org.concord.pedagogica.ui.ClassTree
 
addClassPath(File) - Method in class org.concord.pedagogica.ui.ClassTree
 
addCollisionsListener(CollisionsListener) - Method in class org.concord.collisions.engine.JPartWorld
addCollisionsListener listener will be notified in case of any collision event
addCollisionsListener(CollisionsListener) - Method in class org.concord.collisions.ui.GUIPanel
 
addComponent(NodeViewItem) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
addConditionListener(ConditionListener) - Method in class org.concord.molecular.engine.ConditionValue
 
addContentData(TreeWalker, Vector, Vector) - Method in class org.concord.pedagogica.ui.LogView
 
addDaemonListener(DaemonListener) - Method in class org.concord.collisions.engine.JDaemon
Add a daemon listener
addData(float) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
addDataListener(DataListener) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
addDataListener(DataListener) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
addDataSource(DataSource) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addDebugging(String) - Static method in class org.concord.util.Debug
 
addDirectories(ListTree, File) - Method in class org.concord.pedagogica.engine.LogModel
 
addElement(JWorldElement) - Method in class org.concord.collisions.ui.GUIPanel
add element into the panel
addElseIfExpression(Expression) - Method in class org.concord.util.script.IfThenElseStatement
 
addElseIfStatement(Statement) - Method in class org.concord.util.script.IfThenElseStatement
 
addExpression(Object) - Method in class org.concord.util.script.SequenceLiteral
 
addFamily(Family, int, int) - Method in class org.concord.biologica.ui.PedigreeView
Add a family to this view.
addFamily(Family, int, int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Add a family to this view.
addFamily(PedigreeFamily) - Method in class org.concord.biologica.ui.PedigreeLevel
Add a family to this level.
addField(int) - Method in class org.concord.pedagogica.ui.BlankFill
 
addField(Object) - Method in class org.concord.util.script.ObjectExpression
 
addGlobals(NameStack) - Method in class org.concord.pedagogica.engine.NodeAccess
 
addHandler(HandlerDeclaration) - Method in class org.concord.util.script.Script
 
addHandler(String, String) - Method in class org.concord.util.script.event.EventHandler
 
addHyperlinkListener(HyperlinkListener) - Method in class org.concord.pedagogica.ui.CCXMLText
 
addIfSpeciesAllele(SpeciesAllele) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Adds an if species allele to this rule.
addImport(Statement) - Method in class org.concord.util.script.Script
 
addLocal(String) - Method in class org.concord.util.script.BlockStatement
 
addLocals(Stack, Object[]) - Method in class org.concord.util.script.NameStack
Add parameters and locals to stack frame.
addMapEntry(int, int, int) - Method in class org.concord.util.BarGraph
Add or replace an index map entry.
addMenus(String[][], Object) - Method in class org.concord.util.Editor
 
addMethod(MethodDeclaration) - Method in class org.concord.util.script.Script
 
addMouseListener(FComponent, MouseListener) - Method in class org.concord.flash.player.FMouseSupport
 
addMouseListener(MouseListener) - Method in class org.concord.flash.player.FButton
 
addMovieClip(String, FMovieClip) - Method in class org.concord.flash.player.FMovie
Adds a movie clip to the global name table.
addMovieClipListener(MovieClipListener) - Method in class org.concord.flash.player.FMovieClip
 
addNeighborX(JWorldElement, JWorldElement) - Method in class org.concord.collisions.engine.JWorldElement
 
addNeighborX(JWorldElement, JWorldElement) - Method in class org.concord.collisions.engine.JAtom
 
addNeighborY(JWorldElement, JWorldElement) - Method in class org.concord.collisions.engine.JWorldElement
 
addNeighborY(JWorldElement, JWorldElement) - Method in class org.concord.collisions.engine.JAtom
 
addNewData(float[]) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
addNode(TreeViewNode, TreeViewNode, int) - Method in class org.concord.biologica.ui.TreeView
Add a new node to the tree with the given parent node.
addNotify() - Method in class org.concord.collisions.ui.GUIElementsFrame
 
addNotify() - Method in class org.concord.collisions.ui.GUITestIngrid
 
addNotify() - Method in class org.concord.collisions.ui.IngridProblem
 
addNotify() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.OrganismAllele
Adds a nucleic acid to the holder.
addNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.NucleicAcid
Adds a nucleic acid to the holder.
addNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.SpeciesAllele
Adds a nucleic acid to the holder.
addNucleicAcid(INucleicAcid) - Method in interface org.concord.biologica.engine.INucleicAcidHolder
Adds a nucleic acid to the holder.
addObject(EngineObject, int) - Method in class org.concord.biologica.engine.ImportContext
Add an object to the engine's array of objects, reallocating the array to a larger size if necessary.
addOperand(Expression) - Method in class org.concord.util.script.BinaryExpression
Set the first operand of this expression.
addOperation(Expression) - Method in class org.concord.util.script.BinaryExpression
Set the first operand of this expression.
addOrganism(Organism) - Method in class org.concord.biologica.ui.MultipleOrganismView
Add an organism to this view.
addOrganism(Organism, int, int) - Method in class org.concord.biologica.ui.PedigreeView
Add an organism to this view.
addOrganism(Organism, int, int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Add an organism to this view without any required ties to a family.
addOrganism(Organism, int, int, String) - Method in class org.concord.biologica.ui.PedigreeView
Add an organism to this view and specify the trait to show, which is used only if this is the first organism added to the view.
addOrganism(Organism, int, int, String) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Add an organism to this view without any required ties to a family.
addOrganism(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeLevel
Add an organism to this level.
addParameter(String) - Method in class org.concord.util.script.MethodDeclaration
 
addPassiveElement(PassiveElement) - Method in class org.concord.collisions.ui.GUIPanel
add passive element(Line, Icon, Rectangle, Text) into the panel
addPrefix(String, String) - Method in class org.concord.util.PathDialog
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.engine.EngineObject
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.engine.BioEngine
Add a property change listener for all non-vector properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.UIView
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.FertilizationModel
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.MeiosisModel
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.SelectionSet
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.TreeView
Add a property change listener for properties.
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.collisions.engine.JWorldElement
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.molecular.ui.MolecularView
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.pedagogica.ui.HTMLViewCustomizer
 
addPropertyChangeListener(PropertyChangeListener) - Method in class org.concord.pedagogica.ui.TableInputModel
 
addPropertyComponents(JPanel, JPanel) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
addQuestion(Question) - Method in class org.concord.pedagogica.ui.Quiz
 
addQuestion(QuestionForm) - Method in class org.concord.pedagogica.engine.ActivityNode
 
addQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
addQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.Question
 
addQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
address - Variable in class org.concord.util.NetworkTime
 
addRow(String[]) - Method in class org.concord.pedagogica.ui.TabularView
 
addScreen(int, int, int, int) - Method in class org.concord.collisions.engine.BedSpringWorld
 
addSelectionPresenter(SelectionPresenter) - Method in class org.concord.biologica.ui.SelectionSet
Add a selection presenter
addSoundThread(int) - Method in class org.concord.collisions.engine.JPartWorld
add Thread for playing sounds it will be moved to an other location
addSource(int, int, float, float, float, float, float, float) - Method in class org.concord.collisions.engine.BedSpringWorld
 
addSource(int, int, float, float, float, float, float, float, Color) - Method in class org.concord.collisions.engine.BedSpringWorld
 
addStatement(Statement) - Method in class org.concord.util.script.BlockStatement
 
addStatement(Statement) - Method in class org.concord.util.script.Script
 
addStateVariable(String, Object) - Method in class org.concord.pedagogica.engine.ActivityScript
 
addStepListener(StepListener, int) - Method in class org.concord.collisions.engine.JPartWorld
 
addStudentName(String, String) - Method in class org.concord.pedagogica.engine.Logging
 
addText(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
addTo(int, int) - Method in class org.concord.molecular.engine.IndexList
 
addTool(int) - Method in class org.concord.biologica.ui.ToolView
Add the given tool to the view
addToPath(String) - Method in class org.concord.util.PathDialog
 
addToPath(String, String) - Method in class org.concord.util.PathDialog
 
addValueFunction(ConditionValue) - Method in class org.concord.molecular.engine.AggregateValue
 
addVariable(String) - Method in class org.concord.util.script.Script
 
addView(Container) - Method in class org.concord.biologica.ui.ToolView
Add a view to the list of views that care about which tool in this tool view is active.
addWorldElement(JWorldElement) - Method in class org.concord.collisions.engine.JPartWorld
addWorldElement add JWorldElement into the world
addWorldElement(JWorldElement) - Method in class org.concord.collisions.engine.BedSpringWorld
addWorldElement add JWorldElement into the world
addXAxis(float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addXAxis(float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
addXAxis(String, float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addXAxis(String, float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
addXAxis(String, float, float, CCUnit) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addXAxis(String, float, float, CCUnit) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
addYAxis(float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addYAxis(float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
addYAxis(String, float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addYAxis(String, float, float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
addYAxis(String, float, float, CCUnit) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
addYAxis(String, float, float, CCUnit) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
ADENINE - Static variable in class org.concord.biologica.engine.Base
A purine which links with thymine in DNA and with uracil in RNA.
adjustmentValueChanged(AdjustmentEvent) - Method in class org.concord.biologica.ui.DNAView
Handle adjustment event
advances - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
AggregateValue - class org.concord.molecular.engine.AggregateValue.
 
AggregateValue() - Constructor for class org.concord.molecular.engine.AggregateValue
 
ALA - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Alanine
ALANINE - Static variable in class org.concord.biologica.engine.AminoAcid
Alanine
ALGORITHMIC_NUCLEIC_ACID_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ALGORITHMIC_NUCLEIC_ACID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
XML element names and ids - Please keep these in alphabetical and numeric order.
ALGORITHMIC_NUCLEIC_ACID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ALGORITHMIC_NUCLEIC_ACID_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ALGORITHMIC_NUCLEIC_ACID_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
AlgorithmicNucleicAcid - class org.concord.biologica.engine.AlgorithmicNucleicAcid.
This class represents a nucleic acid whose bases are algorithmically and randomly generated.
AlgorithmicNucleicAcid(INucleicAcidHolder, int, AlgorithmicNucleicAcid) - Constructor for class org.concord.biologica.engine.AlgorithmicNucleicAcid
Create a new algorithmic nucleic acid given another algorithmic nucleic acid to copy.
AlgorithmicNucleicAcid(INucleicAcidHolder, int, int, int) - Constructor for class org.concord.biologica.engine.AlgorithmicNucleicAcid
Create a new algorithmic nucleic acid given a length in codons.
ALIGNMENT_CONTROLS_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
Alignment controls visible in big meiosis view.
ALL_ITEM - Static variable in class org.concord.pedagogica.engine.LogModel
 
ALLELE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ALLELES_ALTERABLE - Static variable in class org.concord.biologica.engine.EngineProp
Alleles alterable flag.
ALLELES_ALTERABLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ALLELES_ALTERABLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ALLELES_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ALLELES_VISIBLE - Static variable in class org.concord.biologica.engine.EngineProp
Alleles visible flag.
ALLELES_VISIBLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ALLELES_VISIBLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
allelesEdited() - Method in class org.concord.biologica.ui.DNAView
Alleles edited
allIndices - Variable in class org.concord.molecular.engine.ConditionValue
 
AllInOneView - class org.concord.biologica.ui.AllInOneView.
This class represents a view which contains and acts as a parent or manager of all of the other views of BioLogica.
AllInOneView() - Constructor for class org.concord.biologica.ui.AllInOneView
Creates BioLogica AllInOne view
AminoAcid - class org.concord.biologica.engine.AminoAcid.
This class represents an amino acid object.
AminoAcid() - Constructor for class org.concord.biologica.engine.AminoAcid
 
amper - Variable in class org.concord.util.CCUnit
 
AndExpression - class org.concord.util.script.AndExpression.
 
AndExpression() - Constructor for class org.concord.util.script.AndExpression
 
animator - Variable in class org.concord.molecular.ui.MolecularView
 
answerFont - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
answerFont - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
answerList - Variable in class org.concord.pedagogica.ui.CustomTableQuestion
 
answers - Variable in class org.concord.util.LogProcess
 
answers - Variable in class org.concord.pedagogica.engine.QuestionState
 
answers - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
answerTable - Variable in class org.concord.pedagogica.ui.CustomTableQuestion
 
appletResize(int, int) - Method in class org.concord.pedagogica.ui.ViewerStub
 
ApplicationFrame - class org.concord.flash.util.ApplicationFrame.
 
ApplicationFrame() - Constructor for class org.concord.flash.util.ApplicationFrame
 
ApplicationFrame(String) - Constructor for class org.concord.flash.util.ApplicationFrame
 
APPLY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Apply button pushed.
applyForce(CCForce) - Method in class org.concord.collisions.engine.JWorldElement
Apply force to the JWorldElement.
applyForce(CCForce) - Method in class org.concord.collisions.engine.JRigidBox
JRigidBox doesn't support applying forces
applyForce(CCForce) - Method in class org.concord.collisions.engine.JWall
JWall doesn't support applying forces
applyForce(CCForce) - Method in class org.concord.collisions.engine.JDaemon
JDaemon doesn't support applying forces
applyPendingChanges() - Method in class org.concord.biologica.ui.DNAView
Apply pending changes made to DNA
arc - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
arcButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
arcDragPoint - Variable in class org.concord.pedagogica.ui.ActivityView
 
arch - Variable in class org.concord.pedagogica.ui.ActivityView
 
arcItems - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
arcNumber - Static variable in class org.concord.pedagogica.ui.ActivityArcItem
 
arcs - Variable in class org.concord.pedagogica.engine.Activity
 
arcSelected(ActivityItemEvent) - Method in class org.concord.pedagogica.PedAgogica
 
arcSelected(ActivityItemEvent) - Method in interface org.concord.pedagogica.ui.event.ActivityItemListener
 
arcThread - Variable in class org.concord.pedagogica.engine.ActivityArc
 
AreaEvent - class org.concord.collisions.event.AreaEvent.
 
AreaEvent(JWorldElement, int, int, int, int) - Constructor for class org.concord.collisions.event.AreaEvent
 
areaListener - Variable in class org.concord.collisions.engine.JWorldElement
 
AreaListener - interface org.concord.collisions.event.AreaListener.
 
areaVisited(AreaEvent) - Method in interface org.concord.collisions.event.AreaListener
 
ARG - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Arginine
ARGININE - Static variable in class org.concord.biologica.engine.AminoAcid
Arginine
args - Variable in class org.concord.util.script.BinaryExpression
 
arrayClass - Variable in class org.concord.util.script.SequenceLiteral
 
ArrayDataSource - class org.concord.pedagogica.graph.ArrayDataSource.
 
ArrayLiteral - class org.concord.util.script.ArrayLiteral.
 
ArrayLiteral(Script) - Constructor for class org.concord.util.script.ArrayLiteral
 
arrowsVelDragMode - Variable in class org.concord.collisions.ui.GUIPanel
 
ASCEND_FROM_NODE - Static variable in class org.concord.pedagogica.ui.ActivityView
 
ASN - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Asparagine
ASP - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Aspartic acid
ASPARAGINE - Static variable in class org.concord.biologica.engine.AminoAcid
Asparagine
ASPARTIC_ACID - Static variable in class org.concord.biologica.engine.AminoAcid
Aspartic acid
assert(boolean, String, Object) - Static method in class org.concord.util.Debug
The classic assert - if the test fails, prints a message and throws an Error.
assert(boolean, String, Object) - Static method in class org.concord.biologica.engine.Debug
The classic assert - if the test fails, prints a message and throws an Error.
ASSERTION_FAILED - Static variable in class org.concord.biologica.engine.EngineStrings
 
assign - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
assignIndNumber(int) - Method in class org.concord.collisions.engine.JWorldElement
 
AssignmentStatement - class org.concord.util.script.AssignmentStatement.
 
AssignmentStatement() - Constructor for class org.concord.util.script.AssignmentStatement
 
atan(double) - Method in class org.concord.flash.player.builtin.FMath
 
atan2(double, double) - Method in class org.concord.flash.player.builtin.FMath
 
atom - Variable in class org.concord.molecular.engine.AtomAccessor
 
ATOM_ATOM_COLLISION - Static variable in class org.concord.collisions.engine.JPartWorld
ATOM_ATOM_COLLISION JPartWorld generates CollisionsEvent if collision was between atom/atom getID method of that CollisionEvent will return ATOM_ATOM_COLLISION value
ATOM_DAEMON_COLLISION - Static variable in class org.concord.collisions.engine.JPartWorld
ATOM_DAEMON_COLLISION JPartWorld generates CollisionsEvent if collision was between atom/daemon getID method of that CollisionEvent will return ATOM_DAEMON_COLLISION value
ATOM_WALL_COLLISION - Static variable in class org.concord.collisions.engine.JPartWorld
ATOM_WALL_COLLISION JPartWorld generates CollisionsEvent if collision was between atom/wall getID method of that CollisionEvent will return ATOM_WALL_COLLISION value
AtomAccessor - class org.concord.molecular.engine.AtomAccessor.
 
AtomAccessor() - Constructor for class org.concord.molecular.engine.AtomAccessor
 
AtomAccessor(Atom) - Constructor for class org.concord.molecular.engine.AtomAccessor
 
AtomDragModePropertyEditor - class org.concord.collisions.engine.AtomDragModePropertyEditor.
 
AtomDragModePropertyEditor() - Constructor for class org.concord.collisions.engine.AtomDragModePropertyEditor
 
AtomDragPropertyEditor - class org.concord.collisions.engine.AtomDragPropertyEditor.
 
AtomDragPropertyEditor() - Constructor for class org.concord.collisions.engine.AtomDragPropertyEditor
 
atomicDataEvent - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
AtomicDataEvent - class org.concord.molecular.engine.AtomicDataEvent.
 
AtomicDataEvent(Object, double, double) - Constructor for class org.concord.molecular.engine.AtomicDataEvent
 
AtomicDataListener - interface org.concord.molecular.engine.AtomicDataListener.
 
atomicDataUpdate(AtomicDataEvent) - Method in interface org.concord.molecular.engine.AtomicDataListener
 
atomicDataUpdate(AtomicDataEvent) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
This is the event handler for the model generated calculation events.
atomicDataUpdate(AtomicDataEvent) - Method in class org.concord.molecular.ui.MolecularView
 
atomicModel - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
AtomicProperty - class org.concord.molecular.engine.AtomicProperty.
 
AtomicProperty() - Constructor for class org.concord.molecular.engine.AtomicProperty
 
AtomicProperty(String) - Constructor for class org.concord.molecular.engine.AtomicProperty
 
AtomicValue - class org.concord.molecular.engine.AtomicValue.
 
AtomicValue() - Constructor for class org.concord.molecular.engine.AtomicValue
 
AtomicValueDispatcher - class org.concord.molecular.ui.AtomicValueDispatcher.
An instance of this class moderates the interaction between a ValueGraph and the DefaultAtomicModel.
AtomicValueDispatcher() - Constructor for class org.concord.molecular.ui.AtomicValueDispatcher
 
atoms - Variable in class org.concord.molecular.engine.AtomicValue
 
atomsDragMode - Variable in class org.concord.collisions.ui.GUIPanel
 
attachArc(ActivityArcItem, int, int) - Method in class org.concord.pedagogica.ui.ActivityView
 
attachGUIElement(JWorldElement) - Method in class org.concord.collisions.ui.DataCrossPanel
 
attributeNames() - Method in class org.concord.util.beans.FeatureDescriptor
Gets an enumeration of the locale-independent names of this feature.
autoCrossing() - Method in class org.concord.biologica.ui.BigMeiosisView
 
autoCrossOver(int, int) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle autoCrossing Over
AUTOMATIC_LOCKED - Static variable in class org.concord.biologica.engine.EngineObject
Automatic lock value.
AUTOMATIC_LOCKED_STRING - Static variable in class org.concord.biologica.engine.EngineObject
 
AUTOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
Chromosome type - autosome (non-sex chromosome)
available - Variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
available() - Method in class org.concord.util.TextInputStream
 
available() - Method in class org.concord.util.TextReader
 
available() - Method in class org.concord.util.script.ScriptFileInputStream
 
ax - Variable in class org.concord.collisions.ui.PassiveElement
 
ay - Variable in class org.concord.collisions.ui.PassiveElement
 

B

B_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
The "B" chromosome of a pair, sometimes of three.
B_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
back() - Method in class org.concord.pedagogica.engine.ActivityNode
 
backColor - Variable in class org.concord.util.LineGraph
 
background - Variable in class org.concord.util.BarGraph
 
background - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
background - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
BACKGROUND - Static variable in class org.concord.biologica.ui.UIProp
The background color changed.
BAD_ALLELE_STRING_SPECIFICATION - Static variable in class org.concord.biologica.engine.EngineStrings
 
BAD_BASE_VALUE - Static variable in class org.concord.biologica.engine.EngineStrings
 
balls - Variable in class org.concord.molecular.ui.MolecularView
 
barColors - Variable in class org.concord.util.Gauge
 
BarGraph - class org.concord.util.BarGraph.
Bar graph component.
BarGraph() - Constructor for class org.concord.util.BarGraph
Bar graph constructor.
bars - Variable in class org.concord.util.Gauge
 
Base - class org.concord.biologica.engine.Base.
This class represents a Base object, as in the base purines and pyrimidines which form DNA and RNA.
BASE_VALUES - Static variable in class org.concord.biologica.engine.EngineProp
Base values in an object containing nucleic acid changed, either the value of a particular base or adding or removing a base.
Base() - Constructor for class org.concord.biologica.engine.Base
 
baseObject - Variable in class org.concord.util.script.Script
 
BASES_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
BASES_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
baseTable - Variable in class org.concord.util.script.Script
 
baseTitle - Static variable in class org.concord.pedagogica.ui.ActivityView
 
baseTitle - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
baseUnit - Variable in class org.concord.util.CCUnit
 
BeanDescriptor - class org.concord.util.beans.BeanDescriptor.
A BeanDescriptor provides global information about a "bean", including its Java class, its displayName, etc.
BeanDescriptor(Class) - Constructor for class org.concord.util.beans.BeanDescriptor
Create a BeanDescriptor for a bean that doesn't have a customizer.
BeanDescriptor(Class, Class) - Constructor for class org.concord.util.beans.BeanDescriptor
Create a BeanDescriptor for a bean that has a customizer.
BeanInfo - interface org.concord.util.beans.BeanInfo.
A bean implementor who wishes to provide explicit information about their bean may provide a BeanInfo class that implements this BeanInfo interface and provides explicit information about the methods, properties, events, etc, of their bean.
BedSpringWorld - class org.concord.collisions.engine.BedSpringWorld.
main class for bed spring simulation contains methods for calculating positions/velocity of particles many methods are duplicated in GUIPanel class
BedSpringWorld(float, float) - Constructor for class org.concord.collisions.engine.BedSpringWorld
 
BedSpringWorld(float, float, float) - Constructor for class org.concord.collisions.engine.BedSpringWorld
 
BedSpringWorld(int) - Constructor for class org.concord.collisions.engine.BedSpringWorld
 
BedSpringWorld(int, float) - Constructor for class org.concord.collisions.engine.BedSpringWorld
 
beginColumn - Variable in class org.concord.util.TextSelection
 
beginColumn - Variable in class org.concord.util.script.ScriptObject
 
beginLine - Variable in class org.concord.util.TextSelection
 
beginLine - Variable in class org.concord.util.script.ScriptObject
 
bends - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
BENGINE - Static variable in class org.concord.util.Debug
 
BENGINE - Static variable in class org.concord.biologica.engine.Debug
 
bevelBorder - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
bi - Variable in class org.concord.util.LineGraph
 
big - Variable in class org.concord.util.LineGraph
 
BIG_FATHER_MEIOSIS_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the big father meiosis view was pushed.
BIG_FERTILIZATION_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the big fertilization view was pushed.
BIG_MOTHER_MEIOSIS_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the big mother meiosis view was pushed.
BigFertilizationView - class org.concord.biologica.ui.BigFertilizationView.
This class represents a view which shows the 2 sex cells of 2 parents in the sex view and has controls for the user to conduct fertilization within this view of those 2 cells.
BigFertilizationView() - Constructor for class org.concord.biologica.ui.BigFertilizationView
Creates a big fertilization view.
BigMeiosisView - class org.concord.biologica.ui.BigMeiosisView.
This class represents a view which shows the sex cell of a parent in the sex view and has controls for the user to conduct meiosis within this view on that sex cell.
BigMeiosisView() - Constructor for class org.concord.biologica.ui.BigMeiosisView
Creates a big meiosis view.
BinaryExpression - class org.concord.util.script.BinaryExpression.
The BinaryExpression class is the base class for all binary operations.
BinaryExpression() - Constructor for class org.concord.util.script.BinaryExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.BinaryExpression
This method should be overridden by a derived class.
binOp(Object, Object) - Method in class org.concord.util.script.NEExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.OrExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.BitAndExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.AndExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.ModulusExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.BitOrExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.LEExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.MinusExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.BitXorExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.EQExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.GEExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.ExponentExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.PlusExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.MultiplyExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.LTExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.GTExpression
 
binOp(Object, Object) - Method in class org.concord.util.script.DivideExpression
 
BioComboBox - class org.concord.biologica.ui.BioComboBox.
This class represents a combobox in BioLogica.
BioComboBox() - Constructor for class org.concord.biologica.ui.BioComboBox
Override the constructor so we can set the model to one that knows how to remove all its items without crashing :-(.
BioComboBoxModel - class org.concord.biologica.ui.BioComboBoxModel.
 
BioComboBoxModel() - Constructor for class org.concord.biologica.ui.BioComboBoxModel
 
BioEngine - class org.concord.biologica.engine.BioEngine.
This class represents the Java Bean representing all of the BioScope engine.
BioEngine() - Constructor for class org.concord.biologica.engine.BioEngine
Creates a bioengine, the main object for the BioScope engine.
BioEngineBeanInfo - class org.concord.biologica.engine.BioEngineBeanInfo.
This class contains the information necessary for a Java Beans builder (e.g.
BioEngineBeanInfo() - Constructor for class org.concord.biologica.engine.BioEngineBeanInfo
Creates the bean info object.
BioLogicaFrame - class org.concord.biologica.ui.BioLogicaFrame.
 
BioLogicaFrame() - Constructor for class org.concord.biologica.ui.BioLogicaFrame
 
BioLogicaFrame(String) - Constructor for class org.concord.biologica.ui.BioLogicaFrame
 
BioLogicaFrame(String, boolean) - Constructor for class org.concord.biologica.ui.BioLogicaFrame
 
BioLogicaSpecies - class org.concord.biologica.engine.BioLogicaSpecies.
 
BioLogicaSpecies(String) - Constructor for class org.concord.biologica.engine.BioLogicaSpecies
 
BioToolBar - class org.concord.biologica.ui.BioToolBar.
This class represents a toolbar in BioLogica.
BioToolBar() - Constructor for class org.concord.biologica.ui.BioToolBar
 
BitAndExpression - class org.concord.util.script.BitAndExpression.
The BitAndExpression class implements the semantic node for bitwise "and".
BitAndExpression() - Constructor for class org.concord.util.script.BitAndExpression
 
BitNotExpression - class org.concord.util.script.BitNotExpression.
The BitNotExpression class implements the semantic node for bitwise "not".
BitNotExpression() - Constructor for class org.concord.util.script.BitNotExpression
 
BitOrExpression - class org.concord.util.script.BitOrExpression.
The BitOrExpression class implements the semantic node for bitwise "or".
BitOrExpression() - Constructor for class org.concord.util.script.BitOrExpression
 
BitXorExpression - class org.concord.util.script.BitXorExpression.
The BitXorExpression class implements the semantic node for bitwise "xor".
BitXorExpression() - Constructor for class org.concord.util.script.BitXorExpression
 
BlankFill - class org.concord.pedagogica.ui.BlankFill.
The BlankFill class is derived from JTextArea and restricts the editable text to the blank areas.
BlankFill() - Constructor for class org.concord.pedagogica.ui.BlankFill
 
BlankFill(String) - Constructor for class org.concord.pedagogica.ui.BlankFill
 
BlockStatement - class org.concord.util.script.BlockStatement.
 
BlockStatement() - Constructor for class org.concord.util.script.BlockStatement
 
bonds - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
BooleanLiteral - class org.concord.util.script.BooleanLiteral.
This node represents a boolean value in the semantic tree.
BooleanLiteral(boolean) - Constructor for class org.concord.util.script.BooleanLiteral
 
BORDERX - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
BORDERY - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
BOTTOM_ALLELE - Static variable in class org.concord.biologica.ui.DNAView
 
BOTTOM_LEFT_GAMETE - Static variable in class org.concord.biologica.ui.MeiosisModel
 
BOTTOM_LEFT_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
BOTTOM_RIGHT_GAMETE - Static variable in class org.concord.biologica.ui.MeiosisModel
 
BOTTOM_RIGHT_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
BOTTOM_STRAND - Static variable in class org.concord.biologica.engine.Gene
Top strand
bound - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
boundary - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
boundaryType - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
boundBox - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
bounds - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
BOUNDS_PROPERTY - Static variable in class org.concord.pedagogica.PedAgogica
 
boundsLabel - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
box(Atom[], int) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
boxLength - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
boxLength - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
boxLength - Static variable in class org.concord.collisions.ui.IngridProblem
 
Branch - class org.concord.biologica.engine.Branch.
 
Branch(OrganismAllele[], Color[], OrganismAllele[], Color[], OrganismAllele[], Color[], OrganismAllele[], Color[]) - Constructor for class org.concord.biologica.engine.Branch
 
Branch(OrganismAllele[], OrganismAllele[], OrganismAllele[], OrganismAllele[]) - Constructor for class org.concord.biologica.engine.Branch
 
Branch(OrganismAllele[], OrganismAllele[], OrganismAllele[], OrganismAllele[], Color) - Constructor for class org.concord.biologica.engine.Branch
 
Branch(OrganismChromosome) - Constructor for class org.concord.biologica.engine.Branch
This class is used to store the chromosome's alleles when the cross over happened,
Branch(OrganismChromosome, Color) - Constructor for class org.concord.biologica.engine.Branch
 
BTEST - Static variable in class org.concord.util.Debug
 
BTEST - Static variable in class org.concord.biologica.engine.Debug
 
buffer - Variable in class org.concord.util.TextReader
 
BUFFER_SIZE - Static variable in class org.concord.util.Transfer
 
build() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
build(Atom[]) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
buildBox(float, float, float, float, float) - Method in class org.concord.collisions.ui.GUIPanel
build square box: 4 walls
buildBox(float, float, float, float, float, float, float, float, float) - Method in class org.concord.collisions.ui.GUIPanel
build square box: 4 walls
but - Variable in class org.concord.flash.player.FMovieBuilder.ButtonActionBuilder
 
buttonData - Variable in class org.concord.pedagogica.ui.ActivityView
 
buttonPanel - Variable in class org.concord.pedagogica.PedAgogica
 
buttonPanel - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
buttonPanel - Variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
buttonPanel - Variable in class org.concord.pedagogica.ui.ActivityView
 
buttonPanel - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
buttons - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
buttonTable - Variable in class org.concord.pedagogica.ui.ActivityView
 

C

C_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
The "C" chromosome of a pair, sometimes of three.
caclulateDistanceToLine(float, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JPartWorld
 
caclulateDistanceToLine(float, float, float, float, float, float, boolean) - Static method in class org.concord.collisions.engine.JPartWorld
 
calcEnergyKoeff(float) - Method in class org.concord.collisions.engine.JWall
 
calculate() - Method in class org.concord.collisions.engine.VelDistFraction
 
calculateAcceleration() - Method in class org.concord.collisions.engine.JAtom
 
calculateAtoms - Variable in class org.concord.collisions.engine.CCGravityForce
 
calculateBoxes - Variable in class org.concord.collisions.engine.CCGravityForce
 
calculateColor(float) - Method in class org.concord.collisions.engine.JPartWorld
calculates color that corresponds to color dependence parameters
calculateDaemons - Variable in class org.concord.collisions.engine.CCGravityForce
 
calculateFrameRate() - Method in class org.concord.flash.player.FFlash
For calculating the actual frame rate
calculateStep() - Method in class org.concord.collisions.engine.JPartWorld
 
calculateStep() - Method in class org.concord.collisions.engine.BedSpringWorld
 
calculateTotalAtomsEnergy() - Method in class org.concord.collisions.engine.JPartWorld
calculates total kinetic energy (atoms only)
calculateTotalAtomsEnergyInRect(float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
retrieves total kinetic energy for atoms existed inside of rectangle with given coordinates
calculateTotalAtomsEnergyXInRect(float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
 
calculateTotalAtomsEnergyYInRect(float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
 
calculateTotalBoxesEnergy() - Method in class org.concord.collisions.engine.JPartWorld
 
calculateTotalWallsEnergy() - Method in class org.concord.collisions.engine.JPartWorld
calculates total kinetic energy (walls only)
calculateWalls - Variable in class org.concord.collisions.engine.CCGravityForce
 
callActionListeners(ActionEvent) - Method in class org.concord.biologica.ui.DNAView
 
callAtomicDataListeners() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
callDeclaredMethod(MethodDeclaration, Object[]) - Method in class org.concord.util.script.Script
 
callMethod(String, Object[]) - Method in class org.concord.util.script.Script
 
callMethod(String, Object[]) - Method in class org.concord.flash.player.FScriptObject
Calls a method on this object.
callMethod(String, Object[]) - Method in class org.concord.flash.player.builtin.FArray
 
callMethod(String, Object[], boolean) - Method in class org.concord.util.script.Script
 
cancelButton - Variable in class org.concord.pedagogica.PedAgogica
 
cancelButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
cancelButton - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
cancelColorTempDependencies() - Method in class org.concord.collisions.engine.JPartWorld
set color dependency parameters between element's temperature and element's color cancel color dependence
cancelColorTempDependencies() - Method in class org.concord.collisions.engine.BedSpringWorld
 
candela - Variable in class org.concord.util.CCUnit
 
CANNOT_CHANGE_PLOIDY_NUMBER_OF_SPECIES_WITH_CHROMOSOMES - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_CLOSE_FILE_INPUT_STREAM_DUE_TO_EXCEPTION - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_CLOSE_FILE_OUTPUT_STREAM_DUE_TO_EXCEPTION - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_CREATE_FILE_INPUT_STREAM_DUE_TO_EXCEPTION - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_CREATE_FILE_OUTPUT_STREAM_DUE_TO_EXCEPTION - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_FIND_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
CANNOT_READ_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
canonicalPathSeparation(String) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
canSqueeze() - Method in class org.concord.biologica.ui.PedigreeObject
Can this object be squeezed? Mainly used for PedigreeFamilies.
canSqueeze() - Method in class org.concord.biologica.ui.PedigreeFamily
Can the family be squeezed any more? Enforces the maximum squeeze factor.
caretUpdate(CaretEvent) - Method in class org.concord.util.Editor
 
caretUpdate(CaretEvent) - Method in class org.concord.pedagogica.PedAgogica
 
caretUpdate(CaretEvent) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
caretUpdate(CaretEvent) - Method in class org.concord.pedagogica.ui.TableInputView
 
caretUpdateEnabled - Variable in class org.concord.pedagogica.PedAgogica
 
catNames - Static variable in class org.concord.util.CCUnit
 
CCBedSpringForce - class org.concord.collisions.engine.CCBedSpringForce.
 
CCBedSpringForce() - Constructor for class org.concord.collisions.engine.CCBedSpringForce
 
CCBedSpringForce(float) - Constructor for class org.concord.collisions.engine.CCBedSpringForce
 
CCBedSpringForce(float, boolean) - Constructor for class org.concord.collisions.engine.CCBedSpringForce
 
CCBedSpringForceCalculator - class org.concord.collisions.engine.CCBedSpringForceCalculator.
 
CCBedSpringForceCalculator(float) - Constructor for class org.concord.collisions.engine.CCBedSpringForceCalculator
 
CCBedSpringForceCalculator(float, boolean) - Constructor for class org.concord.collisions.engine.CCBedSpringForceCalculator
 
CCBedSpringForceCalculator(float, float) - Constructor for class org.concord.collisions.engine.CCBedSpringForceCalculator
 
CCBedSpringForceCalculator(float, float, boolean) - Constructor for class org.concord.collisions.engine.CCBedSpringForceCalculator
 
CCConstantForce - class org.concord.collisions.engine.CCConstantForce.
 
CCConstantForce(CCConstantForce) - Constructor for class org.concord.collisions.engine.CCConstantForce
 
CCConstantForce(float, float) - Constructor for class org.concord.collisions.engine.CCConstantForce
 
CCCoordinateTuner - interface org.concord.collisions.ui.CCCoordinateTuner.
 
CCDefaultForceCalculator - class org.concord.collisions.engine.CCDefaultForceCalculator.
 
CCDefaultForceCalculator() - Constructor for class org.concord.collisions.engine.CCDefaultForceCalculator
 
CCDraggable - interface org.concord.collisions.ui.CCDraggable.
 
CCElementPositionChanger - interface org.concord.collisions.engine.CCElementPositionChanger.
 
CCForce - class org.concord.collisions.engine.CCForce.
 
CCForce() - Constructor for class org.concord.collisions.engine.CCForce
 
CCForceCalculator - interface org.concord.collisions.engine.CCForceCalculator.
 
CCFrictionForce - class org.concord.collisions.engine.CCFrictionForce.
 
CCFrictionForce() - Constructor for class org.concord.collisions.engine.CCFrictionForce
 
CCFrictionForce(float) - Constructor for class org.concord.collisions.engine.CCFrictionForce
 
CCFrictionForce(int) - Constructor for class org.concord.collisions.engine.CCFrictionForce
 
CCFrictionForce(int, float) - Constructor for class org.concord.collisions.engine.CCFrictionForce
 
CCFrictionForceCalculator - class org.concord.collisions.engine.CCFrictionForceCalculator.
 
CCFrictionForceCalculator() - Constructor for class org.concord.collisions.engine.CCFrictionForceCalculator
 
CCFrictionForceCalculator(float) - Constructor for class org.concord.collisions.engine.CCFrictionForceCalculator
 
CCFrictionForceCalculator(int) - Constructor for class org.concord.collisions.engine.CCFrictionForceCalculator
 
CCFrictionForceCalculator(int, float) - Constructor for class org.concord.collisions.engine.CCFrictionForceCalculator
 
ccGraphReady(CCGraphReadyEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
ccGraphReady(CCGraphReadyEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
ccGraphReady(CCGraphReadyEvent) - Method in interface org.concord.pedagogica.graph.CCGraphReadyListener
 
CCGraphReadyEvent - class org.concord.pedagogica.graph.CCGraphReadyEvent.
 
CCGraphReadyEvent(Object) - Constructor for class org.concord.pedagogica.graph.CCGraphReadyEvent
 
CCGraphReadyListener - interface org.concord.pedagogica.graph.CCGraphReadyListener.
 
CCGravityForce - class org.concord.collisions.engine.CCGravityForce.
 
CCGravityForce(CCScalingFactors) - Constructor for class org.concord.collisions.engine.CCGravityForce
 
CCHarmonicPositionChanger - class org.concord.collisions.engine.CCHarmonicPositionChanger.
 
CCHarmonicPositionChanger(float, float, float, float, float, float, float, float) - Constructor for class org.concord.collisions.engine.CCHarmonicPositionChanger
 
CCImpulseForce - class org.concord.collisions.engine.CCImpulseForce.
 
CCImpulseForce(CCImpulseForce) - Constructor for class org.concord.collisions.engine.CCImpulseForce
 
CCImpulseForce(float, float, float) - Constructor for class org.concord.collisions.engine.CCImpulseForce
 
CCImpulseForce(float, float, float, float) - Constructor for class org.concord.collisions.engine.CCImpulseForce
 
CCInfoDrawer - interface org.concord.collisions.ui.CCInfoDrawer.
 
CCJTable - class org.concord.pedagogica.ui.CCJTable.
 
CCJTable() - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCJTable(int, int) - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCJTable(TableModel) - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCJTable(TableModel, TableColumnModel) - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCJTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCJTable(Vector, Vector) - Constructor for class org.concord.pedagogica.ui.CCJTable
 
CCMassive - interface org.concord.collisions.engine.CCMassive.
 
CCPedagogicaGraph - class org.concord.pedagogica.graph.CCPedagogicaGraph.
 
CCPedagogicaGraph() - Constructor for class org.concord.pedagogica.graph.CCPedagogicaGraph
 
CCPedagogicaGraphPanel - class org.concord.pedagogica.graph.CCPedagogicaGraphPanel.
 
CCPedagogicaGraphPanel() - Constructor for class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
CCPedagogicaGraphPanel(Frame) - Constructor for class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
CCPedagogicaGraphPanel(String, Frame) - Constructor for class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
CCPoint - class org.concord.collisions.engine.CCPoint.
utility Class for keeping floating point coordinates Point
CCPoint(float, float) - Constructor for class org.concord.collisions.engine.CCPoint
 
CCScalingFactors - class org.concord.collisions.engine.CCScalingFactors.
 
CCScalingFactors(double, double, double) - Constructor for class org.concord.collisions.engine.CCScalingFactors
 
CCSpring - class org.concord.collisions.engine.CCSpring.
 
CCSpring() - Constructor for class org.concord.collisions.engine.CCSpring
 
CCSpring(double, double) - Constructor for class org.concord.collisions.engine.CCSpring
 
CCTableCellRenderer - class org.concord.pedagogica.ui.CCTableCellRenderer.
 
CCTableCellRenderer.UIResource - class org.concord.pedagogica.ui.CCTableCellRenderer.UIResource.
A subclass of DefaultTableCellRenderer that implements UIResource.
CCTableCellRenderer.UIResource() - Constructor for class org.concord.pedagogica.ui.CCTableCellRenderer.UIResource
 
CCTableCellRenderer() - Constructor for class org.concord.pedagogica.ui.CCTableCellRenderer
Creates a default table cell renderer.
CCTimer - class org.concord.collisions.engine.CCTimer.
 
CCTimer(int, ActionListener, int) - Constructor for class org.concord.collisions.engine.CCTimer
creates new instance of CCTimer
CCUnit - class org.concord.util.CCUnit.
 
CCUnit(String, String, boolean, int, int, int, byte, byte, byte, byte, byte, byte, byte, byte, byte, float, float, boolean, boolean) - Constructor for class org.concord.util.CCUnit
 
CCUnsuppOperationException - exception org.concord.util.CCUnsuppOperationException.
 
CCUnsuppOperationException() - Constructor for class org.concord.util.CCUnsuppOperationException
 
CCUnsuppOperationException(String) - Constructor for class org.concord.util.CCUnsuppOperationException
 
CCXMLDecoder - class org.concord.util.beans.CCXMLDecoder.
This is a bean decoder back-compliant with Java prior-1.4 version using reflection.
CCXMLDecoder(InputStream) - Constructor for class org.concord.util.beans.CCXMLDecoder
 
CCXMLEncoder - class org.concord.util.beans.CCXMLEncoder.
This is a bean encoder back-compliant with Java prior-1.4 version using reflection.
CCXMLEncoder(OutputStream) - Constructor for class org.concord.util.beans.CCXMLEncoder
 
CCXMLText - class org.concord.pedagogica.ui.CCXMLText.
 
CCXMLText() - Constructor for class org.concord.pedagogica.ui.CCXMLText
 
CCXMLText(String) - Constructor for class org.concord.pedagogica.ui.CCXMLText
 
ceil(double) - Method in class org.concord.flash.player.builtin.FMath
 
CELL_SELECTED - Static variable in class org.concord.pedagogica.ui.TableInputModel
 
CELL_TEXT_CHANGED - Static variable in class org.concord.pedagogica.ui.TableInputModel
 
CellArc - class org.concord.biologica.ui.CellArc.
CellArc has the information necessary to draw an arc to represent a portion of a cell boundary.
CellArc(int, int, int, int, int, int) - Constructor for class org.concord.biologica.ui.CellArc
Create a new CellArc
CellBorder - class org.concord.pedagogica.ui.CellBorder.
 
CellBorder() - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellBorder(Color) - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellBorder(Color, int) - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellBorder(Color, int, int) - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellBorder(int) - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellBorder(int, int) - Constructor for class org.concord.pedagogica.ui.CellBorder
 
CellLine - class org.concord.biologica.ui.CellLine.
CellLine has the information necessary to draw a line to represent a portion of a cell boundary.
CellLine() - Constructor for class org.concord.biologica.ui.CellLine
Create a new CellLine
CellLine(int, int, int, int) - Constructor for class org.concord.biologica.ui.CellLine
Create a new CellLine
cellSize - Variable in class org.concord.util.LineGraph
 
CENTER_ORIGIN - Static variable in class org.concord.collisions.ui.PassiveIcon
 
centerOfMass - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
centerOfMass(Atom[]) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
changedUpdate(DocumentEvent) - Method in class org.concord.util.TextReader
 
changedUpdate(DocumentEvent) - Method in class org.concord.util.EditorInternalFrame
 
changeEvent - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
changeHeight - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
changeHeightAndY - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
changes - Variable in class org.concord.biologica.engine.EngineObject
Utility object which manages property change events and listeners.
changes - Variable in class org.concord.biologica.ui.UIView
Utility object which manages property change events and listeners.
changes - Variable in class org.concord.biologica.ui.FertilizationModel
Utility object which manages property change events and listeners.
changes - Variable in class org.concord.biologica.ui.MeiosisModel
Utility object which manages property change events and listeners.
changes - Variable in class org.concord.biologica.ui.SelectionSet
Utility object which manages property change events and listeners.
changes - Variable in class org.concord.biologica.ui.TreeView
Utility object which manages property change events and listeners.
changeScript(Script) - Method in interface org.concord.util.script.ScriptRuntime
 
changeScript(Script) - Method in class org.concord.util.script.ECMA
 
changeWidth - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
changeWidthAndX - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
Characteristic - class org.concord.biologica.engine.Characteristic.
This class represents a characteristic of a trait of a species.
CHARACTERISTIC_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was added to a Trait.
CHARACTERISTIC_ADDED_TO_COLUMN - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was added to a SpeciesImageColumn.
CHARACTERISTIC_ADDED_TO_ROW - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was added to a SpeciesImageRow.
CHARACTERISTIC_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHARACTERISTIC_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_IDS_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_IDS_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
CHARACTERISTIC_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
CHARACTERISTIC_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was removed from a Trait.
CHARACTERISTIC_REMOVED_FROM_COLUMN - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was removed from a SpeciesImageColumn.
CHARACTERISTIC_REMOVED_FROM_ROW - Static variable in class org.concord.biologica.engine.EngineProp
A Characteristic object was removed from a SpeciesImageRow.
Characteristic(Trait, String, int) - Constructor for class org.concord.biologica.engine.Characteristic
Creates a new characteristic with the given name.
Characteristic(Trait, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Characteristic
Create a new Characteristic and start handling XML parsing events to set the properties of this object.
CHARACTERISTICS_TEXT_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The flag indicating whether a view should draw the text for an organism's characteristics under the organism has changed.
characteristicsTextVisible - Variable in class org.concord.biologica.ui.OrganismView
Characteristics text visible boolean flag.
CharacterLiteral - class org.concord.util.script.CharacterLiteral.
This node represents a character value in the semantic tree.
CharacterLiteral(String) - Constructor for class org.concord.util.script.CharacterLiteral
 
characters(char[], int, int) - Method in class org.concord.util.LogProcess
 
characters(char[], int, int) - Method in class org.concord.biologica.engine.World
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.OrganismAllele
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Environment
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImage
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Species
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesAllele
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Organism
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Family
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.OrganismImage
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Characteristic
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.OrganismChromosome
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Gene
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.ElementContext
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Trait
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.OrganismAllelePair
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImageRow
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.Terrain
Receive notification of character data.
characters(char[], int, int) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
characters(char[], int, int) - Method in class org.concord.biologica.engine.RawNucleicAcid
Receive notification of character data.
check(double) - Method in class org.concord.molecular.engine.ConditionValue
 
checkDTCollision(float) - Method in class org.concord.collisions.engine.JPartWorld
 
checkForSingleAtomAtomCollision(float, JAtom, JAtom) - Method in class org.concord.collisions.engine.JPartWorld
 
checkForSingleAtomBoxCollision(float, JAtom, float, float, float, JRigidBox) - Method in class org.concord.collisions.engine.JPartWorld
 
checkForSingleAtomDaemonCollision(float, JAtom, float, float, float, JDaemon) - Method in class org.concord.collisions.engine.JPartWorld
 
checkForSingleAtomWallCollision(float, JAtom, float, float, float, JWall) - Method in class org.concord.collisions.engine.JPartWorld
 
checkImage(Dimension) - Method in class org.concord.flash.player.FFlash
 
checkingCollisionsSensitive() - Method in class org.concord.collisions.engine.JDaemon
 
checkPause() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
CHILD_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A child organism was added to a family.
CHILD_FAMILY_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A child Family object was added to an organism.
CHILD_FAMILY_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A child Family object was removed from an organism.
CHILD_IDS_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
CHILD_IDS_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
CHILD_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A child organism was removed from a family.
CHILDREN_ADDED_TO_VIEW - Static variable in class org.concord.biologica.ui.UIProp
Children have been added to a family in the view.
choiceQuestion - Variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
ChoiceQuestion - class org.concord.pedagogica.ui.ChoiceQuestion.
 
ChoiceQuestion() - Constructor for class org.concord.pedagogica.ui.ChoiceQuestion
 
choices - Variable in class org.concord.pedagogica.engine.QuestionState
 
choices - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
CHROMOSOME - Static variable in class org.concord.biologica.ui.Tool
 
CHROMOSOME_BOTTOM_LENGTH - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_BOTTOM_SECTION_BOTTOM - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_BOTTOM_SECTION_TOP - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_COLON_X - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_COLON_Y - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_IMAGE_HEIGHT - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_IMAGE_HEIGHT - Static variable in class org.concord.biologica.ui.ObjectPropertiesView
 
CHROMOSOME_IMAGE_WIDTH - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_IMAGE_WIDTH - Static variable in class org.concord.biologica.ui.ObjectPropertiesView
 
CHROMOSOME_MID_POINT - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_NAME - Static variable in class org.concord.biologica.ui.Tool
 
CHROMOSOME_PAIR_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_PAIR_XX - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_PAIR_XY - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_PAIR_YX - Static variable in class org.concord.biologica.engine.EngineStrings
 
CHROMOSOME_TOOL_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The enabled state of the chromosome tool has changed.
CHROMOSOME_TOOL_PICK_ON_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
Chromosome tool was used to pick on an organism.
CHROMOSOME_TOOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the chromosome tool has changed.
CHROMOSOME_TOP_LENGTH - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_TOP_SECTION_BOTTOM - Static variable in class org.concord.biologica.ui.ChromosomeView
 
CHROMOSOME_TOP_SECTION_TOP - Static variable in class org.concord.biologica.ui.ChromosomeView
Chromosome image values, used to draw genes and alleles on them
CHROMOSOME_TOTAL_LENGTH - Static variable in class org.concord.biologica.ui.ChromosomeView
 
ChromosomePracticeView - class org.concord.biologica.ui.ChromosomePracticeView.
 
ChromosomePracticeView(JFrame) - Constructor for class org.concord.biologica.ui.ChromosomePracticeView
 
CHROMOSOMES_TO_SHOW - Static variable in class org.concord.biologica.ui.UIProp
Chromosomes to show in the chromosome view.
ChromosomeSpecification - class org.concord.biologica.engine.ChromosomeSpecification.
This class represents the specification of a particular chromosome for use in creating an organism.
ChromosomeSpecification(Species, SpeciesChromosome, Vector) - Constructor for class org.concord.biologica.engine.ChromosomeSpecification
Create a new chromosome specification.
chromosomeToolCursor - Static variable in class org.concord.biologica.ui.Tool
 
chromosomeToolImageIcon - Static variable in class org.concord.biologica.ui.Tool
 
ChromosomeView - class org.concord.biologica.ui.ChromosomeView.
The chromosome view of BioLogica.
ChromosomeView() - Constructor for class org.concord.biologica.ui.ChromosomeView
Creates a chromosome view.
classes - Variable in class org.concord.pedagogica.ui.LoginPanel
 
classField - Variable in class org.concord.pedagogica.ui.LoginPanel
 
classLevels - Variable in class org.concord.pedagogica.ui.LoginPanel
 
className - Variable in class org.concord.util.LogProcess
 
className - Variable in class org.concord.util.script.HandlerDeclaration
 
ClassTree - class org.concord.pedagogica.ui.ClassTree.
 
ClassTree() - Constructor for class org.concord.pedagogica.ui.ClassTree
 
clear() - Method in class org.concord.pedagogica.ui.TabularView
 
clear() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
clearAll() - Method in class org.concord.collisions.ui.GUIPanel
remove all elements from the panel
clearAll() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
clearAllAtomsTrace() - Method in class org.concord.collisions.engine.JPartWorld
clear all traces
clearAllText() - Method in class org.concord.pedagogica.ui.TableInputView
A method which can be applied to every cell in a Punnett Square or TableInputView object.
clearAtoms() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
clearBackground(int) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
 
clearBackgroundIcon() - Method in class org.concord.collisions.ui.GUIPanel
 
clearConsole - Variable in class org.concord.pedagogica.PedAgogica
 
clearConsole() - Method in class org.concord.util.Editor
 
clearConstraints() - Method in class org.concord.collisions.engine.JWorldElement
 
clearDirtyBit() - Method in class org.concord.biologica.engine.OrganismImage
 
clearEdit() - Method in class org.concord.util.Editor
 
clearFilter() - Method in class org.concord.collisions.engine.JDaemon
 
clearForces() - Method in class org.concord.collisions.engine.JWorldElement
remove all applied forces
clearGrid() - Method in class org.concord.collisions.ui.GUIPanel
 
clearIcon() - Method in class org.concord.collisions.engine.JAtom
sets icon to don't show
clearLastError() - Method in class org.concord.pedagogica.engine.ActivityScript
 
clearLastError() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
clearLastError() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
clearLastError() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
clearMap() - Method in class org.concord.util.BarGraph
Resets the index mapping.
clearNodeFromTitle() - Method in class org.concord.pedagogica.ui.RunActivity
 
clearOriginElement() - Method in class org.concord.collisions.ui.GUIPanel
 
clearSearchResult() - Method in class org.concord.pedagogica.ui.ActivityView
 
clearSelected() - Method in class org.concord.pedagogica.ui.ActivityView
 
clearSound() - Method in class org.concord.collisions.engine.JPartWorld
set soundOn property to false so you won't be able to use sound threads
clearStatus() - Method in interface org.concord.util.script.ScriptRuntime
 
clearStatus() - Method in class org.concord.util.script.ECMA
 
clearTemporaryOffsets() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Clear temporary offsets.
clearTemporaryOffsets() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Clear temporary offsets.
clearTrace() - Method in class org.concord.collisions.engine.JAtom
clears trace
clearWorld() - Method in class org.concord.collisions.engine.JPartWorld
remove walls and atoms from the world
client - Variable in class org.concord.pedagogica.engine.Logging
 
clip - Variable in class org.concord.flash.player.FMovieBuilder
 
clone() - Method in class org.concord.flash.player.FScriptObject
 
clone() - Method in class org.concord.flash.player.builtin.FArray
 
clone() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
cloneView - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
close() - Method in class org.concord.util.TextReader
 
close() - Method in class org.concord.util.TextWriter
 
close() - Method in class org.concord.util.TextOutputStream
 
close() - Method in class org.concord.util.beans.XMLDecoder
This method closes the input stream associated with this stream.
close() - Method in class org.concord.util.beans.CCXMLEncoder
 
close() - Method in class org.concord.util.beans.CCXMLDecoder
 
close() - Method in class org.concord.util.beans.XMLEncoder
This method calls flush, writes the closing postamble and then closes the output stream associated with this stream.
close() - Method in class org.concord.util.script.ScriptFileOutputStream
 
close() - Method in class org.concord.util.script.ScriptFileInputStream
 
close() - Method in class org.concord.biologica.engine.World
Close the current engine, which is identical to delete -- I think!
closeAll() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
closeDialog - Variable in class org.concord.pedagogica.PedAgogica
 
closeDocument() - Method in class org.concord.util.Editor
 
closeEverything() - Method in class org.concord.pedagogica.graph.GenericDataSource
 
closeEverything() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
closeEverything() - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
closeFrame(JInternalFrame) - Method in class org.concord.util.Editor.EditorDesktopManager
 
closeLabel - Variable in class org.concord.pedagogica.PedAgogica
 
closePanel - Variable in class org.concord.pedagogica.PedAgogica
 
closer - Variable in class org.concord.pedagogica.ui.RunActivity
 
code - Variable in class org.concord.util.CCUnit
 
codes - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
Codon - class org.concord.biologica.engine.Codon.
This class represents a Codon object, groups of 3 bases which code for particular amino acids.
Codon() - Constructor for class org.concord.biologica.engine.Codon
 
COHORTS - Static variable in class org.concord.util.LogProcess
 
CollControl - interface org.concord.collisions.ui.CollControl.
 
collectData() - Method in class org.concord.pedagogica.graph.GenericDataSource
 
collidedObject - Variable in class org.concord.collisions.event.CollisionsEvent
 
collisionHistory - Variable in class org.concord.collisions.engine.JDaemon
 
collisionOccured(CollisionsEvent) - Method in interface org.concord.collisions.event.CollisionsListener
 
collisionOccured(CollisionsEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
collisionOccured(CollisionsEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
collisionOccured(CollisionsEvent) - Method in class org.concord.collisions.ui.IngridProblem
 
CollisionsEvent - class org.concord.collisions.event.CollisionsEvent.
 
CollisionsEvent(Object, Object, int, long, int, int) - Constructor for class org.concord.collisions.event.CollisionsEvent
 
CollisionsListener - interface org.concord.collisions.event.CollisionsListener.
 
collSensitive - Variable in class org.concord.collisions.engine.JWorldElement
 
color - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
color - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
color - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
COLOR - Static variable in class org.concord.biologica.engine.EngineProp
The color of an engine object.
COLOR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
COLOR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
color(Color) - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
colorList - Variable in class org.concord.util.LineGraph
 
colors - Static variable in interface org.concord.util.ValueGraph
 
ColorUtil - class org.concord.biologica.datasupport.ColorUtil.
 
ColorUtil() - Constructor for class org.concord.biologica.datasupport.ColorUtil
 
COLUMN_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
COLUMN_INDEX - Static variable in class org.concord.biologica.engine.EngineProp
The column index of an OrganismImage in its SpeciesImage object.
COLUMN_INDEX_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
COLUMN_INDEX_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
columnCount - Variable in class org.concord.pedagogica.ui.TabularView
 
columnLabel - Variable in class org.concord.pedagogica.PedAgogica
 
columnStatus - Variable in class org.concord.pedagogica.PedAgogica
 
columnWidths - Variable in class org.concord.pedagogica.ui.TabularView
 
COMMA - Static variable in class org.concord.biologica.engine.EngineStrings
 
COMMAND_CHROMOSOME - Static variable in class org.concord.biologica.ui.Tool
 
COMMAND_CROSS - Static variable in class org.concord.biologica.ui.Tool
 
COMMAND_PEDIGREE - Static variable in class org.concord.biologica.ui.Tool
 
COMMAND_SELECTION - Static variable in class org.concord.biologica.ui.Tool
 
COMMAND_SNIP - Static variable in class org.concord.biologica.ui.Tool
 
compareCharacteristics(Organism) - Method in class org.concord.biologica.engine.Organism
 
compareTo(Object) - Method in class org.concord.flash.player.FComponent
Used to sort a collection of component by its depth.
component - Variable in class org.concord.pedagogica.engine.NodeAccess
 
component - Variable in class org.concord.pedagogica.ui.RunActivity
 
component - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.PedigreeView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.ToolView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Component events
componentHidden(ComponentEvent) - Method in class org.concord.biologica.ui.SexView
Component events
componentList - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
componentList - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.PedigreeView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.ToolView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
 
componentMoved(ComponentEvent) - Method in class org.concord.biologica.ui.SexView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.PedigreeView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.ToolView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
 
componentResized(ComponentEvent) - Method in class org.concord.biologica.ui.SexView
 
components - Variable in class org.concord.pedagogica.engine.NodeAccess
 
components - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
componentScroll - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.PedigreeView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.ToolView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
 
componentShown(ComponentEvent) - Method in class org.concord.biologica.ui.SexView
 
componentTable - Variable in class org.concord.pedagogica.engine.NodeAccess
 
computeBounds(FontMetrics) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
concat(Object[]) - Method in class org.concord.flash.player.builtin.FArray
 
conditionEvent - Variable in class org.concord.molecular.engine.ConditionValue
 
ConditionEvent - class org.concord.molecular.engine.ConditionEvent.
 
ConditionEvent(Object) - Constructor for class org.concord.molecular.engine.ConditionEvent
 
ConditionListener - interface org.concord.molecular.engine.ConditionListener.
 
conditionUpdate(ConditionEvent) - Method in interface org.concord.molecular.engine.ConditionListener
 
ConditionValue - class org.concord.molecular.engine.ConditionValue.
 
ConditionValue() - Constructor for class org.concord.molecular.engine.ConditionValue
 
consoleScroll - Variable in class org.concord.pedagogica.PedAgogica
 
consoleText - Variable in class org.concord.pedagogica.PedAgogica
 
consoleText - Variable in class org.concord.pedagogica.ui.ActivityView
 
constructor - Variable in class org.concord.util.script.InvocationExpression
 
constructor - Variable in class org.concord.util.script.IndexExpression
 
contains(EngineObject) - Method in class org.concord.biologica.ui.SelectionSet
Returns whether or not this selection set contains the given object.
contains(int, int) - Method in class org.concord.biologica.ui.CellArc
 
contains(PedigreeFamily) - Method in class org.concord.biologica.ui.PedigreeLevel
Does this level contain this pedigreeFamily
contains(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeLevel
Does this level contain this pedigreeOrganism? Looks within families and at stand-alone organisms.
contains(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeFamily
Does this family contain this pedigreeOrganism
contains(Rectangle) - Method in class org.concord.biologica.ui.CellArc
 
containsCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.Organism
Returns true or false on whether this organism contains the given characteristic.
containsCharacteristic(String) - Method in class org.concord.biologica.engine.Organism
Returns true or false on whether this organism contains the a characteristic with the given name.
containsFatalCharacteristic() - Method in class org.concord.biologica.engine.Organism
Returns true or false on whether this organism contains a fatal characteristic.
containsIfSpeciesAllele(SpeciesAllele) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return if the if species alleles contains the given species allele
containsOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeView
Returns whether or not the given organism is in this view.
containsOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Returns whether or not the given organism is in this view.
containsOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeLevel
Does this level contain this organism? Looks within families and at stand-alone organisms.
containsOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeFamily
Does this family contain this Organism?
contentData - Variable in class org.concord.pedagogica.ui.LogView
 
contentPane - Variable in class org.concord.util.PathDialog
 
contentPane - Variable in class org.concord.pedagogica.PedAgogica
 
contentPane - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
contentPane - Variable in class org.concord.pedagogica.ui.VariableDialog
 
contentPane - Variable in class org.concord.pedagogica.ui.RunActivity
 
contentPane - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
context - Variable in class org.concord.util.script.Script
 
continueSteps() - Method in class org.concord.collisions.engine.JPartWorld
continueSteps continues simulation all timers will be started
continueSteps() - Method in class org.concord.collisions.engine.BedSpringWorld
 
continueSteps() - Method in class org.concord.collisions.ui.GUIPanel
continue simulation
controllable - Variable in class org.concord.collisions.engine.JWorldElement
 
controlMenu - Variable in class org.concord.pedagogica.ui.ActivityView
 
controlPanel - Variable in class org.concord.util.PathDialog
 
controlPanel - Variable in class org.concord.pedagogica.ui.VariableDialog
 
convertChromosomeNumberTypeToString(int) - Static method in class org.concord.biologica.engine.SpeciesChromosome
Convert a chromosome number type to a string.
convertFileName(String) - Method in class org.concord.pedagogica.engine.Logging
 
convertStringToChromosomeNumberType(String) - Static method in class org.concord.biologica.engine.SpeciesChromosome
Convert a chromosome number type string to an int
convertToBoolean(Object) - Method in class org.concord.flash.player.StackFrame4
 
convertToFloat(Object) - Method in class org.concord.flash.player.StackFrame4
 
convertToInt(Object) - Method in class org.concord.flash.player.StackFrame4
 
convertTransform(Transform) - Static method in class org.concord.flash.player.FUtil
Creates a java transform from a Flash transform.
convertTransform(Transform, double, double) - Static method in class org.concord.flash.player.FUtil
Creates a java transform from a Flash transform.
convertTransform2(Transform) - Static method in class org.concord.flash.player.FUtil
Creates a java transform from a Flash transform.
convertTransform3(Transform) - Static method in class org.concord.flash.player.FUtil
Creates a java transform from a Flash transform.
COPY_SELECTED - Static variable in class org.concord.pedagogica.ui.ActivityView
 
copy(File, File) - Method in class org.concord.pedagogica.ui.ActivityView
 
copyButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
copyEdit() - Method in class org.concord.util.Editor
 
copySelectedItems() - Method in class org.concord.pedagogica.ui.ActivityView
 
correctV(float) - Method in class org.concord.collisions.engine.JAtom
 
cos(double) - Method in class org.concord.flash.player.builtin.FMath
 
cos(float) - Static method in class org.concord.collisions.engine.JPartWorld
 
count - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
COUNT - Static variable in class org.concord.molecular.engine.ConditionValue
 
count(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
courseLevel - Variable in class org.concord.pedagogica.engine.Logging
 
courseName - Variable in class org.concord.pedagogica.engine.Logging
 
CREATE_ARC_ITEM - Static variable in class org.concord.pedagogica.ui.ActivityView
 
CREATE_NODE_ITEM - Static variable in class org.concord.pedagogica.ui.ActivityView
 
create(Class, Object, String) - Static method in class org.concord.util.beans.EventHandler
Creates an implementation of listenerInterface in which all of the methods in the listener interface apply the handler's action to the target.
create(Class, Object, String, String) - Static method in class org.concord.util.beans.EventHandler
Creates an implementation of listenerInterface in which all of the methods pass the value of the event expression, eventPropertyName, to the final method in the statement, action, which is applied to the target.
create(Class, Object, String, String, String) - Static method in class org.concord.util.beans.EventHandler
Creates an implementation of listenerInterface in which the method named listenerMethodName passes the value of the event expression, eventPropertyName, to the final method in the statement, action, which is applied to the target.
create(float[], LabBookSession) - Static method in class org.concord.pedagogica.graph.ArrayDataSource
 
create(LabBookSession, float) - Static method in class org.concord.pedagogica.graph.GenericDataSource
 
create(String) - Method in interface org.concord.pedagogica.engine.DomainView
 
create(String) - Method in interface org.concord.pedagogica.engine.DomainModel
 
create(String) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
createArcItem(Vector, Vector, int, int) - Method in class org.concord.pedagogica.ui.ActivityView
 
createArrayDataSource(float[]) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
createAtom(float, float, float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default radius and mass).
createAtom(float, float, float, float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default mass).
createAtom(GUIPanel, float, float, float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default radius and mass).
createAtom(GUIPanel, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default mass).
createBedSpringWorld() - Method in class org.concord.collisions.ui.GUIElementsFrame
 
createBooster(float, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JBooster
Creates a new booster
createButton() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
createButton() - Method in class org.concord.pedagogica.ui.SurveyChoice
 
createButton() - Method in class org.concord.pedagogica.ui.MultipleChoice
 
createCCFontFromFONTElement(Element, CCXMLText.CCFont) - Static method in class org.concord.pedagogica.ui.CCXMLText
 
createCCFontFromTEXTElement(Element, CCXMLText.CCFont) - Static method in class org.concord.pedagogica.ui.CCXMLText
 
createChildNodes() - Method in class org.concord.biologica.ui.TreeViewNode
Create the child nodes of this node.
createComponent(Attributes) - Method in class org.concord.pedagogica.engine.NodeAccess
 
createComponent(Attributes) - Method in class org.concord.pedagogica.ui.RunActivity
 
createComponent(Attributes) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
createConstantForceDaemon(float, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JImpulseDaemon
 
createdArc - Variable in class org.concord.pedagogica.ui.ActivityView
 
createDefaultCalculator() - Method in class org.concord.collisions.engine.JWorldElement
 
createEventHandlerClass(String) - Method in class org.concord.util.script.ScriptClassLoader
 
createGenericDataSource(float) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
createGraphView() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
createGrid(int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createHashIndex(int, int) - Static method in class org.concord.biologica.datasupport.ImageReader
 
createIcon(String, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createIcon(String, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createIcon(String, int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createImpulseDaemon(float, float, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JImpulseDaemon
Creates a new impulse daemon
createInstance(String) - Method in class org.concord.pedagogica.engine.NodeAccess
 
createLine(int, int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createLine(int, int, int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createModifyValueDialog(JFrame) - Method in class org.concord.pedagogica.ui.VariableDialog
 
createModifyValueDialog(JFrame) - Method in class org.concord.pedagogica.ui.StringDialog
 
createMotionlessAtom(float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default mass).
createMotionlessAtom(float, float, float) - Static method in class org.concord.collisions.engine.JAtom
factory method (default mass).
createNodeItem(Vector, int, int) - Method in class org.concord.pedagogica.ui.ActivityView
 
createObj(String, LObjDictionaryView) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
createOrganism(String, int) - Method in class org.concord.biologica.ui.PracticeView
 
createOval(int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createPlacement(Attributes) - Method in class org.concord.pedagogica.engine.NodeAccess
 
createPlacement(Attributes) - Method in class org.concord.pedagogica.ui.RunActivity
 
createPlacement(Attributes) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
createPopupMenu(int) - Method in class org.concord.collisions.ui.DataCrossPanel
 
createPopupMenu(JWorldElement) - Method in class org.concord.collisions.ui.GUIPanel
 
createPopupMenu(PassiveElement) - Method in class org.concord.collisions.ui.GUIPanel
 
createRectangle(int, int, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createRectangle(int, int, int, int, boolean) - Static method in class org.concord.collisions.ui.PassiveElement
 
createRectangle2DDouble(double, double, double, double) - Method in class org.concord.molecular.ui.MolecularView
 
createRectangle2DFloat(float, float, float, float) - Method in class org.concord.molecular.ui.MolecularView
 
createRigidBox(float, float, float, float, float) - Static method in class org.concord.collisions.engine.JRigidBox
 
createSolarSystemFactors() - Static method in class org.concord.collisions.engine.CCScalingFactors
 
createText(String, int, int) - Static method in class org.concord.collisions.ui.PassiveElement
 
createTransferClient(String, int, String) - Static method in class org.concord.util.Transfer
 
createTransferClient(String, String) - Static method in class org.concord.util.Transfer
 
createTransferServer(int) - Static method in class org.concord.util.Transfer
 
createTreeWalker(String) - Method in class org.concord.pedagogica.ui.LogView
 
createView(Attributes) - Method in class org.concord.pedagogica.engine.NodeAccess
 
createView(Attributes) - Method in class org.concord.pedagogica.ui.RunActivity
 
createView(Attributes) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
createViewItem(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
createWall(float, float, float, float, boolean) - Static method in class org.concord.collisions.engine.JWall
factory method
createWall(float, float, float, float, float) - Static method in class org.concord.collisions.engine.JWall
factory method
createWall(GUIPanel, float, float, float, float, boolean) - Static method in class org.concord.collisions.engine.JWall
factory method
createWall(GUIPanel, float, float, float, float, float) - Static method in class org.concord.collisions.engine.JWall
factory method
createWorld(float, float) - Method in class org.concord.collisions.ui.GUIPanel
 
CRICKIUM - Static variable in class org.concord.molecular.ui.MolecularView
 
CROSS - Static variable in class org.concord.biologica.ui.Tool
 
CROSS_FAILED - Static variable in class org.concord.biologica.ui.UIProp
A cross failed in the pedigree view, usually because the user tried to cross to organisms of the same sex.
CROSS_NAME - Static variable in class org.concord.biologica.ui.Tool
 
CROSS_SUCCEEDED - Static variable in class org.concord.biologica.ui.UIProp
A cross was done successfully in the pedigree view.
CROSS_TOOL_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The enabled state of the cross tool has changed.
CROSS_TOOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the cross tool has changed.
CrossOver - class org.concord.biologica.engine.CrossOver.
 
CROSSOVER_CONTROLS_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
Crossover controls visible in big meiosis view.
CrossOver() - Constructor for class org.concord.biologica.engine.CrossOver
 
crossOverOrganism(Organism) - Method in class org.concord.biologica.engine.CrossOver
create a fake
crossOverWith(Branch) - Method in class org.concord.biologica.engine.Branch
 
crossToolCursor - Static variable in class org.concord.biologica.ui.Tool
 
crossToolImageIcon - Static variable in class org.concord.biologica.ui.Tool
 
Crypt - class org.concord.util.Crypt.
jcrypt.java Java-based implementation of the unix crypt command Based upon C source code written by Eric Young, eay@psych.uq.oz.au
crypt(String, String) - Static method in class org.concord.util.Crypt
 
CURRENT_SPECIES - Static variable in class org.concord.biologica.engine.EngineProp
The current species in a world changed.
CURRENT_TERRAIN - Static variable in class org.concord.biologica.engine.EngineProp
The current terrain in a world changed.
currentActionItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
currentActivationStep - Variable in class org.concord.collisions.engine.JDaemon
 
currentColor - Variable in class org.concord.pedagogica.ui.ActivityView
 
currentFrame - Variable in class org.concord.util.script.ScriptThread
 
currentFrame() - Method in class org.concord.flash.player.FMovieBuilder
 
currentLocation - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
currentNode - Variable in class org.concord.pedagogica.engine.Activity
 
currentNode - Variable in class org.concord.pedagogica.ui.RunActivity
 
currentNodeDone() - Method in class org.concord.pedagogica.engine.Activity
 
currentString - Variable in class org.concord.pedagogica.engine.Activity
 
currentString - Variable in class org.concord.pedagogica.ui.ActivityView
 
currentText - Variable in class org.concord.util.LogProcess
 
curriculum - Variable in class org.concord.pedagogica.engine.Activity
 
currx - Variable in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
curry - Variable in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
cursorColor - Variable in class org.concord.biologica.ui.DNAView
Cursor color
CursorText - class org.concord.biologica.ui.CursorText.
 
CursorText(Component, String) - Constructor for class org.concord.biologica.ui.CursorText
 
curve(int, int, int, int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
CustomChoiceQuestion - class org.concord.pedagogica.ui.CustomChoiceQuestion.
 
CustomChoiceQuestion() - Constructor for class org.concord.pedagogica.ui.CustomChoiceQuestion
 
CustomEssayFill - class org.concord.pedagogica.ui.CustomEssayFill.
 
CustomEssayFill() - Constructor for class org.concord.pedagogica.ui.CustomEssayFill
 
CustomEssayFill(String) - Constructor for class org.concord.pedagogica.ui.CustomEssayFill
 
CustomQuestion - class org.concord.pedagogica.ui.CustomQuestion.
 
CustomQuestion() - Constructor for class org.concord.pedagogica.ui.CustomQuestion
 
CustomTableQuestion - class org.concord.pedagogica.ui.CustomTableQuestion.
 
CustomTableQuestion() - Constructor for class org.concord.pedagogica.ui.CustomTableQuestion
 
CUT_SELECTED - Static variable in class org.concord.pedagogica.ui.ActivityView
 
cutButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
cutEdit() - Method in class org.concord.util.Editor
 
cutSelectedItems() - Method in class org.concord.pedagogica.ui.ActivityView
 
cxform - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
CYS - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Cysteine
CYSTEINE - Static variable in class org.concord.biologica.engine.AminoAcid
Cysteine
CYTOSINE - Static variable in class org.concord.biologica.engine.Base
A purine which links with guanine in DNA and RNA.

D

daemonActivated(DaemonEvent) - Method in interface org.concord.collisions.event.DaemonListener
 
daemonDeactivated(DaemonEvent) - Method in interface org.concord.collisions.event.DaemonListener
 
DaemonEvent - class org.concord.collisions.event.DaemonEvent.
 
DaemonEvent(Object) - Constructor for class org.concord.collisions.event.DaemonEvent
 
daemonFinished(DaemonEvent) - Method in interface org.concord.collisions.event.DaemonListener
 
DaemonListener - interface org.concord.collisions.event.DaemonListener.
 
daemonsDragMode - Variable in class org.concord.collisions.ui.GUIPanel
 
daemonStarted(DaemonEvent) - Method in interface org.concord.collisions.event.DaemonListener
 
DASH - Static variable in class org.concord.biologica.engine.EngineStrings
 
DataCrossPanel - class org.concord.collisions.ui.DataCrossPanel.
 
DataCrossPanel() - Constructor for class org.concord.collisions.ui.DataCrossPanel
 
DataCrossPanel(float) - Constructor for class org.concord.collisions.ui.DataCrossPanel
 
DataOrganism - class org.concord.biologica.datasupport.DataOrganism.
 
DataOrganism() - Constructor for class org.concord.biologica.datasupport.DataOrganism
 
dataOutput - Variable in class org.concord.util.LogProcess
 
DATE - Static variable in class org.concord.util.LogProcess
 
deactivate() - Method in class org.concord.collisions.engine.JDaemon
 
deactivate() - Method in class org.concord.collisions.engine.CCImpulseForce
 
deactivate() - Method in class org.concord.pedagogica.engine.ActivityArc
 
debug - Static variable in class org.concord.util.Debug
 
debug - Static variable in class org.concord.util.script.ScriptObject
 
debug - Variable in class org.concord.util.script.ScriptThread
 
debug - Variable in class org.concord.pedagogica.ui.ActivityView
 
debug - Variable in class org.concord.pedagogica.ui.RunActivity
 
Debug - class org.concord.util.Debug.
Debug contains useful code and constants for debugging.
Debug - class org.concord.biologica.engine.Debug.
Debug contains useful code and constants for debugging.
DEBUG - Static variable in class org.concord.util.Debug
Debug constant.
DEBUG - Static variable in class org.concord.biologica.engine.Debug
Debug constant.
Debug() - Constructor for class org.concord.util.Debug
 
Debug() - Constructor for class org.concord.biologica.engine.Debug
 
debugAll - Static variable in class org.concord.util.script.ScriptThread
 
decapitalize(String) - Static method in class org.concord.util.beans.Introspector
Utility method to take a string and convert it to normal Java variable name capitalization.
decrementStep() - Method in class org.concord.biologica.ui.FertilizationModel
Decrement the current step of the fertilization, returning the new current step value.
decrementStep() - Method in class org.concord.biologica.ui.MeiosisModel
Decrement the current step of the meiosis, returning the new current step value.
DEFAULT - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_CALC_DT - Static variable in class org.concord.collisions.engine.JPartWorld
 
DEFAULT_COURSE - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_CUTOFF - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_DELAY - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_DELTA - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_DESCENT - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_DRAW_DT - Static variable in class org.concord.collisions.engine.JPartWorld
 
DEFAULT_FONT - Static variable in class org.concord.pedagogica.ui.CustomQuestion
 
DEFAULT_FONT - Static variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
DEFAULT_FONT - Static variable in class org.concord.pedagogica.ui.CustomEssayFill
 
DEFAULT_GAUGE_WIDTH - Static variable in class org.concord.util.BarGraph
 
DEFAULT_HEIGHT - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_HEIGHT - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
DEFAULT_HOST - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_INSTRUCTOR - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_INTERVAL - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_INTERVAL - Static variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
DEFAULT_LINE - Static variable in class org.concord.pedagogica.ui.EssayFill
 
DEFAULT_LOG_PATH - Static variable in class org.concord.pedagogica.engine.LogModel
 
DEFAULT_MASS - Static variable in class org.concord.collisions.engine.JRigidBox
 
DEFAULT_MASS - Static variable in class org.concord.collisions.engine.JWall
 
DEFAULT_MASS - Static variable in class org.concord.collisions.engine.JAtom
 
DEFAULT_MAX_CONSTRAINT - Static variable in class org.concord.collisions.engine.JWorldElement
 
DEFAULT_MAX_VALUE - Static variable in class org.concord.util.Gauge
 
DEFAULT_MIN_CONSTRAINT - Static variable in class org.concord.collisions.engine.JWorldElement
 
DEFAULT_MIN_VALUE - Static variable in class org.concord.util.Gauge
 
DEFAULT_NUMBER_OF_GAUGES - Static variable in class org.concord.util.BarGraph
 
DEFAULT_PORT - Static variable in class org.concord.util.Transfer
 
DEFAULT_PORT - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_RADIUS - Static variable in class org.concord.collisions.engine.JAtom
 
DEFAULT_SITE - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_SKIN - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_TEMPERATURE - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_THICKNESS - Static variable in class org.concord.collisions.engine.JRigidBox
 
DEFAULT_THICKNESS - Static variable in class org.concord.collisions.engine.JWall
 
DEFAULT_USER - Static variable in class org.concord.pedagogica.engine.Logging
 
DEFAULT_VALUE - Static variable in class org.concord.util.Gauge
 
DEFAULT_WIDTH - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DEFAULT_WIDTH - Static variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
DEFAULT_WIDTH - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
DEFAULT_WIDTH - Static variable in class org.concord.pedagogica.ui.EssayFill
 
DefaultAtomicModel - class org.concord.molecular.engine.DefaultAtomicModel.
This class is a convenience class for using the Oslet AtomicModel It attempts to simplify the use of this view in activity by providing a specific set of methods for parameterizing the model.
DefaultAtomicModel() - Constructor for class org.concord.molecular.engine.DefaultAtomicModel
 
DefaultAtomicModel(int, int) - Constructor for class org.concord.molecular.engine.DefaultAtomicModel
 
DefaultMolecularModel - class org.concord.molecular.engine.DefaultMolecularModel.
 
DefaultMolecularModel() - Constructor for class org.concord.molecular.engine.DefaultMolecularModel
 
DefaultMolecularModel(int, int) - Constructor for class org.concord.molecular.engine.DefaultMolecularModel
 
DefaultPersistenceDelegate - class org.concord.util.beans.DefaultPersistenceDelegate.
The DefaultPersistenceDelegate is a concrete implementation of the abstract PersistenceDelegate class and is the delegate used by default for classes about which no information is available.
DefaultPersistenceDelegate() - Constructor for class org.concord.util.beans.DefaultPersistenceDelegate
Creates a persistence delegate for a class with a nullary constructor.
DefaultPersistenceDelegate(String[]) - Constructor for class org.concord.util.beans.DefaultPersistenceDelegate
Creates a default persistence delegate for a class with a constructor whose arguments are the values of the property names as specified by constructorPropertyNames.
DefaultPrinter - class org.concord.pedagogica.ui.DefaultPrinter.
 
DefaultPrinter() - Constructor for class org.concord.pedagogica.ui.DefaultPrinter
 
defaultSize - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
defaultStep - Variable in class org.concord.molecular.ui.MolecularView
 
defaultWorldFile - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
DEFER_APPLY - Static variable in class org.concord.biologica.ui.UIProp
Defer Apply flag changed.
DEFER_REVERT - Static variable in class org.concord.biologica.ui.UIProp
Defer Revert flag changed.
defGlyphs - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
defineClass(String, byte[], Object) - Method in class org.concord.util.script.Script.ScriptSecuritySupport
Define and load a Java class.
defineElementA(double, double, double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
defineElementB(double, double, double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
defineElementC(double, double, double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
defineElementD(double, double, double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
defineFillStyle(Color) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
defineFillStyle(int, Matrix, boolean) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
defineFillStyle(Matrix, int[], Color[], boolean) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
defineLineStyle(int, Color) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
delay - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DELETE_SELECTED - Static variable in class org.concord.pedagogica.ui.ActivityView
 
delete() - Method in class org.concord.util.script.ScriptObject
 
delete() - Method in class org.concord.util.script.BinaryExpression
 
delete() - Method in class org.concord.util.script.FactAssignStatement
 
delete() - Method in class org.concord.util.script.UnaryExpression
 
delete() - Method in class org.concord.util.script.InvocationExpression
 
delete() - Method in class org.concord.util.script.ExpressionStatement
 
delete() - Method in class org.concord.util.script.ListenStatement
 
delete() - Method in class org.concord.util.script.SequenceLiteral
 
delete() - Method in class org.concord.util.script.LoopStatement
 
delete() - Method in class org.concord.util.script.BlockStatement
 
delete() - Method in class org.concord.util.script.NameStack
 
delete() - Method in class org.concord.util.script.ImportDeclaration
 
delete() - Method in class org.concord.util.script.AssignmentStatement
 
delete() - Method in class org.concord.util.script.IndexExpression
 
delete() - Method in class org.concord.util.script.Script
 
delete() - Method in class org.concord.util.script.IfThenElseStatement
 
delete() - Method in class org.concord.util.script.ObjectExpression
 
delete() - Method in class org.concord.util.script.MethodDeclaration
 
delete() - Method in class org.concord.util.script.HandlerDeclaration
 
delete() - Method in class org.concord.util.script.ReturnStatement
 
delete() - Method in class org.concord.util.script.ExtendsDeclaration
 
delete() - Method in class org.concord.util.script.ReferenceExpression
 
delete() - Method in class org.concord.biologica.engine.EngineObject
Deletes the object, notifying any containing objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.World
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.SpeciesChromosome
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.OrganismAllele
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Environment
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.SpeciesImage
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Species
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.NucleicAcid
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.SpeciesAllele
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Organism
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Family
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.OrganismImage
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Characteristic
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in interface org.concord.biologica.engine.INucleicAcid
Delete this nucleic acid - redundant with EngineObject in most cases.
delete() - Method in class org.concord.biologica.engine.OrganismChromosome
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Gene
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Trait
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.OrganismAllelePair
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.SpeciesImageRow
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.Terrain
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.engine.RawNucleicAcid
Delete this object, notifying parent objects and deleting any child objects.
delete() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Delete this chromosome model.
delete() - Method in class org.concord.biologica.ui.FertilizationModel
Deletes this model and associated models
delete() - Method in class org.concord.biologica.ui.MeiosisModel
Deletes this model and associated models
delete() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Delete this chromosome model.
delete() - Method in class org.concord.pedagogica.engine.ActivityScript
 
delete() - Method in class org.concord.pedagogica.engine.ActivityNode
 
delete() - Method in class org.concord.pedagogica.engine.ActivityArc
Delete the ActivityArc object.
delete() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
delete() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
delete() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
delete(boolean) - Method in class org.concord.biologica.engine.World
 
delete(boolean) - Method in class org.concord.biologica.engine.SpeciesChromosome
 
delete(boolean) - Method in class org.concord.biologica.engine.OrganismAllele
 
delete(boolean) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
 
delete(boolean) - Method in class org.concord.biologica.engine.SpeciesImageColumn
 
delete(boolean) - Method in class org.concord.biologica.engine.Environment
 
delete(boolean) - Method in class org.concord.biologica.engine.SpeciesImage
 
delete(boolean) - Method in class org.concord.biologica.engine.Species
 
delete(boolean) - Method in class org.concord.biologica.engine.NucleicAcid
 
delete(boolean) - Method in class org.concord.biologica.engine.SpeciesAllele
 
delete(boolean) - Method in class org.concord.biologica.engine.Organism
 
delete(boolean) - Method in class org.concord.biologica.engine.Family
 
delete(boolean) - Method in class org.concord.biologica.engine.OrganismImage
 
delete(boolean) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
 
delete(boolean) - Method in class org.concord.biologica.engine.Characteristic
 
delete(boolean) - Method in class org.concord.biologica.engine.OrganismChromosomePair
 
delete(boolean) - Method in interface org.concord.biologica.engine.INucleicAcid
Delete this nucleic acid - redundant with EngineObject in most cases.
delete(boolean) - Method in class org.concord.biologica.engine.OrganismChromosome
 
delete(boolean) - Method in class org.concord.biologica.engine.Gene
 
delete(boolean) - Method in class org.concord.biologica.engine.Trait
 
delete(boolean) - Method in class org.concord.biologica.engine.OrganismAllelePair
 
delete(boolean) - Method in class org.concord.biologica.engine.SpeciesImageRow
 
delete(boolean) - Method in class org.concord.biologica.engine.Terrain
 
delete(boolean) - Method in class org.concord.biologica.engine.RawNucleicAcid
 
delete(boolean, boolean) - Method in class org.concord.biologica.engine.Family
 
deleteAll() - Method in class org.concord.util.script.NameStack
 
deleteAllFamilies(boolean, boolean) - Method in class org.concord.biologica.engine.World
 
deleteAllOrganisms(boolean) - Method in class org.concord.biologica.engine.World
 
deleteButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
deleteButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
deleteConfirmed - Variable in class org.concord.pedagogica.ui.ActivityView
 
deleted - Variable in class org.concord.util.script.ScriptObject
 
deleted - Variable in class org.concord.biologica.engine.EngineObject
Indicates if this object has been deleted and is waiting for garbage collection.
DELETED - Static variable in class org.concord.biologica.engine.EngineProp
DELETED simple property name.
DELETED_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
DELETED_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
deleteDialog - Variable in class org.concord.pedagogica.ui.ActivityView
 
deleteLabel - Variable in class org.concord.pedagogica.ui.ActivityView
 
deleteNode(ActivityNode) - Method in class org.concord.pedagogica.engine.Activity
 
deletePanel - Variable in class org.concord.pedagogica.ui.ActivityView
 
deletePlacement - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
deleteSelectedItems() - Method in class org.concord.pedagogica.ui.ActivityView
 
deleteSpecifiedFamilies(Vector, boolean, boolean) - Method in class org.concord.biologica.engine.World
 
deleteSpecifiedOrganisms(Vector, boolean) - Method in class org.concord.biologica.engine.World
 
delta - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
deltaX - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
deltaX - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
deltaX - Static variable in class org.concord.collisions.ui.IngridProblem
 
deltaY - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
deltaY - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
deltaY - Static variable in class org.concord.collisions.ui.IngridProblem
 
depth - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
derived - Variable in class org.concord.util.CCUnit
 
DESCEND_INTO_NODE - Static variable in class org.concord.pedagogica.ui.ActivityView
 
descent - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
DESCRIPTION - Static variable in class org.concord.biologica.engine.EngineProp
Description, indicating that the description string for an object has changed.
DESCRIPTION_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
DESCRIPTION_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
deselectAll() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
deselectAllObjects() - Method in class org.concord.biologica.ui.SelectionSet
Deselect all objects
deselectObject(EngineObject) - Method in class org.concord.biologica.ui.SelectionSet
Deselect the given object.
destGlobalUnit - Static variable in class org.concord.util.CCUnit
 
df - Static variable in class org.concord.collisions.ui.GUIPanel
 
differentBaseColor - Variable in class org.concord.biologica.ui.DNAView
Different base color
dimLess - Variable in class org.concord.util.CCUnit
 
DIPLOID_TYPE - Static variable in class org.concord.biologica.engine.EngineProp
Diploid type of a species changed, indicating that the rule for which is female or male has changed.
DIPLOID_TYPE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
DIPLOID_TYPE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
DIPLOID_TYPE_NO_SEX_CHROMOSOMES - Static variable in class org.concord.biologica.engine.Species
Third type of diploid species - no sex chromosomes (e.g.
DIPLOID_TYPE_NO_SEX_CHROMOSOMES_STRING - Static variable in class org.concord.biologica.engine.Species
 
DIPLOID_TYPE_XX_FEMALE_XY_MALE - Static variable in class org.concord.biologica.engine.Species
One type of diploid species - XX female, XY male (e.g.
DIPLOID_TYPE_XX_FEMALE_XY_MALE_STRING - Static variable in class org.concord.biologica.engine.Species
 
DIPLOID_TYPE_XY_FEMALE_XX_MALE - Static variable in class org.concord.biologica.engine.Species
Second type of diploid species - XY female, XX male (e.g.
DIPLOID_TYPE_XY_FEMALE_XX_MALE_STRING - Static variable in class org.concord.biologica.engine.Species
 
directoryName - Variable in class org.concord.pedagogica.engine.Logging
 
directoryPath - Variable in class org.concord.pedagogica.ui.LogView
 
DIRTY - Static variable in class org.concord.biologica.engine.EngineProp
Dirty property, indicating that the current Engine state has been modified since the state was last saved to a file.
dispose() - Method in class org.concord.collisions.ui.PassiveElement
 
dispose() - Method in class org.concord.collisions.ui.PassiveIcon
 
distributeAtoms() - Method in class org.concord.collisions.ui.GUIElementsFrame
 
distributeAtoms() - Method in class org.concord.collisions.ui.GUITestIngrid
 
distributeAtoms() - Method in class org.concord.collisions.ui.IngridProblem
 
distributeAtomsRandomly(int, float, float, float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
distribute atoms in given rectangle (random position and velocity) with default mass and radius
distributeAtomsRandomly(int, float, float, float, float, float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
distribute atoms in given rectangle (random position and velocity)
distributeAtomsRandomlyConstVel(int, float, float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
distribute atoms in given rectangle (random position and const velocityvalue but random direction)
distributeAtomsRandomlyConstVel(int, float, float, float, float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
distribute atoms in given rectangle (random position and const velocityvalue but random direction)
DivideExpression - class org.concord.util.script.DivideExpression.
The DivideExpression class implements the semantic node for divide.
DivideExpression() - Constructor for class org.concord.util.script.DivideExpression
 
DNA_ALTERABLE - Static variable in class org.concord.biologica.engine.EngineProp
DNA alterable flag.
DNA_ALTERABLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
DNA_ALTERABLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
DNA_AREA_DOUBLE_HEIGHT - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_AREA_GAP - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_AREA_LEFT - Static variable in class org.concord.biologica.ui.DNAView
DNA area static values, used in drawing and picking on the DNA area
DNA_AREA_SINGLE_HEIGHT - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_AREA_TOP - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_AREA_WIDTH - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_BOTTOM_STRAND - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_BOTTOM_STRAND_Y - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_CMD_APPLY - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_CMD_REVERT - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_CURSOR_HEIGHT - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_ARROWS_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_AT_DARK_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_AT_DARK_SELECTED_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_AT_LIGHT_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_CG_DARK_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_CG_DARK_SELECTED_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_CG_LIGHT_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_GC_DARK_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_GC_DARK_SELECTED_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_GC_LIGHT_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_HEIGHT - Static variable in class org.concord.biologica.ui.DNAView
DNA image values, used to draw base pairs
DNA_IMAGE_MAX_BASES - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_TA_DARK_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_TA_DARK_SELECTED_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_TA_LIGHT_INDEX - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_IMAGE_WIDTH - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_SCROLLBAR_AREA_OFFSET - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_SCROLLBAR_GARBAGE_WIDTH_IN_BASES - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_SCROLLBAR_HEIGHT - Static variable in class org.concord.biologica.ui.DNAView
Scrollbar values
DNA_TOP_STRAND - Static variable in class org.concord.biologica.ui.DNAView
Strand values
DNA_TOP_STRAND_Y - Static variable in class org.concord.biologica.ui.DNAView
 
DNA_VISIBLE - Static variable in class org.concord.biologica.engine.EngineProp
DNA visible flag.
DNA_VISIBLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
DNA_VISIBLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
DNAView - class org.concord.biologica.ui.DNAView.
The chromosome view of BioLogica.
DNAView() - Constructor for class org.concord.biologica.ui.DNAView
Creates a chromosome view.
doConversion - Variable in class org.concord.util.script.ScriptObject
 
doCrossingOver() - Method in class org.concord.biologica.ui.BigMeiosisView
Do the actual crossing over now given the current crossing over state.
document - Variable in class org.concord.util.TextReader
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JRigidBox
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JWall
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JDaemon
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JBooster
 
doDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.ui.PassiveElement
 
doDrag(CCCoordinateTuner, int, int) - Method in interface org.concord.collisions.ui.CCDraggable
 
DOMAIN - Static variable in class org.concord.util.LogProcess
 
DomainEngine - interface org.concord.pedagogica.engine.DomainEngine.
 
DomainEvent - class org.concord.pedagogica.engine.DomainEvent.
 
DomainEvent(Class, Class) - Constructor for class org.concord.pedagogica.engine.DomainEvent
 
DomainMethod - class org.concord.pedagogica.engine.DomainMethod.
 
DomainMethod(Method) - Constructor for class org.concord.pedagogica.engine.DomainMethod
 
DomainModel - interface org.concord.pedagogica.engine.DomainModel.
 
DomainView - interface org.concord.pedagogica.engine.DomainView.
 
doMetricPrefix - Variable in class org.concord.util.CCUnit
 
done - Variable in class org.concord.pedagogica.engine.Activity
 
done() - Method in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
All actions are done - place the instance
done() - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
done() - Method in class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
done() - Method in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
done() - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
done() - Method in class org.concord.pedagogica.engine.ActivityNode
 
doneButton - Variable in class org.concord.util.PathDialog
 
doneButton - Variable in class org.concord.pedagogica.ui.VariableDialog
 
doneButton - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
doOneStep() - Method in class org.concord.collisions.engine.JPartWorld
doOneStep does only one step all timers will be started
doOneStep() - Method in class org.concord.collisions.engine.BedSpringWorld
 
doOneStep() - Method in class org.concord.collisions.ui.GUIPanel
make only one simulation's step
doProjection - Variable in class org.concord.collisions.engine.JWorldElement
 
doSelectionOrganismStuff(Organism) - Method in class org.concord.biologica.ui.AllInOneView
Do selection organism stuff
dot - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
DOUBLECLICK_INTERVAL - Static variable in class org.concord.pedagogica.ui.ActivityView
 
DOWN_STATE - Static variable in class org.concord.flash.player.FButton
 
down(float, float, JComponent) - Method in class org.concord.collisions.engine.JRigidBox
shift wall down
down(float, float, JComponent) - Method in class org.concord.collisions.engine.JWall
shift wall down
downButton - Variable in class org.concord.util.PathDialog
 
downButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
DRAG_ARROW_VEL_NONE - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_ARROW_VEL_ONLYX - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_ARROW_VEL_ONLYY - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_ARROW_VEL_XY - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_DELAY - Static variable in class org.concord.pedagogica.ui.NodeViewEditor
 
DRAG_MODE_NONE - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_MODE_NORMAL - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_MODE_ONLYVX - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_MODE_ONLYVY - Static variable in class org.concord.collisions.ui.GUIPanel
 
DRAG_MODE_VEL - Static variable in class org.concord.collisions.ui.GUIPanel
 
drag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
dragArc - Variable in class org.concord.pedagogica.ui.ActivityView
 
draggable - Variable in class org.concord.collisions.engine.JWorldElement
 
draggable - Variable in class org.concord.collisions.ui.PassiveElement
 
dragGauge - Variable in class org.concord.util.Gauge
 
dragged - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
dragSelections(int, int) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
DRAW_MODE_FLAME - Static variable in class org.concord.collisions.engine.CCConstantForce
 
DRAW_MODE_ROCKET - Static variable in class org.concord.collisions.engine.CCConstantForce
 
DRAW_MODE_SIMPLE - Static variable in class org.concord.collisions.engine.CCConstantForce
 
draw(Graphics) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
drawBoundary - Variable in class org.concord.util.Gauge
 
drawBoundsValues - Variable in class org.concord.util.LineGraph
 
drawDashedStraightLine(Graphics, int, int, int, int, int, int) - Static method in class org.concord.collisions.ui.GUIPanel
used for drawing velocity projections
drawDataImage(Graphics, int, int, int, Component) - Method in class org.concord.biologica.engine.SpeciesImage
 
drawDataImage(Graphics, int, int, int, int, int, Component) - Method in class org.concord.biologica.engine.SpeciesImage
 
drawDataImage(int[], int, int, int, int, int) - Method in class org.concord.biologica.engine.SpeciesImage
 
drawLine(Graphics) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
drawMaxVelMenu(Graphics) - Method in class org.concord.collisions.ui.DataCrossPanel
 
drawNode(Graphics) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
drawSelected(Graphics) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
drawSelected(Graphics) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
drawSpring(Graphics, float, float) - Method in class org.concord.collisions.engine.CCSpring
 
drawTriangle(Graphics) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
DumpSWF - class org.concord.flash.util.DumpSWF.
Reads and parses a SWF file and dumps a textual representation to System.out.
DumpSWF() - Constructor for class org.concord.flash.util.DumpSWF
 
dynamics - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 

E

E - Static variable in class org.concord.flash.player.builtin.FMath
 
easlRuntime - Static variable in class org.concord.pedagogica.engine.NodeAccess
 
easterEggs - Variable in class org.concord.pedagogica.ui.RunActivity
 
ECMA - class org.concord.util.script.ECMA.
 
ECMA_EXT - Static variable in class org.concord.util.script.ECMA
 
ECMA() - Constructor for class org.concord.util.script.ECMA
The constructor for the ECMA parser/interpreter.
ECMA(Reader, PrintWriter) - Constructor for class org.concord.util.script.ECMA
The constructor for the ECMA parser/interpreter.
ecmaRuntime - Static variable in class org.concord.pedagogica.engine.NodeAccess
 
ecmaScript - Variable in class org.concord.util.script.Script
 
ecmaText - Variable in class org.concord.util.script.Script
 
editable - Variable in class org.concord.util.BarGraph
 
editable - Variable in class org.concord.util.Gauge
 
editable - Variable in class org.concord.collisions.ui.GUIPanel
 
Editable - interface org.concord.util.Editable.
 
editButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
editControlPanel - Variable in class org.concord.pedagogica.PedAgogica
 
editHandlerButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
editItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
Editor - class org.concord.util.Editor.
 
Editor.EditorDesktopManager - class org.concord.util.Editor.EditorDesktopManager.
 
Editor.EditorDesktopManager(Editor) - Constructor for class org.concord.util.Editor.EditorDesktopManager
 
Editor(Editable) - Constructor for class org.concord.util.Editor
 
EditorInternalFrame - class org.concord.util.EditorInternalFrame.
 
EditorInternalFrame(JDesktopPane, String, String, UndoManager) - Constructor for class org.concord.util.EditorInternalFrame
 
EditorInternalFrame(JDesktopPane, UndoManager) - Constructor for class org.concord.util.EditorInternalFrame
 
editPanel - Variable in class org.concord.pedagogica.PedAgogica
 
editPathDialog - Variable in class org.concord.pedagogica.ui.ActivityView
 
editSaved() - Method in interface org.concord.util.Editable
 
editStringDialog - Variable in class org.concord.pedagogica.ui.ActivityView
 
editStringItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
elapsedTime() - Method in class org.concord.util.LogProcess
 
ELASTIC_MODEL - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
elasticModel() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
ElementContext - class org.concord.biologica.engine.ElementContext.
This class represents a context for an XML element during the process of reading that element in from a BioLogica XML file.
ElementContext(DocumentHandler, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.ElementContext
Creates a new ElementContext.
elementList - Variable in class org.concord.pedagogica.ui.LogView
 
Elements - class org.concord.biologica.engine.Elements.
This class contains the name strings and ids for engine XML elements.
Elements() - Constructor for class org.concord.biologica.engine.Elements
 
elementScroll - Variable in class org.concord.pedagogica.ui.LogView
 
elemSource - Variable in class org.concord.collisions.engine.JWorldElementFilter
 
ELSE_CHARACTERISTIC - Static variable in class org.concord.biologica.engine.EngineProp
The "else characteristic" of a genotype to phenotype rule changed.
ELSE_CHARACTERISTIC_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ELSE_CHARACTERISTIC_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
elseIfExpressions - Variable in class org.concord.util.script.IfThenElseStatement
 
elseIfStatements - Variable in class org.concord.util.script.IfThenElseStatement
 
elseStatement - Variable in class org.concord.util.script.IfThenElseStatement
 
empty - Static variable in class org.concord.util.script.Statement
 
EMPTY_VIEW - Static variable in class org.concord.biologica.ui.SmallMeiosisView
 
emptyBorder - Variable in class org.concord.pedagogica.ui.LogView
 
emptyTrace() - Method in class org.concord.collisions.engine.JAtom
 
Encoder - class org.concord.util.beans.Encoder.
An Encoder is a class which can be used to create files or streams that encode the state of a collection of JavaBeans in terms of their public APIs.
Encoder() - Constructor for class org.concord.util.beans.Encoder
 
end - Variable in class org.concord.pedagogica.ui.ActivitySearchResult
 
endAllLogs() - Static method in class org.concord.pedagogica.engine.Logging
 
endBounds - Variable in class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
endColumn - Variable in class org.concord.util.TextSelection
 
endColumn - Variable in class org.concord.util.script.ScriptObject
 
endDocument() - Method in class org.concord.util.LogProcess
 
endDocument() - Method in class org.concord.biologica.engine.World
Handle notification that a document parse has ended.
endDocument() - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JRigidBox
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JWall
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JDaemon
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
endDrag(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.ui.PassiveElement
 
endDrag(CCCoordinateTuner, int, int) - Method in interface org.concord.collisions.ui.CCDraggable
 
endElement(String) - Method in class org.concord.biologica.engine.World
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.SpeciesChromosome
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.OrganismAllele
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Environment
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.SpeciesImage
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Species
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.SpeciesAllele
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Organism
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Family
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.OrganismImage
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Characteristic
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.OrganismChromosome
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Gene
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.ElementContext
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Trait
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in interface org.concord.biologica.engine.INucleicAcidHolder
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.OrganismAllelePair
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.SpeciesImageRow
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.Terrain
Handle notification that the parsing of the given element has ended.
endElement(String) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
endElement(String) - Method in class org.concord.biologica.engine.RawNucleicAcid
Handle notification that the parsing of the given element has ended.
endElement(String, String, String) - Method in class org.concord.util.LogProcess
 
endElement(String, String, String) - Method in class org.concord.pedagogica.engine.NodeAccess
 
endLine - Variable in class org.concord.util.TextSelection
 
endLine - Variable in class org.concord.util.script.ScriptObject
 
endLog() - Method in class org.concord.pedagogica.engine.Logging
 
enforceFileExtension(File, String) - Method in class org.concord.biologica.ui.AllInOneView
Enforce the proper file extension, if possible
EngineObject - class org.concord.biologica.engine.EngineObject.
This abstract class is the base for all BioScope engine classes and defines the basic API's that all engine classes must implement.
EngineObject() - Constructor for class org.concord.biologica.engine.EngineObject
Creates engine object, giving the object a proper ID.
EngineProp - class org.concord.biologica.engine.EngineProp.
This class contains definitions for BioLogica engine simple and vector property names.
EngineProp() - Constructor for class org.concord.biologica.engine.EngineProp
 
EngineStrings - class org.concord.biologica.engine.EngineStrings.
This class contains the strings for the engine package.
EngineStrings() - Constructor for class org.concord.biologica.engine.EngineStrings
 
enqueueEvent(Object[]) - Method in class org.concord.util.script.event.EventHandler
 
enter() - Method in class org.concord.pedagogica.engine.ActivityNode
 
enter() - Method in class org.concord.pedagogica.engine.Activity
 
enter(String, Object) - Method in class org.concord.util.script.NameStack
Set a variable value in the stack frame.
enter(String, Object, boolean) - Method in class org.concord.util.script.NameStack
 
enterCount - Variable in class org.concord.pedagogica.engine.ActivityNode
 
entryNameTable - Static variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
Enumerator - class org.concord.util.Enumerator.
 
Enumerator(Enumeration) - Constructor for class org.concord.util.Enumerator
 
Environment - class org.concord.biologica.engine.Environment.
This class represents an environment.
ENVIRONMENT_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
An Environment object was added.
ENVIRONMENT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ENVIRONMENT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ENVIRONMENT_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ENVIRONMENT_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ENVIRONMENT_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ENVIRONMENT_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
An Environment object was removed.
Environment(World, String, int, int) - Constructor for class org.concord.biologica.engine.Environment
Creates a new environment with the given name.
Environment(World, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Environment
Create a new environment and start handling XML parsing events to set the properties of this object.
epsilon1 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
epsilon1 - Variable in class org.concord.molecular.ui.MolecularView
 
epsilon2 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
epsilon2 - Variable in class org.concord.molecular.ui.MolecularView
 
epsilon3 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
epsilon3 - Variable in class org.concord.molecular.ui.MolecularView
 
epsilon4 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
epsilon4 - Variable in class org.concord.molecular.ui.MolecularView
 
EQExpression - class org.concord.util.script.EQExpression.
The EQExpression class implements the semantic node for "equals".
EQExpression() - Constructor for class org.concord.util.script.EQExpression
 
equalBaseColor - Variable in class org.concord.biologica.ui.DNAView
Equal base color
equals(Object) - Method in class org.concord.util.beans.PropertyDescriptor
Compares this PropertyDescriptor against the specified object.
equals(Object) - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Compares this PropertyDescriptor against the specified object.
error - Variable in class org.concord.pedagogica.engine.NodeAccess
 
ERROR - Static variable in class org.concord.util.Debug
 
ERROR - Static variable in class org.concord.biologica.engine.Debug
 
ERROR - Static variable in class org.concord.biologica.engine.EngineStrings
 
ERROR_PARSING_XML_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
errorConvertStatus - Static variable in class org.concord.util.CCUnit
 
errorHandler - Variable in class org.concord.pedagogica.engine.ActivityScript
 
errorHandler - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
errorHandler - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
errorPrint(Throwable, PrintWriter) - Method in class org.concord.util.script.ScriptThread
 
essayFill - Variable in class org.concord.pedagogica.ui.EssayFill
 
EssayFill - class org.concord.pedagogica.ui.EssayFill.
 
EssayFill() - Constructor for class org.concord.pedagogica.ui.EssayFill
 
EssayFill(String) - Constructor for class org.concord.pedagogica.ui.EssayFill
 
etchedBorder - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
EventHandler - class org.concord.util.beans.EventHandler.
The EventHandler class provides support for dynamically generating event listeners whose methods execute a simple statement involving an incoming event object and a target object.
EventHandler - class org.concord.util.script.event.EventHandler.
 
EventHandler(Object, String, String, String) - Constructor for class org.concord.util.beans.EventHandler
Creates a new EventHandler object; you generally use one of the create methods instead of invoking this constructor directly.
EventHandler(Script, String) - Constructor for class org.concord.util.script.event.EventHandler
 
eventQueue - Variable in class org.concord.util.script.Script
 
EventSetDescriptor - class org.concord.util.beans.EventSetDescriptor.
An EventSetDescriptor describes a group of events that a given Java bean fires.
EventSetDescriptor(Class, String, Class, String) - Constructor for class org.concord.util.beans.EventSetDescriptor
Creates an EventSetDescriptor assuming that you are following the most simple standard design pattern where a named event "fred" is (1) delivered as a call on the single method of interface FredListener, (2) has a single argument of type FredEvent, and (3) where the FredListener may be registered with a call on an addFredListener method of the source component and removed with a call on a removeFredListener method.
EventSetDescriptor(Class, String, Class, String[], String, String) - Constructor for class org.concord.util.beans.EventSetDescriptor
Creates an EventSetDescriptor from scratch using string names.
EventSetDescriptor(Class, String, Class, String[], String, String, String) - Constructor for class org.concord.util.beans.EventSetDescriptor
This constructor creates an EventSetDescriptor from scratch using string names.
EventSetDescriptor(String, Class, Method[], Method, Method) - Constructor for class org.concord.util.beans.EventSetDescriptor
Creates an EventSetDescriptor from scratch using java.lang.reflect.Method and java.lang.Class objects.
EventSetDescriptor(String, Class, Method[], Method, Method, Method) - Constructor for class org.concord.util.beans.EventSetDescriptor
This constructor creates an EventSetDescriptor from scratch using java.lang.reflect.Method and java.lang.Class objects.
EventSetDescriptor(String, Class, MethodDescriptor[], Method, Method) - Constructor for class org.concord.util.beans.EventSetDescriptor
Creates an EventSetDescriptor from scratch using java.lang.reflect.MethodDescriptor and java.lang.Class objects.
eventThread - Variable in class org.concord.util.script.Script
 
ExceptionListener - interface org.concord.util.beans.ExceptionListener.
An ExceptionListener is notified of internal exceptions.
exceptionThrown(Exception) - Method in interface org.concord.util.beans.ExceptionListener
This method is called when a recoverable exception has been caught.
execute() - Method in class org.concord.util.beans.Statement
The execute method finds a method whose name is the same as the methodName property, and invokes the method on the target.
execute(Object[]) - Method in class org.concord.flash.player.FFunction
Executes this function.
executeActions() - Method in interface org.concord.flash.player.FActionable
 
executeActions() - Method in class org.concord.flash.player.FFrame
Executes the actions for this frame.
executeFrame(int) - Method in class org.concord.flash.player.FMovieClip
Executes code at the specified frame
executeFrame(String) - Method in class org.concord.flash.player.FMovieClip
Executes code at the specified frame
EXHAUSTED_AVAILABLE_OBJECT_IDS - Static variable in class org.concord.biologica.engine.EngineStrings
 
exists() - Method in class org.concord.util.script.ScriptFile
 
exit() - Method in class org.concord.pedagogica.engine.ActivityNode
 
exit() - Method in class org.concord.pedagogica.engine.Activity
 
exp(double) - Method in class org.concord.flash.player.builtin.FMath
 
expandNode(TreeViewNode) - Method in class org.concord.biologica.ui.TreeView
Expand the given node
ExponentExpression - class org.concord.util.script.ExponentExpression.
The ExponentExpression class implements the semantic node for exponentiation.
ExponentExpression() - Constructor for class org.concord.util.script.ExponentExpression
 
exportButton - Variable in class org.concord.pedagogica.ui.LogView
 
exportData() - Method in class org.concord.pedagogica.ui.LogView
 
exportItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
exportTo(File) - Method in class org.concord.biologica.engine.Species
Export this species to a species file.
expression - Variable in class org.concord.util.script.ExpressionStatement
 
expression - Variable in class org.concord.util.script.AssignmentStatement
 
expression - Variable in class org.concord.util.script.ReturnStatement
 
Expression - class org.concord.util.beans.Expression.
An Expression object represents a primitive expression in which a single method is applied to a target and a set of arguments to return a result - as in "a.getFoo()".
Expression - class org.concord.util.script.Expression.
This class is for instanceof checks.
Expression() - Constructor for class org.concord.util.script.Expression
 
Expression(Object, Object, String, Object[]) - Constructor for class org.concord.util.beans.Expression
Creates a new Expression object for a method that returns a result.
Expression(Object, String, Object[]) - Constructor for class org.concord.util.beans.Expression
Creates a new Statement object with a target, methodName and arguments as per the parameters.
Expression(Script) - Constructor for class org.concord.util.script.Expression
 
expressions - Variable in class org.concord.util.script.SequenceLiteral
 
ExpressionStatement - class org.concord.util.script.ExpressionStatement.
 
ExpressionStatement() - Constructor for class org.concord.util.script.ExpressionStatement
 
ext - Variable in class org.concord.pedagogica.engine.ActivityScript
 
ExtendsDeclaration - class org.concord.util.script.ExtendsDeclaration.
The extend statement allows a script to extend an existing java object.
ExtendsDeclaration(Script) - Constructor for class org.concord.util.script.ExtendsDeclaration
 

F

FactAssignStatement - class org.concord.util.script.FactAssignStatement.
The FactAssignStatement class implements the node that supports the semantics of the "fact assignment" statement.
FactAssignStatement() - Constructor for class org.concord.util.script.FactAssignStatement
 
FActionable - interface org.concord.flash.player.FActionable.
 
factory - Variable in class org.concord.pedagogica.ui.HelpView
 
FALSE - Static variable in class org.concord.biologica.engine.EngineObject
FALSE Boolean object.
Family - class org.concord.biologica.engine.Family.
This class represents a family of diploid organisms consisting of a female parent organism, a male parent organism and a set of child organisms.
FAMILY_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Family object was added to a world.
FAMILY_ADDED_TO_VIEW - Static variable in class org.concord.biologica.ui.UIProp
A Family object has been added to a view.
FAMILY_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
FAMILY_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FAMILY_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FAMILY_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FAMILY_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FAMILY_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Family object was removed.
FAMILY_REMOVED_FROM_VIEW - Static variable in class org.concord.biologica.ui.UIProp
A Family object has been removed from a view.
Family(Organism, Organism, int) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents, creating the number of children specified.
Family(Organism, Organism, int, boolean) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents, creating the number of children specified and also respecting whether or not the children should all be alive.
Family(Organism, Organism, int, int) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents, creating the number of female and male children specified.
Family(Organism, Organism, int, int, boolean) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents, creating the number of female and male children specified.
Family(Organism, Organism, Organism) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents and one child.
Family(Organism, Organism, Vector) - Constructor for class org.concord.biologica.engine.Family
Create a family from a given set of 2 parents and optionally some children.
Family(World, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Family
Create a new family and start handling XML parsing events to set the properties of this object.
FArray - class org.concord.flash.player.FArray.
 
FArray - class org.concord.flash.player.builtin.FArray.
 
FArray(String, FScriptObject, int) - Constructor for class org.concord.flash.player.FArray
 
FArray(String, FScriptObject, int) - Constructor for class org.concord.flash.player.builtin.FArray
 
FATAL - Static variable in class org.concord.biologica.engine.EngineProp
Fatal characteristic simple property name.
FATAL_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FATAL_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FATHER_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
The father organism shown in a view has changed from one organism to another.
FATHER_VIEW - Static variable in class org.concord.biologica.ui.SmallMeiosisView
 
FButton - class org.concord.flash.player.FButton.
Object for handling button objects in flash.
FColorFillMethod - class org.concord.flash.player.fill.FColorFillMethod.
 
FColorFillMethod(Shape.ColorFill) - Constructor for class org.concord.flash.player.fill.FColorFillMethod
 
FComponent - class org.concord.flash.player.FComponent.
Models a placeable object.
FeatureDescriptor - class org.concord.util.beans.FeatureDescriptor.
The FeatureDescriptor class is the common baseclass for PropertyDescriptor, EventSetDescriptor, and MethodDescriptor, etc.
FeatureDescriptor() - Constructor for class org.concord.util.beans.FeatureDescriptor
Constructs a FeatureDescriptor.
FEditField - class org.concord.flash.player.FEditField.
Implements an edit field.
FEMALE - Static variable in class org.concord.biologica.engine.Organism
 
FEMALE_AND_MALE - Static variable in class org.concord.biologica.engine.Species
Gender values used in defining genotype to phenotype rules, species image columns and species image rows.
FEMALE_AND_MALE_STRING - Static variable in class org.concord.biologica.engine.Species
 
FEMALE_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.FertilizationChromosomeModel
Types of fertilization chromosome models
FEMALE_ONLY - Static variable in class org.concord.biologica.engine.Species
 
FEMALE_ONLY_STRING - Static variable in class org.concord.biologica.engine.Species
 
FEMALE_PARENT_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FEMALE_PARENT_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FEMALE_STRING - Static variable in class org.concord.biologica.engine.Organism
 
FERTILIZATION_GAMETES - Static variable in class org.concord.biologica.ui.UIProp
The fertilization gametes have changed.
FERTILIZATION_MANUALLY_DISABLED - Static variable in class org.concord.biologica.ui.UIProp
Fertilization manual disabled state changed.
FERTILIZATION_MODEL - Static variable in class org.concord.biologica.ui.UIProp
The fertilization model has changed.
FERTILIZATION_OFFSPRING_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
The fertilization offspring organism has changed, usually either becoming null or becoming non-null.
FERTILIZATION_STARTED - Static variable in class org.concord.biologica.ui.UIProp
Fertilization has started (scripts shouldn't use this - it's internal) New and old values are integers (the new and old steps).
FERTILIZATION_STARTED_AND_STOPPED - Static variable in class org.concord.biologica.ui.UIProp
Fertilization has started and was stopped.
FERTILIZATION_STEP - Static variable in class org.concord.biologica.ui.UIProp
The fertilization step has changed.
FertilizationChromosomeModel - class org.concord.biologica.ui.FertilizationChromosomeModel.
FertilizationChromosomeModel contains the data describing the fertilization state for a given chromosome.
FertilizationChromosomeModel(int, FertilizationModel, MeiosisChromosomeModel, Rectangle) - Constructor for class org.concord.biologica.ui.FertilizationChromosomeModel
Creates a new instance of FertilizationChromosomeModel with the given type, fertilization model and meiosis chromosome model.
FertilizationModel - class org.concord.biologica.ui.FertilizationModel.
FertilizationModel contains the data describing the fertilization process state for the fertilization of 2 gametes to form a single offspring organism.
FertilizationModel() - Constructor for class org.concord.biologica.ui.FertilizationModel
Creates an empty instance of FertilizationModel
FFillMethod - class org.concord.flash.player.fill.FFillMethod.
Interface for handling various fill methods
FFillMethod() - Constructor for class org.concord.flash.player.fill.FFillMethod
 
FFlash - class org.concord.flash.player.FFlash.
timer Main class for handling flash files.
FFlash() - Constructor for class org.concord.flash.player.FFlash
After calling this constructor, setInputStream MUST be called with the InputStream of the flash file in order to "play" the flash file.
FFlash(InputStream) - Constructor for class org.concord.flash.player.FFlash
Constructor for creating a flash.
FFrame - class org.concord.flash.player.FFrame.
This class handles frames in a movie clip.
FFunction - class org.concord.flash.player.FFunction.
 
FFunction(String, FScriptObject, Actions, String[]) - Constructor for class org.concord.flash.player.FFunction
 
FFunction(String, FScriptObject, ArrayList, String[], HashMap) - Constructor for class org.concord.flash.player.FFunction
 
FGradientFillMethod - class org.concord.flash.player.fill.FGradientFillMethod.
 
FGradientFillMethod(Shape.GradientFill) - Constructor for class org.concord.flash.player.fill.FGradientFillMethod
 
file - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
file - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
FILE - Static variable in class org.concord.biologica.engine.EngineProp
File simple property name.
fileFilter - Variable in class org.concord.pedagogica.ui.ActivityView
 
fileList - Variable in class org.concord.pedagogica.ui.LogView
 
fileLocate - Variable in class org.concord.util.LogProcess
 
fileName - Variable in class org.concord.pedagogica.engine.Logging
 
FILENAME - Static variable in class org.concord.biologica.engine.EngineProp
Filename simple property name.
files - Variable in class org.concord.biologica.engine.BioLogicaSpecies
 
fileTable - Variable in class org.concord.pedagogica.engine.LogModel
 
fillAtoms() - Method in class org.concord.collisions.engine.BedSpringWorld
 
FilledCircle - class org.concord.biologica.ui.FilledCircle.
FilledCircle has the information necessary to draw a filled circle to represent a portion of a cell boundary.
FilledCircle(int, int, int, int) - Constructor for class org.concord.biologica.ui.FilledCircle
Create a new FilledCircle
fillLine(int, int, int, int, int[]) - Method in class org.concord.flash.player.fill.FFillMethod
 
fillLine(int, int, int, int, int[]) - Method in class org.concord.flash.player.fill.FGradientFillMethod
 
fillLine(int, int, int, int, int[]) - Method in class org.concord.flash.player.fill.FColorFillMethod
 
fillLine(int, int, int, int, int[]) - Method in class org.concord.flash.player.fill.FImageFillMethod
 
filter - Static variable in class org.concord.pedagogica.ui.ClassTree
 
filter(JWorldElement) - Method in class org.concord.collisions.engine.JWorldElementFilter
filter an element
filter(JWorldElement) - Method in class org.concord.collisions.engine.JPropertyFilter
filter an element
filterValue(String) - Method in class org.concord.util.Query
 
FImage - class org.concord.flash.player.fill.FImage.
 
FImage(String, FScriptObject) - Constructor for class org.concord.flash.player.fill.FImage
 
FImageFillMethod - class org.concord.flash.player.fill.FImageFillMethod.
 
FImageFillMethod(Shape.ImageFill) - Constructor for class org.concord.flash.player.fill.FImageFillMethod
 
findActivityScript(String) - Method in class org.concord.pedagogica.engine.Activity
 
findAllelePair(OrganismAllele) - Method in class org.concord.biologica.engine.Organism
Find an organism allele pair given an organism allele
findAllelePair(Organism, OrganismAllele) - Method in class org.concord.biologica.ui.MutationsPracticeView
 
findAtom(float, float) - Method in class org.concord.collisions.engine.JPartWorld
 
findBarIndex(int, int) - Method in class org.concord.util.Gauge
 
findButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
findCellLocation(Object) - Method in class org.concord.pedagogica.ui.TableInputView
Method that determines the upper lefthand point location of an individual cell in the table that has experienced a mouse press.
findClass(String) - Method in class org.concord.util.script.Script
 
findClass(String, boolean) - Method in class org.concord.util.script.Script
 
findComponent(String) - Method in class org.concord.pedagogica.engine.NodeAccess
 
findComponent(String, boolean) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
findConstructor(String, Object[]) - Method in class org.concord.util.script.ScriptObject
This method finds the appropriate consructor given the class name and the parameters.
findFile(File, String) - Method in class org.concord.pedagogica.engine.LogModel
 
findFrame(Component) - Method in class org.concord.biologica.ui.CursorText
 
findLevelForFamily(PedigreeFamily) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Find the level containing the pedigreeFamily
findLevelForOrganism(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Find the level containing the pedigreeOrganism
findMethod(String) - Method in class org.concord.util.script.Script
 
findMethod(String, Object, Object[]) - Method in class org.concord.util.script.ScriptObject
This method finds the appropriate method given the method name, the object and the parameters.
findOrganismAllele(Vector, String) - Method in class org.concord.biologica.engine.Organism
 
findPedigreeFamily(Family) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Find the pedigreeFamily corresponding to a given family
findPedigreeFamily(Family) - Method in class org.concord.biologica.ui.PedigreeLevel
Find the PedigreeFamily at this level given the Family
findPedigreeFamily(Family, int[]) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Find the PedigreeFamily for the given Family
findPedigreeOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Find the pedigreeOrganism corresponding to a given organism.
findPedigreeOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeLevel
Find the Pedigree Organism at this level given the Organism
findPedigreeOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeFamily
Find the PedigreeOrganism given the Organism.
findSelected(int, int) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
finished - Variable in class org.concord.util.script.NameStack
 
finished() - Method in class org.concord.pedagogica.ui.Quiz
 
finishShapes() - Method in class org.concord.flash.player.FMovieBuilder
 
FinishStatement - class org.concord.util.script.FinishStatement.
The FinishStatement class implements the node that supports the semantics of the "finish" statement.
FinishStatement() - Constructor for class org.concord.util.script.FinishStatement
 
fireActionEvent(String) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
firePropertyChange(String, boolean, boolean) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
firePropertyChange(String, Object, Object) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
FIRST_ORGANISM_ALLELE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FIRST_ORGANISM_ALLELE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FIRST_ORGANISM_CHROMOSOME_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
FIRST_ORGANISM_CHROMOSOME_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
FIRST_STRAND - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
firstClick - Variable in class org.concord.pedagogica.ui.ActivityView
 
firstDate - Variable in class org.concord.util.LogProcess
 
firstTime - Variable in class org.concord.util.LogProcess
 
FIXED_NUMBER_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The fixed number of children from a breeding has changed.
fixTransform(Transform) - Static method in class org.concord.flash.player.FUtil
 
FJPEGImage - class org.concord.flash.player.fill.FJPEGImage.
 
FJPEGImage(String, FScriptObject, Image.JPEG) - Constructor for class org.concord.flash.player.fill.FJPEGImage
 
flashing - Variable in class org.concord.collisions.engine.JWorldElement
 
flashState - Variable in class org.concord.collisions.engine.JAtom
creates instance of the JAtom class with default mass and default radius
FloatLiteral - class org.concord.util.script.FloatLiteral.
This node represents a float value in the semantic tree.
FloatLiteral(String) - Constructor for class org.concord.util.script.FloatLiteral
 
FloatPair - class org.concord.collisions.engine.FloatPair.
 
FloatPair(float, float) - Constructor for class org.concord.collisions.engine.FloatPair
 
floor(double) - Method in class org.concord.flash.player.builtin.FMath
 
FLosslessImage - class org.concord.flash.player.fill.FLosslessImage.
 
FLosslessImage(String, FScriptObject, Image.Lossless) - Constructor for class org.concord.flash.player.fill.FLosslessImage
 
flush() - Method in class org.concord.util.TextWriter
 
flush() - Method in class org.concord.util.TextOutputStream
 
flush() - Method in class org.concord.util.beans.CCXMLEncoder
 
flush() - Method in class org.concord.util.beans.XMLEncoder
This method writes out the preamble associated with the XML encoding if it has not been written already and then writes out all of the values that been written to the stream since the last time flush was called.
flush() - Method in class org.concord.util.script.ScriptFileOutputStream
 
flushCaches() - Static method in class org.concord.util.beans.Introspector
Flush all of the Introspector's internal caches.
flushFromCaches(Class) - Static method in class org.concord.util.beans.Introspector
Flush the Introspector's internal cached information for a given class.
FMath - class org.concord.flash.player.builtin.FMath.
 
FMath(String, FScriptObject) - Constructor for class org.concord.flash.player.builtin.FMath
 
FMorphShape - class org.concord.flash.player.FMorphShape.
Handles morphed shapes.
FMorphShape(String, FScriptObject, MorphShape) - Constructor for class org.concord.flash.player.FMorphShape
 
FMouseSupport - class org.concord.flash.player.FMouseSupport.
Handles mouse movement/hits, Mainly because all mouse events go to the AWT component -- FFlash object.
FMouseSupport(AffineTransform) - Constructor for class org.concord.flash.player.FMouseSupport
 
FMovie - class org.concord.flash.player.FMovie.
Represents the whole movie.
FMovieBuilder - class org.concord.flash.player.FMovieBuilder.
An implementation of the SWFTagTypes interface that builds a Movie object
FMovieBuilder.ActionsBuilder - class org.concord.flash.player.FMovieBuilder.ActionsBuilder.
A SWFActions implementation that breaks multiple action arrays into separate Actions objects
FMovieBuilder.ActionsBuilder(int) - Constructor for class org.concord.flash.player.FMovieBuilder.ActionsBuilder
 
FMovieBuilder.ButtonActionBuilder - class org.concord.flash.player.FMovieBuilder.ButtonActionBuilder.
 
FMovieBuilder.ButtonActionBuilder(FMovieBuilder, Button, int) - Constructor for class org.concord.flash.player.FMovieBuilder.ButtonActionBuilder
 
FMovieBuilder.ClipActionBuilder - class org.concord.flash.player.FMovieBuilder.ClipActionBuilder.
 
FMovieBuilder.ClipActionBuilder(FMovieBuilder, Symbol, Matrix, AlphaTransform, int, String, int, boolean) - Constructor for class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
FMovieBuilder.GlyphBuilder - class org.concord.flash.player.FMovieBuilder.GlyphBuilder.
 
FMovieBuilder.GlyphBuilder(FMovieBuilder, FontDefinition, Font, int) - Constructor for class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
FMovieBuilder.GlyphBuilder(FMovieBuilder, FontDefinition, Font, int[], int[], Rect[]) - Constructor for class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
FMovieBuilder.MorphShapeBuilder - class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder.
 
FMovieBuilder.MorphShapeBuilder(FMovieBuilder, int, Rect, Rect) - Constructor for class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
FMovieBuilder.ShapeBuilder - class org.concord.flash.player.FMovieBuilder.ShapeBuilder.
SWFShape implementation that builds a Shape
FMovieBuilder.ShapeBuilder(FMovieBuilder, Shape) - Constructor for class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
FMovieBuilder.TextBuilder - class org.concord.flash.player.FMovieBuilder.TextBuilder.
A SWFText implementation that builds a Text object
FMovieBuilder.TextBuilder(FMovieBuilder, Text) - Constructor for class org.concord.flash.player.FMovieBuilder.TextBuilder
 
FMovieBuilder() - Constructor for class org.concord.flash.player.FMovieBuilder
Build a new Movie
FMovieBuilder(FMovieBuilder, MovieClip) - Constructor for class org.concord.flash.player.FMovieBuilder
Build the timeline of a MovieClip
FMovieBuilder(Movie) - Constructor for class org.concord.flash.player.FMovieBuilder
Append to an existing movie (do not change size,rate,color,version etc)
FMovieClip - class org.concord.flash.player.FMovieClip.
Parent class for both FMovie and FSprite.
FMovieClip(String, FScriptObject) - Constructor for class org.concord.flash.player.FMovieClip
 
FMovieClip(String, FScriptObject, MovieClip) - Constructor for class org.concord.flash.player.FMovieClip
 
FMovieClip(String, FScriptObject, MovieClip, Instance) - Constructor for class org.concord.flash.player.FMovieClip
 
focusGained(FocusEvent) - Method in class org.concord.biologica.ui.PedigreeView
Handle focus gained event - do nothing in most cases.
focusGained(FocusEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle focus gained event - do nothing in most cases.
focusLost(FocusEvent) - Method in class org.concord.biologica.ui.PedigreeView
Handle focus lost event - check text in most cases.
focusLost(FocusEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle focus lost event - check text in most cases.
font - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
font - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
FONT - Static variable in class org.concord.biologica.ui.UIProp
The font changed.
font(int, int) - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
fontAscent - Variable in class org.concord.biologica.ui.UIView
Font ascent
fontDef - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
fontDescent - Variable in class org.concord.biologica.ui.UIView
Font descent
fontGlyphs - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
fontHeight - Variable in class org.concord.biologica.ui.UIView
Font height
fontMetrics - Variable in class org.concord.biologica.ui.UIView
Font metrics
fontSize - Static variable in class org.concord.pedagogica.ui.CustomQuestion
 
FOREGROUND - Static variable in class org.concord.biologica.ui.UIProp
The foreground color changed.
format - Variable in class org.concord.util.LineGraph
 
foundList - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
foundScroll - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
frame - Variable in class org.concord.flash.player.FMovieBuilder
 
frame - Variable in class org.concord.pedagogica.engine.NodeAccess
 
frame - Variable in class org.concord.pedagogica.ui.ActivityView
 
frame - Variable in class org.concord.pedagogica.ui.RunActivity
 
frame - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
frame - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
frameChanged(MovieClipEvent) - Method in interface org.concord.flash.player.event.MovieClipListener
 
framePlacement - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
frameSize - Variable in class org.concord.util.script.NameStack
 
frameViewItem - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
FScriptObject - class org.concord.flash.player.FScriptObject.
Root class for all the objects used in this Flash player.
FScriptObject() - Constructor for class org.concord.flash.player.FScriptObject
 
FScriptObject(String, FScriptObject) - Constructor for class org.concord.flash.player.FScriptObject
 
FShape - class org.concord.flash.player.FShape.
Object to handle shapes.
FShape(String, FScriptObject, Shape) - Constructor for class org.concord.flash.player.FShape
 
FSprite - class org.concord.flash.player.FSprite.
Handles sprites.
FText - class org.concord.flash.player.FText.
Handles Text.
FULL_MODEL - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
fullModel() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
functions - Variable in class org.concord.util.LineGraph
 
functions - Variable in class org.concord.molecular.engine.AggregateValue
 
FUndefined - class org.concord.flash.player.FUndefined.
Used in scripting to specify values that are not defined.
FUtil - class org.concord.flash.player.FUtil.
Set of useful utility functions
FUtil() - Constructor for class org.concord.flash.player.FUtil
 

G

G_TO_P_RULE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
GAMETE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Gamete object was added.
GAMETE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Gamete object was removed.
gamma - Static variable in class org.concord.collisions.engine.CCGravityForce
 
Gauge - class org.concord.util.Gauge.
Value gauge.
Gauge() - Constructor for class org.concord.util.Gauge
Gauge constructor.
gaugeHeight - Variable in class org.concord.util.Gauge
 
gauges - Variable in class org.concord.util.BarGraph
 
gaugeValues - Variable in class org.concord.util.Gauge
 
gaugeWidth - Variable in class org.concord.util.BarGraph
 
gaugeWidth - Variable in class org.concord.util.Gauge
 
GEExpression - class org.concord.util.script.GEExpression.
The GEExpression class implements the semantic node for "greater or equal".
GEExpression() - Constructor for class org.concord.util.script.GEExpression
 
GENDER - Static variable in class org.concord.biologica.engine.EngineProp
An object's gender changed.
GENDER_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENDER_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
genders - Variable in class org.concord.pedagogica.ui.LoginPanel
 
Gene - class org.concord.biologica.engine.Gene.
This class represents a gene.
GENE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Gene object was added to a species chromosome.
GENE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
GENE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
GENE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
GENE_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
GENE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Gene object was removed from a species chromosome.
Gene(SpeciesChromosome, String, int, int) - Constructor for class org.concord.biologica.engine.Gene
Create a new gene given a species chromosome.
Gene(SpeciesChromosome, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Gene
Create a new gene and start handling XML parsing events to set the properties of this object.
generateEventHandler(Class, String, String) - Method in class org.concord.util.script.ScriptClassLoader
 
generateMethods(Class, Query, String, String) - Method in class org.concord.util.script.ScriptClassLoader
 
generateQuestionEvent() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
generateQuestionID() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
GENERATION_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENERATION_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
GenericDataSource - class org.concord.pedagogica.graph.GenericDataSource.
 
genoPhenoPracticeView - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
GENOTYPE_TO_PHENOTYPE_RULE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A GenotypeToPhenotypeRule object was added.
GENOTYPE_TO_PHENOTYPE_RULE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENOTYPE_TO_PHENOTYPE_RULE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
GENOTYPE_TO_PHENOTYPE_RULE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
GENOTYPE_TO_PHENOTYPE_RULE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
GENOTYPE_TO_PHENOTYPE_RULE_MOVED - Static variable in class org.concord.biologica.engine.EngineProp
A GenotypeToPhenotypeRule object was moved.
GENOTYPE_TO_PHENOTYPE_RULE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A GenotypeToPhenotypeRule object was removed.
GenotypeToPhenotypeRule - class org.concord.biologica.engine.GenotypeToPhenotypeRule.
This class represents a rule for choosing a phenotype from a genotype.
GenotypeToPhenotypeRule(Species, String) - Constructor for class org.concord.biologica.engine.GenotypeToPhenotypeRule
Creates a new genotype to phenotype rule with the given name.
GenotypeToPhenotypeRule(Species, String, GenotypeToPhenotypeRule, SpeciesAllele, SpeciesAllele) - Constructor for class org.concord.biologica.engine.GenotypeToPhenotypeRule
Creates a new genotype to phenotype rule with the given name, an existing rule as a template and 2 species alleles.
GenotypeToPhenotypeRule(Species, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.GenotypeToPhenotypeRule
Create a new genotype to phenotype rule and start handling XML parsing events to set the properties of this object.
get_alpha() - Method in class org.concord.flash.player.FComponent
 
get_currentframe() - Method in class org.concord.flash.player.FMovieClip
Gets the current frame number
get_name() - Method in class org.concord.flash.player.FComponent
 
get_rotation() - Method in class org.concord.flash.player.FComponent
 
get_visible() - Method in class org.concord.flash.player.FComponent
 
get_x() - Method in class org.concord.flash.player.FComponent
 
get_xscale() - Method in class org.concord.flash.player.FComponent
 
get_y() - Method in class org.concord.flash.player.FComponent
 
get_yscale() - Method in class org.concord.flash.player.FComponent
 
get(int) - Method in class org.concord.molecular.engine.IndexList
 
get(Object) - Method in class org.concord.util.beans.Encoder
Returns a tentative value for oldInstance in the environment created by this stream.
getAccelerationKoeff() - Method in class org.concord.collisions.engine.JWorldElement
 
getAccelerationKoeff() - Method in class org.concord.collisions.engine.JPartWorld
 
getAccelerations(JWorldElement) - Method in class org.concord.collisions.engine.CCDefaultForceCalculator
 
getAccelerations(JWorldElement) - Method in interface org.concord.collisions.engine.CCForceCalculator
 
getAction() - Method in class org.concord.util.beans.EventHandler
Returns the name of the target's writable property that this event handler will set, or the name of the method that this event handler will invoke on the target.
getActions() - Method in class org.concord.flash.player.FMovieBuilder.ActionsBuilder
 
getActivationStepTime() - Method in class org.concord.collisions.engine.JDaemon
 
getActivationStepTime(int) - Method in class org.concord.collisions.engine.JDaemon
 
getActiveCollision(JWorldElement) - Method in class org.concord.collisions.engine.JDaemon
Retrieve the active collision for an element
getActiveColor() - Method in class org.concord.collisions.engine.JDaemon
 
getActiveTool() - Method in class org.concord.biologica.ui.PedigreeView
Get the active tool.
getActiveTool() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the active tool.
getActiveTool() - Method in class org.concord.biologica.ui.ToolView
Get the active tool id.
getActivityAlias() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getActivityAlias() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getActivityAlias() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getActivityAlias() - Method in class org.concord.pedagogica.ui.BlankFill
 
getActivityAlias() - Method in class org.concord.pedagogica.ui.EssayFill
 
getActivityArcs() - Method in class org.concord.pedagogica.engine.Activity
 
getActivityItem() - Method in class org.concord.pedagogica.ui.ActivitySearchResult
 
getActivityNode() - Method in class org.concord.pedagogica.ui.ActivityView
 
getActivityNodes() - Method in class org.concord.pedagogica.engine.Activity
 
getActTime() - Method in class org.concord.collisions.engine.CCImpulseForce
 
getActuals() - Method in class org.concord.util.script.InvocationExpression
 
getActuals() - Method in class org.concord.util.script.IndexExpression
 
getAdditionalBeanInfo() - Method in class org.concord.util.beans.SimpleBeanInfo
Claim there are no other relevant BeanInfo objects.
getAdditionalBeanInfo() - Method in interface org.concord.util.beans.BeanInfo
This method allows a BeanInfo object to return an arbitrary collection of other BeanInfo objects that provide additional information on the current bean.
getAdditionalBeanInfo() - Method in class org.concord.util.script.ScriptObject
 
getAdditionalBeanInfo() - Method in class org.concord.biologica.engine.BioEngineBeanInfo
Gets a BeanInfo for the superclass of this bean.
getAdditionalBeanInfo() - Method in class org.concord.collisions.engine.JDaemonBeanInfo
 
getAdditionalBeanInfo() - Method in class org.concord.collisions.engine.JWorldElementBeanInfo
 
getAdditionalBeanInfo() - Method in class org.concord.collisions.engine.JAtomBeanInfo
 
getAdditionalBeanInfo() - Method in class org.concord.collisions.ui.PassiveElementBeanInfo
 
getAddListenerMethod() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the method used to add event listeners.
getAllelePendingTextSymbol(int) - Method in class org.concord.biologica.ui.DNAView
Get the text symbol of the top or bottom allele if the pending changes are made to that allele.
getAllelesAsString() - Method in class org.concord.biologica.engine.Branch
 
getAllImages() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getAllMembers() - Method in class org.concord.flash.player.FScriptObject
Gets the enumeration of all the members (e.g.
getAminoAcidForCodon(byte, byte, byte) - Static method in class org.concord.biologica.engine.Codon
Get the amino acid, stop or start for a given codon.
getAnglePStrandAtCentromereAtLastStep() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the angle of the P strand of the chromosome at the centromere at the last step of this chromosome's portion of meiosis.
getAngleQStrandAtCentromereAtLastStep() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the angle of the Q strand of the chromosome at the centromere at the last step of this chromosome's portion of meiosis.
getAnimator() - Method in class org.concord.molecular.ui.MolecularView
Returns the AnimatorPanel of this view.
getAnswer(int) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.BlankFill
 
getAnswer(int) - Method in class org.concord.pedagogica.ui.EssayFill
 
getAnswerComponent() - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
getAnswerFont() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getAnswerFont() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getAnswerLength() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.BlankFill
 
getAnswerLength() - Method in class org.concord.pedagogica.ui.EssayFill
 
getAnswers() - Method in class org.concord.pedagogica.engine.QuestionState
 
getAnswers() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getAnswers() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getAnswers() - Method in class org.concord.pedagogica.ui.CustomTableQuestion
 
getAnswers() - Method in class org.concord.pedagogica.ui.Question
This gets the String array of answers from the particular question type.
getAnswers() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getAnswers() - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
getAnswers() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getAnswers() - Method in class org.concord.pedagogica.ui.QuestionEvent
 
getAnswers() - Method in class org.concord.pedagogica.ui.BlankFill
 
getAnswers() - Method in class org.concord.pedagogica.ui.EssayFill
 
getAnswers(int) - Method in class org.concord.pedagogica.ui.Quiz
 
getApplet(String) - Method in class org.concord.pedagogica.ui.ViewerContext
 
getAppletContext() - Method in class org.concord.pedagogica.ui.ViewerStub
 
getApplets() - Method in class org.concord.pedagogica.ui.ViewerContext
 
getArc() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getArcItems() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getARGBColor(Color, ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
getArgumentNames() - Method in class org.concord.flash.player.FFunction
 
getArguments() - Method in class org.concord.util.beans.Statement
Returns the arguments of this statement.
getArray() - Method in class org.concord.molecular.engine.IndexList
 
getArrayValue(Object, int[]) - Method in class org.concord.util.script.ScriptObject
 
getArrowsVelDragMode() - Method in class org.concord.collisions.ui.GUIPanel
 
getAssignVelocities() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getAsText() - Method in class org.concord.collisions.engine.AtomDragPropertyEditor
 
getAsText() - Method in class org.concord.collisions.engine.AtomDragModePropertyEditor
 
getAtom(String) - Method in class org.concord.util.script.ScriptObject
 
getAtomByName(String) - Method in class org.concord.collisions.engine.JPartWorld
 
getAtomDraggable(int) - Method in class org.concord.collisions.engine.JAtom
 
getAtomicModel() - Method in class org.concord.molecular.ui.MolecularView
Returns atomic model.
getAtomPropertiesEditor() - Method in class org.concord.molecular.ui.MolecularView
 
getAtoms() - Method in class org.concord.collisions.engine.JPartWorld
 
getAtoms() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getAtomsDragMode() - Method in class org.concord.collisions.ui.GUIPanel
setting drag mode for the atoms
getAudioClip(URL) - Method in class org.concord.pedagogica.ui.ViewerContext
 
getAwtColor(Color, ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
getAwtFont(Font) - Static method in class org.concord.flash.player.FUtil
 
getAx() - Method in class org.concord.collisions.ui.PassiveElement
 
getAy() - Method in class org.concord.collisions.ui.PassiveElement
 
getBackColor() - Method in class org.concord.collisions.ui.PassiveElement
 
getBackground() - Method in class org.concord.util.BarGraph
 
getBackground() - Method in class org.concord.pedagogica.ui.Quiz
 
getBarValue(int, int, int) - Method in class org.concord.util.Gauge
 
getBase(int) - Method in class org.concord.biologica.engine.OrganismAllele
Returns the base value at the given index in this allele.
getBase(int) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the base value at the given index in this raw nucleic acid.
getBase(int) - Method in class org.concord.biologica.engine.NucleicAcid
Returns the base value at the given index in this sequence.
getBase(int) - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the base value at the given index in this allele.
getBase(int) - Method in interface org.concord.biologica.engine.INucleicAcid
Returns the base value at the given index in this acid.
getBase(int) - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the base value at the given index in this chromosome.
getBase(int) - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the base value at the given index in this raw nucleic acid.
getBaseMethod(String, Object[]) - Method in class org.concord.util.script.Script
 
getBaseObject() - Method in class org.concord.util.script.Script
 
getBases() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the base values array for this allele.
getBases() - Method in class org.concord.biologica.engine.RawNucleicAcid
Get the bases of this raw nucleic acid as an array of bytes.
getBasesAsString() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the bases as a String of characters A,T,C and G.
getBeanClass() - Method in class org.concord.util.beans.BeanDescriptor
Gets the bean's Class object.
getBeanDescriptor() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge about the class and customizer of the bean.
getBeanDescriptor() - Method in interface org.concord.util.beans.BeanInfo
Gets the beans BeanDescriptor.
getBeanDescriptor() - Method in class org.concord.util.script.ScriptObject
 
getBeanDescriptor() - Method in class org.concord.biologica.engine.BioEngineBeanInfo
Gets the BeanDescriptor for this bean.
getBeanDescriptor() - Method in class org.concord.collisions.engine.JDaemonBeanInfo
 
getBeanDescriptor() - Method in class org.concord.collisions.engine.JWorldElementBeanInfo
 
getBeanDescriptor() - Method in class org.concord.collisions.engine.JAtomBeanInfo
 
getBeanDescriptor() - Method in class org.concord.collisions.ui.PassiveElementBeanInfo
 
getBeanDescriptor() - Method in class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
getBeanInfo(Class) - Static method in class org.concord.util.beans.Introspector
Introspect on a Java Bean and learn about all its properties, exposed methods, and events.
getBeanInfo(Class, Class) - Static method in class org.concord.util.beans.Introspector
Introspect on a Java bean and learn all about its properties, exposed methods, below a given "stop" point.
getBeanInfo(Class, int) - Static method in class org.concord.util.beans.Introspector
Introspect on a Java bean and learn about all its properties, exposed methods, and events, subject to some control flags.
getBeanInfoSearchPath() - Static method in class org.concord.util.beans.Introspector
Gets the list of package names that will be used for finding BeanInfo classes.
getBeginColumn() - Method in interface org.concord.util.TextBounds
 
getBeginLine() - Method in interface org.concord.util.TextBounds
 
getBends() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getBigFertilizationView() - Method in class org.concord.biologica.ui.SexView
 
getBigMeiosisView() - Method in class org.concord.biologica.ui.SexView
 
getBlank() - Method in class org.concord.pedagogica.ui.BlankFill
 
getBonds() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getBooleanFromString(String) - Static method in class org.concord.util.Util
 
getBottomLeftGameteChromosomeModels() - Method in class org.concord.biologica.ui.MeiosisModel
Return an enumeration of the bottom left gamete chromosome models.
getBottomMidPoint() - Method in class org.concord.biologica.ui.PedigreeObject
Get midpoint along bottom of object .
getBottomMostChild() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the bottommost child organism.
getBottomRightGameteChromosomeModels() - Method in class org.concord.biologica.ui.MeiosisModel
Return an enumeration of the bottom right gamete chromosome models.
getBoundaries() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getBoundary() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getBoundaryType() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getBounds() - Method in class org.concord.flash.player.FComponent
 
getBounds2D() - Method in class org.concord.flash.player.FComponent
 
getBounds2D(AffineTransform) - Method in class org.concord.flash.player.FMovieClip
 
getBounds2D(AffineTransform) - Method in class org.concord.flash.player.FEditField
 
getBoxByName(String) - Method in class org.concord.collisions.engine.JPartWorld
 
getBoxes() - Method in class org.concord.collisions.engine.JPartWorld
 
getBranchs() - Method in class org.concord.biologica.ui.MeiosisModel
 
getButton() - Method in class org.concord.flash.player.FMovieClip
Hack, for getting the first button in the first frame
getButton() - Method in class org.concord.flash.player.FFrame
Retrieves the first button in this frame.
getButtonGroup() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getButtonGroup() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getButtonPanel() - Method in class org.concord.pedagogica.ui.ActivityView
 
getButtons() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getButtons() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getCalcDT() - Method in class org.concord.collisions.engine.JPartWorld
 
getCalculateNeighbors() - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
getCalculateTime() - Method in class org.concord.collisions.engine.JPartWorld
 
getCaretPoint() - Method in class org.concord.util.EditorInternalFrame
 
getCatUnitAbbrev(int) - Static method in class org.concord.util.CCUnit
 
getCCXMLTextHeader() - Static method in class org.concord.pedagogica.ui.CCXMLText
 
getCellBoundaries() - Method in class org.concord.biologica.ui.FertilizationModel
Get CellArc and CellLine enumeration to use when drawing boundaries and spindles of cell(s).
getCellBoundaries() - Method in class org.concord.biologica.ui.MeiosisModel
Get CellArc and CellLine enumeration to use when drawing boundaries and spindles of cell(s).
getCellSize() - Method in class org.concord.util.LineGraph
 
getCellText(int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
getCharacteristicCount(String) - Method in class org.concord.biologica.engine.Family
 
getCharacteristicOfTrait(String) - Method in class org.concord.biologica.engine.Organism
Returns the characteristic of a trait of the given name for this organism.
getCharacteristicOfTrait(Trait) - Method in class org.concord.biologica.engine.Organism
Returns the characteristic of a given trait for this organism.
getCharacteristics() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Returns an enumeration over the vector of characteristics in this column.
getCharacteristics() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of characteristics of this organism.
getCharacteristics() - Method in class org.concord.biologica.engine.Trait
Returns an enumeration over the vector of characteristics in this trait.
getCharacteristics() - Method in class org.concord.biologica.engine.SpeciesImageRow
Returns an enumeration over the vector of characteristics in this row.
getCharacteristicsVector() - Method in class org.concord.biologica.engine.Species
Returns a vector of the Characteristics in this species.
getChildAt(int) - Method in class org.concord.biologica.ui.TreeViewNode
Return the child at the given index.
getChildCount() - Method in class org.concord.biologica.ui.TreeViewNode
Return the number of children.
getChildFamilies() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of child families in this organism.
getChildPedigreeOrganisms() - Method in class org.concord.biologica.ui.PedigreeFamily
Get an enumeration over the set of child pedigree organisms in this family
getChildren() - Method in class org.concord.biologica.engine.Family
Returns an enumeration over the children organisms of this family.
getChoices() - Method in class org.concord.pedagogica.engine.QuestionState
 
getChoices() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getChoices() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getChromosome() - Method in class org.concord.biologica.engine.Branch
 
getChromosome() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the chromosome for this model.
getChromosomeModelEnumerations() - Method in class org.concord.biologica.ui.FertilizationModel
Get vector of the appropriate enumerations of chromosome models in this fertilization model.
getChromosomeModelEnumerations() - Method in class org.concord.biologica.ui.MeiosisModel
Get vector of the appropriate enumerations of chromosome models in this meiosis model.
getChromosomeModelType() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the chromosome model type of this chromosome model
getChromosomePaintInfo() - Method in class org.concord.biologica.engine.Organism
 
getChromosomePairNumberType() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Get the chromosome pair number number type.
getChromosomes() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of all chromosomes, sex and non-sex, in this organism.
getChromosomeSpecification() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get a ChromosomeSpecification for this model.
getChromosomesToShow() - Method in class org.concord.biologica.ui.ChromosomeView
Get the chromosomes to show.
getChromosomeType() - Method in class org.concord.biologica.engine.SpeciesChromosome
Get the chromosome type (autosome or sex chromosome).
getChromosomeType() - Method in interface org.concord.biologica.engine.IChromosome
Get the chromosome type (autosome or sex chromosome).
getChromosomeType() - Method in class org.concord.biologica.engine.OrganismChromosome
Get the chromosome type (autosome or sex chromosome).
getChromosomeView() - Method in class org.concord.biologica.ui.AllInOneView
Get the chromosome view
getChromosomeViewHeight() - Method in class org.concord.biologica.engine.OrganismChromosome
 
getClassContext() - Method in class org.concord.util.script.Script.ScriptSecuritySupport
Get the current class Context.
getClassName() - Method in class org.concord.pedagogica.ui.LoginPanel
 
getClassName() - Method in class org.concord.pedagogica.ui.ClassTree
 
getClipDepth() - Method in class org.concord.flash.player.FComponent
 
getClosestX(int) - Method in class org.concord.collisions.ui.PassiveGrid
 
getClosestY(int) - Method in class org.concord.collisions.ui.PassiveGrid
 
getCmFromPx(float) - Static method in class org.concord.collisions.engine.JPartWorld
 
getCMPoint() - Method in class org.concord.collisions.engine.JPartWorld
 
getCMPointX() - Method in class org.concord.collisions.engine.JPartWorld
 
getCMPointX() - Method in interface org.concord.collisions.engine.CCMassive
calculates X coordinate of center of mass
getCMPointX() - Method in class org.concord.collisions.engine.JRigidBox
calculates X coordinate of center of mass
getCMPointX() - Method in class org.concord.collisions.engine.JWall
calculates X coordinate of center of mass
getCMPointX() - Method in class org.concord.collisions.engine.JImpulseDaemon
calculates X coordinate of center of mass
getCMPointX() - Method in class org.concord.collisions.engine.JAtom
calculates X coordinate of center of mass
getCMPointX() - Method in class org.concord.collisions.engine.JBooster
calculates X coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JPartWorld
 
getCMPointY() - Method in interface org.concord.collisions.engine.CCMassive
calculates Y coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JRigidBox
calculates Y coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JWall
calculates Y coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JImpulseDaemon
calculates Y coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JAtom
calculates Y coordinate of center of mass
getCMPointY() - Method in class org.concord.collisions.engine.JBooster
calculates Y coordinate of center of mass
getCmUnit() - Static method in class org.concord.collisions.engine.JPartWorld
 
getCodeBase() - Method in class org.concord.pedagogica.ui.ViewerStub
 
getCollidedObject() - Method in class org.concord.collisions.event.CollisionsEvent
 
getCollidedParticle() - Method in class org.concord.collisions.engine.JWorldElement
 
getCollisionHistory() - Method in class org.concord.collisions.engine.JDaemon
Get the collision history of the daemon
getColor() - Method in class org.concord.util.Gauge
Returns color associated with a particular index.
getColor() - Method in class org.concord.biologica.engine.Terrain
Get the color of this terrain
getColor() - Method in class org.concord.collisions.engine.JWorldElement
 
getColor() - Method in class org.concord.collisions.engine.JWall
 
getColor() - Method in class org.concord.collisions.engine.JDaemon
 
getColor() - Method in class org.concord.collisions.engine.JAtom
 
getColor(int) - Method in class org.concord.util.BarGraph
Returns color associated with a particular index.
getColor(int) - Method in class org.concord.util.Gauge
Returns color associated with a particular index.
getColor(int) - Method in interface org.concord.util.ValueGraph
 
getColor(int) - Method in class org.concord.util.LineGraph
Returns color associated with a particular index.
getColorTransform() - Method in class org.concord.flash.player.FComponent
 
getColumn() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
getColumnIndex() - Method in class org.concord.biologica.engine.OrganismImage
Return the column index of this organism image in its corresponding species image.
getCommandString(int) - Static method in class org.concord.biologica.ui.Tool
Get the command string for the given tool.
getComponent(Object) - Method in class org.concord.pedagogica.engine.NodeAccess
 
getComponent(Object) - Method in class org.concord.pedagogica.ui.RunActivity
 
getComponentName(Object) - Method in class org.concord.pedagogica.engine.NodeAccess
 
getComponentName(Object) - Method in class org.concord.pedagogica.ui.RunActivity
 
getComponents() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getCondition() - Method in class org.concord.flash.player.event.MovieClipEvent
 
getConditionValue() - Method in class org.concord.molecular.engine.ConditionEvent
 
getConsoleText() - Method in class org.concord.pedagogica.ui.ActivityView
 
getCreateNames() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
getCrossoverChromosomeModel(MeiosisChromosomeModel) - Method in class org.concord.biologica.ui.MeiosisModel
Get the chromosome model for the chromosome that can crossover with the given chromosome model chromosome.
getCrossOverFamily(Organism, Organism, int, boolean) - Method in class org.concord.biologica.engine.CrossOver
create a new family when doing crossover
getCrossOverFamily(Organism, Organism, int, int, boolean) - Method in class org.concord.biologica.engine.CrossOver
Create a new family when doing crossover
getCrossOverTurnOn() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Is cross over turn on?
getCurrentChromosome() - Method in class org.concord.biologica.ui.ChromosomeView
 
getCurrentFrame() - Method in class org.concord.util.script.ScriptObject
 
getCurrentFrame() - Method in class org.concord.util.script.ScriptThread
 
getCurrentFrame() - Method in class org.concord.flash.player.FMovieClip
 
getCurrentNode() - Method in class org.concord.pedagogica.engine.Activity
 
getCurrentScript() - Static method in class org.concord.util.script.Script
 
getCurrentSpecies() - Method in class org.concord.biologica.engine.World
Get the current species.
getCursor(int) - Static method in class org.concord.biologica.ui.Tool
Get the cursor for the given tool.
getCursorColor() - Method in class org.concord.biologica.ui.DNAView
Get the cursor color
getCustomizerClass() - Method in class org.concord.util.beans.BeanDescriptor
Gets the Class object for the bean's customizer.
getDaemons() - Method in class org.concord.collisions.engine.JPartWorld
 
getDaemonsDragMode() - Method in class org.concord.collisions.ui.GUIPanel
determine drag mode for the daemons
getData(String, String) - Method in class org.concord.util.Query
 
getDataFileName() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getDataPanel() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getDataPathName(String) - Method in class org.concord.biologica.engine.SpeciesImage
 
getDataResource(String) - Method in class org.concord.biologica.engine.SpeciesImage
 
getDataSourceImage(int[], int, int, int, int, int, int[], int[]) - Method in class org.concord.biologica.engine.SpeciesImage
 
getDataSourceImage(int, int, int, int[], int[], Component) - Method in class org.concord.biologica.engine.SpeciesImage
 
getDataURLString(int, int) - Static method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getDataViewable() - Method in class org.concord.molecular.ui.MolecularView
Returns boolean viewable state.
getDefaultCalculateDT() - Static method in class org.concord.collisions.engine.JPartWorld
 
getDefaultCursorColor() - Static method in class org.concord.biologica.ui.DNAView
Get the default cursor color
getDefaultDifferentBaseColor() - Static method in class org.concord.biologica.ui.DNAView
Get the default different base color
getDefaultEqualBaseColor() - Static method in class org.concord.biologica.ui.DNAView
Get the default equal base color
getDefaultEventIndex() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge of a default event.
getDefaultEventIndex() - Method in interface org.concord.util.beans.BeanInfo
A bean may have a "default" event that is the event that will mostly commonly be used by humans when using the bean.
getDefaultEventIndex() - Method in class org.concord.util.script.ScriptObject
 
getDefaultHeatConductKoeff() - Static method in class org.concord.collisions.engine.JWall
 
getDefaultHighlightColor() - Static method in class org.concord.biologica.ui.OrganismView
Get the default selection color
getDefaultPropertyIndex() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge of a default property.
getDefaultPropertyIndex() - Method in interface org.concord.util.beans.BeanInfo
A bean may have a "default" property that is the property that will mostly commonly be initially chosen for update by human's who are customizing the bean.
getDefaultPropertyIndex() - Method in class org.concord.util.script.ScriptObject
 
getDefaultPropertyIndex() - Method in class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
getDefaultSelectionColor() - Static method in class org.concord.biologica.ui.ChromosomeView
Get the default selection color
getDefaultSelectionColor() - Static method in class org.concord.biologica.ui.OrganismView
Get the default selection color
getDefaultSelectionColor() - Static method in class org.concord.biologica.ui.TreeView
Get the default selection color
getDefaultSelectionSet() - Static method in class org.concord.biologica.ui.SelectionSet
Get default selection set
getDefaultThickness() - Static method in class org.concord.collisions.engine.JWall
retrieves default thickness
getDeferApply() - Method in class org.concord.biologica.ui.DNAView
Get the defer apply setting.
getDeferRevert() - Method in class org.concord.biologica.ui.DNAView
Get the defer revert setting.
getDefinedSymbols() - Method in class org.concord.flash.player.FMovieBuilder
Get the defined symbols - keyed by Integer( symbolId )
getDelay() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getDelta() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getDeltaVelColor() - Method in class org.concord.collisions.engine.JBooster
 
getDeltaVx() - Method in class org.concord.collisions.engine.JBooster
get delta vel
getDeltaVy() - Method in class org.concord.collisions.engine.JBooster
get delta vel
getDepth() - Method in class org.concord.flash.player.FComponent
 
getDescription() - Method in class org.concord.biologica.engine.Species
Return the description of this species.
getDescription() - Method in class org.concord.biologica.engine.SpeciesAllele
Return the description of this allele.
getDescription() - Method in class org.concord.biologica.engine.Gene
Return the description of this gene.
getDescription() - Method in class org.concord.biologica.ui.WorldFileFilter
 
getDescription() - Method in class org.concord.biologica.ui.XMLFileFilter
 
getDescription() - Method in class org.concord.biologica.ui.SpeciesFileFilter
 
getDescription() - Method in class org.concord.biologica.ui.GifFileFilter
 
getDifferentBaseColor() - Method in class org.concord.biologica.ui.DNAView
Get the different base color
getDiploidType() - Method in class org.concord.biologica.engine.Species
Returns diploid type of this species, which may either be DIPLOID_TYPE_XX_FEMALE_XY_MALE, DIPLOID_TYPE_XY_FEMALE_XX_MALE or DIPLOID_TYPE_NO_SEX_CHROMOSOMES.
getDiploidTypeAsString() - Method in class org.concord.biologica.engine.Species
Returns diploid type of this species, which may either be DIPLOID_TYPE_XX_FEMALE_XY_MALE, DIPLOID_TYPE_XY_FEMALE_XX_MALE or DIPLOID_TYPE_NO_SEX_CHROMOSOMES.
getDirectory() - Method in class org.concord.util.EditorInternalFrame
 
getDisplayName() - Method in class org.concord.util.beans.FeatureDescriptor
Gets the localized display name of this feature.
getDocumentBase() - Method in class org.concord.pedagogica.ui.ViewerStub
 
getDomainModels() - Method in interface org.concord.pedagogica.engine.DomainEngine
 
getDomainViews() - Method in interface org.concord.pedagogica.engine.DomainEngine
 
getDoProjection() - Method in class org.concord.collisions.engine.JWorldElement
 
getDot() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getDot() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getDot() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getDownConstraint() - Method in class org.concord.collisions.engine.JWorldElement
 
getDownConstraint() - Method in class org.concord.collisions.engine.JRigidBox
 
getDownConstraint() - Method in class org.concord.collisions.engine.JWall
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JRigidBox
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JWall
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JDaemon
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JAtom
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
getDraggableOwner() - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
getDraggableOwner() - Method in class org.concord.collisions.ui.PassiveElement
 
getDraggableOwner() - Method in interface org.concord.collisions.ui.CCDraggable
 
getDragMode() - Method in class org.concord.collisions.engine.JDaemon
 
getDragMode() - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
getDrawMode() - Method in class org.concord.collisions.engine.CCConstantForce
 
getDynamics() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getEditable() - Method in class org.concord.util.Gauge
Returns editable state.
getEditable() - Method in class org.concord.collisions.ui.GUIPanel
 
getEditable() - Method in class org.concord.molecular.ui.MolecularView
Returns boolean editable state.
getEffectiveCollisionsRadius() - Method in class org.concord.collisions.engine.JDaemon
 
getElement(int) - Method in class org.concord.flash.player.FArray
 
getElement(int) - Method in class org.concord.flash.player.builtin.FArray
 
getElementID() - Method in class org.concord.biologica.engine.ElementContext
Return the element id
getElementName() - Method in class org.concord.biologica.engine.ElementContext
Return the element name
getElementText(Shape.Element) - Static method in class org.concord.flash.player.FUtil
 
getElseCharacteristic() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the else characteristic of this genotype to phenotype rule.
getElseStatement() - Method in class org.concord.util.script.IfThenElseStatement
 
getEnabledPropertyChangeEvent(int) - Static method in class org.concord.biologica.ui.Tool
Get the enabled property change event for the given tool.
getEndColumn() - Method in interface org.concord.util.TextBounds
 
getEndLine() - Method in interface org.concord.util.TextBounds
 
getEnterCount() - Method in class org.concord.pedagogica.engine.ActivityNode
 
getEnvironments() - Method in class org.concord.biologica.engine.World
Returns an enumeration over the vector of environments in this engine.
getEqualBaseColor() - Method in class org.concord.biologica.ui.DNAView
Get the equal base color
getEventPropertyName() - Method in class org.concord.util.beans.EventHandler
Returns the property of the event that should be used in the action applied to the target.
getEventQueue() - Method in class org.concord.util.script.Script
 
getEventSetDescriptors() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge of event sets.
getEventSetDescriptors() - Method in interface org.concord.util.beans.BeanInfo
Gets the beans EventSetDescriptors.
getEventSetDescriptors() - Method in class org.concord.util.script.ScriptObject
 
getEventSetDescriptors() - Method in class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
getEventThread() - Method in class org.concord.util.script.Script
 
getExceptionListener() - Method in class org.concord.util.beans.XMLDecoder
Gets the exception handler for this stream.
getExceptionListener() - Method in class org.concord.util.beans.Encoder
Gets the exception handler for this stream.
getExpression() - Method in class org.concord.util.script.ExpressionStatement
 
getExpression() - Method in class org.concord.util.script.AssignmentStatement
 
getExtension() - Method in interface org.concord.util.script.ScriptRuntime
 
getExtension() - Method in class org.concord.util.script.ECMA
 
getExtension(String) - Static method in class org.concord.pedagogica.engine.NodeAccess
 
getFamilies() - Method in class org.concord.biologica.engine.World
Returns an enumeration over the vector of families in this engine.
getFamilies() - Method in class org.concord.biologica.ui.PedigreeView
Get the set of pedigreeFamilies in this view.
getFamilies() - Method in class org.concord.biologica.ui.PedigreeOrganismView
 
getFamily() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the family for this PedigreeFamily.
getFamilyForParents(Organism, Organism) - Method in class org.concord.biologica.ui.PedigreeView
Get the Family for the given parent Organisms
getFamilyForParents(Organism, Organism) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the Family for the given parent Organisms
getFatherMeiosisModel() - Method in class org.concord.biologica.ui.SexView
Get the father's meiosis model
getFatherOrganism() - Method in class org.concord.biologica.ui.SexView
Get the father organism for this view
getFatherPedigreeOrganism() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the father PedigreeOrganism
getFatherSmallMeiosisView() - Method in class org.concord.biologica.ui.SexView
 
getFemaleParent() - Method in class org.concord.biologica.engine.Family
Returns the female parent organism.
getField(Object, String) - Method in class org.concord.util.script.ScriptObject
 
getFieldValue(Object, String) - Method in class org.concord.util.script.ScriptObject
 
getFile() - Method in class org.concord.util.EditorInternalFrame
 
getFile() - Method in class org.concord.biologica.engine.World
Return the current world file.
getFileControlsVisible() - Method in class org.concord.biologica.ui.AllInOneView
Get file controls visible
getFileData(String) - Method in class org.concord.util.Query
 
getFileList() - Method in class org.concord.pedagogica.engine.LogModel
 
getFileLocate() - Method in class org.concord.util.LogProcess
 
getFileNames(String) - Method in class org.concord.util.LogProcess
 
getFileNames(String, String, String) - Method in class org.concord.util.LogProcess
 
getFileNames(String, Vector) - Method in class org.concord.util.LogProcess
 
getFillMethod(Shape.FillStyle) - Static method in class org.concord.flash.player.fill.FFillMethod
 
getFirstOrganismAllele() - Method in class org.concord.biologica.engine.OrganismAllelePair
Get the first organism allele of this pair.
getFirstOrganismChromosome() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Get the first organism chromosome of this pair.
getFixedNumberChildren() - Method in class org.concord.biologica.ui.PedigreeView
Get the fixed number of children from a breeding.
getFixedNumberChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the fixed number of children from a breeding.
getFlashingColor() - Method in class org.concord.collisions.engine.JWorldElement
 
getFloatFromString(String) - Static method in class org.concord.util.Util
 
getFont() - Method in class org.concord.collisions.ui.PassiveText
 
getFontBold12() - Static method in class org.concord.biologica.ui.UIGraphics
Returns bold size 12 font
getForceCalculator() - Method in class org.concord.collisions.engine.JPartWorld
 
getForeColor() - Method in class org.concord.collisions.ui.PassiveElement
 
getFrame() - Method in class org.concord.pedagogica.ui.ActivityView
 
getFrame() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getFrameNumber() - Method in class org.concord.flash.player.event.MovieClipEvent
 
getFullEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getFullXEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getFullYEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getFunction(String) - Method in class org.concord.flash.player.FMovie
Gets a function from the function list.
getGameteChromosomeModels(int) - Method in class org.concord.biologica.ui.MeiosisModel
Return an enumeration of the appropriate gamete chromosome models.
getGameteChromosomeModels(int) - Method in class org.concord.biologica.ui.BigMeiosisView
 
getGauge(int) - Method in class org.concord.util.BarGraph
Returns the gauge component at a particular index.
getGaugeWidth() - Method in class org.concord.util.BarGraph
Gets value that determines pixel spaceing between gauges.
getGender() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the gender of images in this column, which will be one of Species.FEMALE_AND_MALE, Species.FEMALE_ONLY or Species.MALE_ONLY.
getGender() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the gender of this rule, which will be one of Species.FEMALE_AND_MALE, Species.FEMALE_ONLY or Species.MALE_ONLY.
getGender() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the gender of images in this row, which will be one of Species.FEMALE_AND_MALE, Species.FEMALE_ONLY or Species.MALE_ONLY.
getGenderAsString() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the gender of images in this column, which will be one of Species.FEMALE_AND_MALE_STRING, Species.FEMALE_ONLY_STRING or Species.MALE_ONLY_STRING.
getGenderAsString() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the gender of this rule, which will be one of Species.FEMALE_AND_MALE_STRING, Species.FEMALE_ONLY_STRING or Species.MALE_ONLY_STRING.
getGenderAsString() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the gender of images in this row, which will be one of Species.FEMALE_AND_MALE_STRING, Species.FEMALE_ONLY_STRING or Species.MALE_ONLY_STRING.
getGene() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the allele's gene.
getGene() - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the allele's gene.
getGene() - Method in class org.concord.biologica.ui.OrganismAlleleControl
Get the Gene associated with this control
getGene(String) - Method in class org.concord.biologica.engine.Species
Returns the gene of this species with the given name.
getGeneOrganismAllele(Gene, String) - Method in class org.concord.biologica.engine.Organism
Get an organism allele in this organism that has the given gene and with the given allele symbol
getGeneOrganismAllele(String, String) - Method in class org.concord.biologica.engine.Organism
Get an organism allele in this organism that has the gene with the given name and with the given allele symbol
getGeneOrganismAlleles(Gene) - Method in class org.concord.biologica.engine.Organism
Get a vector of organism alleles in this organism for the given gene.
getGeneOrganismAlleles(String) - Method in class org.concord.biologica.engine.Organism
Get a vector of organism alleles in this organism for the gene with the given name.
getGeneration() - Method in class org.concord.biologica.engine.Organism
Get the generation of this organism.
getGeneration() - Method in class org.concord.biologica.engine.Family
Get the generation of this family.
getGenes() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns an enumeration over the vector of genes in this chromosome.
getGenotypeToPhenotypeRules() - Method in class org.concord.biologica.engine.Species
Returns an enumeration over the vector of genotype to phenotype rules in this species.
getGetListenerMethod() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the method used to access the registered event listeners.
getGIFDirectory() - Static method in class org.concord.biologica.engine.PathStrings
Get the Gif Directory, which will end with a file separator
getGIFURL(String) - Static method in class org.concord.biologica.engine.PathStrings
 
getGlobals() - Method in class org.concord.util.script.NameStack
 
getGlobals() - Method in class org.concord.util.script.ECMA
 
getGlobals() - Method in class org.concord.util.script.Script
 
getGraphWindow() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
getGravityX() - Method in class org.concord.collisions.engine.JWorldElement
 
getGravityX() - Method in class org.concord.collisions.engine.JPartWorld
 
getGravityY() - Method in class org.concord.collisions.engine.JWorldElement
 
getGravityY() - Method in class org.concord.collisions.engine.JPartWorld
 
getGrid() - Method in class org.concord.collisions.ui.GUIPanel
 
getHalfThickness(float) - Static method in class org.concord.collisions.engine.JRigidBox
 
getHalfThickness(float) - Static method in class org.concord.collisions.engine.JWall
 
getHandler() - Method in class org.concord.util.script.HandlerDeclaration
 
getHandlerName() - Method in class org.concord.util.script.HandlerDeclaration
 
getHasAlpha() - Method in class org.concord.flash.player.FShape
 
getHasFocus() - Method in class org.concord.biologica.ui.TreeViewNode
Get whether this node has focus.
getHashKey(int, int, int, int) - Static method in class org.concord.biologica.datasupport.DataOrganism
 
getHeatConductKoeff() - Method in class org.concord.collisions.engine.JWall
 
getHeight() - Method in class org.concord.biologica.engine.Environment
Get the height of the environment
getHeight() - Method in class org.concord.biologica.ui.PedigreeObject
Get the height
getHeight() - Method in class org.concord.biologica.ui.FilledCircle
Return height
getHeight() - Method in class org.concord.biologica.ui.PedigreeLevel
Get our height.
getHeight() - Method in class org.concord.biologica.ui.CellArc
Return height
getHeight() - Method in class org.concord.collisions.engine.JDaemon
Get the height of the daemon
getHeight() - Method in class org.concord.collisions.event.AreaEvent
 
getHeight() - Method in class org.concord.flash.player.fill.FImage
 
getHeight() - Method in class org.concord.flash.player.fill.FLosslessImage
 
getHeight() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getHighlightColor() - Method in class org.concord.biologica.ui.OrganismView
Get the highlight color
getHolder() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the raw nucleic acid's holder.
getHolder() - Method in class org.concord.biologica.engine.NucleicAcid
Returns the raw nucleic acid's holder.
getHolder() - Method in interface org.concord.biologica.engine.INucleicAcid
Returns the nucleic acid's holder.
getHolder() - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the raw nucleic acid's holder.
getHotspot(int) - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the given hotspot location.
getHotspotColor() - Method in class org.concord.biologica.engine.SpeciesImage
Get the hotspot color of this species image
getHotspotRadius() - Method in class org.concord.biologica.engine.SpeciesImage
Get the hotspot radius for this species image.
getHSize() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getHTMLDirectory() - Static method in class org.concord.biologica.engine.PathStrings
 
getHtmlPage() - Method in class org.concord.pedagogica.ui.HTMLView
 
getHTMLURL(String) - Static method in class org.concord.biologica.engine.PathStrings
 
getIcon(int) - Method in class org.concord.util.beans.SimpleBeanInfo
Claim there are no icons available.
getIcon(int) - Method in interface org.concord.util.beans.BeanInfo
This method returns an image object that can be used to represent the bean in toolboxes, toolbars, etc.
getIcon(int) - Method in class org.concord.util.script.ScriptObject
 
getIcon(int) - Method in class org.concord.biologica.engine.BioEngineBeanInfo
Gets an image that may be used to visually represent this bean (in the toolbar, on a form, etc).
getIcon(int) - Method in class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
getIconHeight() - Method in class org.concord.collisions.ui.PassiveIcon
 
getIconWidth() - Method in class org.concord.collisions.ui.PassiveIcon
 
getID() - Method in class org.concord.biologica.engine.EngineObject
Returns the ID of this object.
getID() - Method in interface org.concord.biologica.engine.INucleicAcidHolder
Returns the ID of this object.
getID() - Method in class org.concord.collisions.event.CollisionsEvent
 
getID() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getID() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getID() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getIfExpression() - Method in class org.concord.util.script.IfThenElseStatement
 
getIfSpeciesAlleles() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Returns an enumeration over the rule's if species alleles.
getIfStatement() - Method in class org.concord.util.script.IfThenElseStatement
 
getImage(int, Component) - Method in class org.concord.biologica.engine.SpeciesImage
Get the actual Image object for this species image.
getImage(URL) - Method in class org.concord.pedagogica.ui.ViewerContext
 
getImageByColor(Image, int) - Static method in class org.concord.biologica.datasupport.ImageReader
 
getImageColumnWidth(int) - Method in class org.concord.biologica.engine.Species
Returns image column width of this species.
getImageData() - Method in class org.concord.flash.player.fill.FImage
 
getImageData() - Method in class org.concord.flash.player.fill.FLosslessImage
 
getImageIcon(int) - Static method in class org.concord.biologica.ui.Tool
Get the image icon for the given tool.
getImageID() - Method in class org.concord.biologica.engine.Characteristic
Return the image ID of this characteristic.
getImageNumber() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the image number of this chromosome.
getImageNumber() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the image number of this chromosome.
getImagePathName(String) - Method in class org.concord.biologica.engine.SpeciesImage
 
getImageRowHeight(int) - Method in class org.concord.biologica.engine.Species
Returns image row height of this species.
getImageType() - Method in class org.concord.biologica.engine.SpeciesImage
Get the image type for this species image.
getImageType() - Method in class org.concord.biologica.engine.OrganismImage
Get the image type for this organism image.
getImportClass() - Method in class org.concord.util.script.ImportDeclaration
 
getImportContext() - Method in class org.concord.biologica.engine.ElementContext
Return the import context.
getImportName() - Method in class org.concord.util.script.ImportDeclaration
 
getImportPackage() - Method in class org.concord.util.script.ImportDeclaration
 
getImports() - Method in class org.concord.util.script.NameStack
 
getInactiveColor() - Method in class org.concord.collisions.engine.JDaemon
 
getIndex() - Method in class org.concord.collisions.engine.JWorldElement
 
getIndexedPropertyType() - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Gets the Class object of the indexed properties' type.
getIndexedReadMethod() - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Gets the method that should be used to read an indexed property value.
getIndexedWriteMethod() - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Gets the method that should be used to write an indexed property value.
getIndexOfGenotypeToPhenotypeRule(GenotypeToPhenotypeRule) - Method in class org.concord.biologica.engine.Species
Get index of the given genotype to phenotype rule in this species
getInDNAOrRNA() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns whether this nucleic acid is in DNA or RNA.
getInDNAorRNAasInt(String) - Static method in class org.concord.biologica.engine.Base
Convert an int inDNAorRNA value to a String.
getInDNAorRNAasString(int) - Static method in class org.concord.biologica.engine.Base
Convert an int inDNAorRNA value to a String.
getIndNumber() - Method in class org.concord.collisions.engine.JWorldElement
 
getInFile() - Method in class org.concord.util.Editor
 
getInitDelay() - Method in class org.concord.collisions.engine.CCImpulseForce
 
getInitializer() - Method in class org.concord.pedagogica.engine.Activity
 
getInputStream() - Method in class org.concord.util.script.ScriptFile
 
getInstance(int) - Method in class org.concord.flash.player.FMovieBuilder
 
getIntColorFromStringColor(String) - Static method in class org.concord.util.Util
 
getInterval() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getInterval() - Method in class org.concord.molecular.ui.AtomicValueDispatcher
This returns the graph interval.
getIntFromHexChar(char) - Static method in class org.concord.util.Util
 
getIntFromHexString(String) - Static method in class org.concord.util.Util
 
getIntFromString(String) - Static method in class org.concord.util.Util
 
getItemName() - Method in class org.concord.pedagogica.ui.ActivityView
 
getJavaHome() - Method in class org.concord.util.PathDialog
 
getJavaHome() - Method in class org.concord.pedagogica.ui.ActivityView
 
getJavaHome() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getJumpMap() - Method in class org.concord.flash.player.FFunction
 
getKineticEnergy() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getKineticEnergy() - Method in class org.concord.molecular.engine.AtomicDataEvent
 
getLabBookSession() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
getLabel() - Method in class org.concord.flash.player.FFrame
 
getLabObjGraph() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
getLargeHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the large hotspot location.
getLastError() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getLastError() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getLastError() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getLastError() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getLeftConstraint() - Method in class org.concord.collisions.engine.JWorldElement
 
getLeftConstraint() - Method in class org.concord.collisions.engine.JRigidBox
 
getLeftConstraint() - Method in class org.concord.collisions.engine.JWall
 
getLeftMostChild() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the leftmost child organism.
getLeftMostParentX() - Method in class org.concord.biologica.ui.PedigreeObject
Get X position of leftmost parent.
getLeftMostParentX() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the X location of the leftmost parent in this family.
getLength() - Method in class org.concord.flash.player.builtin.FArray
 
getLengthInBases() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the length of the chromosome in bases.
getLengthInBases() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the length of the allele in bases.
getLengthInBases() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the length of the algorithmic nucleic acid in bases.
getLengthInBases() - Method in interface org.concord.biologica.engine.IChromosome
Returns the length of chromosome in bases.
getLengthInBases() - Method in class org.concord.biologica.engine.NucleicAcid
Returns the length of the nucleic acid by summing up the lengths of all of the child nucleic acids.
getLengthInBases() - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the length of the allele in bases.
getLengthInBases() - Method in interface org.concord.biologica.engine.INucleicAcid
Returns the length of the nucleic acid in bases (vs.
getLengthInBases() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the length of the chromosome in bases.
getLengthInBases() - Method in class org.concord.biologica.engine.Gene
Returns the length of this gene in bases.
getLengthInBases() - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the length of the raw nucleic acid in bases.
getLengthInCodons() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the length of the chromosome in codons, calculated by dividing the number of bases by 3, ignoring remainder.
getLengthInCodons() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the length of the allele in codons.
getLengthInCodons() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the length of the algoritmic nucleic acid in codons.
getLengthInCodons() - Method in interface org.concord.biologica.engine.IChromosome
Returns the length of the chromosome in codons, calculated by dividing the number of bases by 3, ignoring remainder.
getLengthInCodons() - Method in class org.concord.biologica.engine.NucleicAcid
Returns the length of the nucleic acid in codons by summing up the lengths in codons of all of the child nucleic acids.
getLengthInCodons() - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the length of the allele in codons.
getLengthInCodons() - Method in interface org.concord.biologica.engine.INucleicAcid
Returns the length of the nucleic acid in codons (vs.
getLengthInCodons() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the length of the chromosome in codons.
getLengthInCodons() - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the length of the raw nucleic acid in codons, which is calculated by dividing the length in bases by 3, ignoring any remainder.
getLevel() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getLHS() - Method in class org.concord.util.script.FactAssignStatement
 
getLineText(String, int) - Method in class org.concord.util.script.Script
 
getListenerMethodDescriptors() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the MethodDescriptors of the target listener interface.
getListenerMethodName() - Method in class org.concord.util.beans.EventHandler
Returns the name of the method that will trigger the action.
getListenerMethods() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the methods of the target listener interface.
getListenerType() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the Class object for the target interface.
getLocalImage(String) - Static method in class org.concord.biologica.ui.UIView
 
getLocals() - Method in class org.concord.util.script.Statement
 
getLocation() - Method in class org.concord.biologica.ui.PedigreeLevel
Get our location.
getLockedState() - Method in class org.concord.biologica.engine.EngineObject
Get locked state of this object.
getLockedStateAsString() - Method in class org.concord.biologica.engine.EngineObject
Get locked state of this object as a string.
getLogDirectory() - Method in class org.concord.pedagogica.engine.LogModel
 
getLogging() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getLogging() - Method in class org.concord.pedagogica.engine.Activity
 
getLoginButton() - Method in class org.concord.pedagogica.ui.LoginPanel
 
getLogLevel() - Static method in class org.concord.util.Debug
Get the log level.
getLogLevel() - Static method in class org.concord.biologica.engine.Debug
Get the log level.
getLosslessFormatString(int) - Static method in class org.concord.flash.player.FUtil
 
getMainSession() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
getMakeSound() - Method in class org.concord.collisions.engine.CCImpulseForce
 
getMaleParent() - Method in class org.concord.biologica.engine.Family
Returns the male parent organism.
getMass() - Method in class org.concord.collisions.engine.JWorldElement
 
getMass() - Method in class org.concord.collisions.engine.JPartWorld
 
getMass() - Method in interface org.concord.collisions.engine.CCMassive
 
getMax() - Method in class org.concord.util.BarGraph
 
getMax() - Method in class org.concord.util.Gauge
Get the maximum value of the gauge.
getMax() - Method in class org.concord.util.LineGraph
 
getMaxColor() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getMaximumNumberChildren() - Method in class org.concord.biologica.ui.PedigreeView
Get the maximum number of children from a breeding.
getMaximumNumberChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the maximum number of children from a breeding.
getMaximumSize() - Method in class org.concord.flash.player.FFlash
 
getMaxScroll() - Method in class org.concord.flash.player.FEditField
Gets the maximum line number that this edit field will scroll to.
getMaxVel() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getMaxVelIcon() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getMediumHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the medium hotspot location.
getMember(String) - Method in class org.concord.flash.player.FScriptObject
Gets the value of a member field.
getMembers() - Method in class org.concord.util.script.NameStack
 
getMemberValue(String) - Method in class org.concord.util.script.Script
 
getMemoryMenuVisible() - Method in class org.concord.biologica.ui.AllInOneView
Get memory menu visible
getMenuBar() - Method in class org.concord.flash.util.ApplicationFrame
 
getMenus() - Method in interface org.concord.util.Editable
 
getMethod() - Method in class org.concord.util.beans.MethodDescriptor
Gets the method that this MethodDescriptor encapsualtes.
getMethodDescriptors() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge of methods.
getMethodDescriptors() - Method in interface org.concord.util.beans.BeanInfo
Gets the beans MethodDescriptors.
getMethodDescriptors() - Method in class org.concord.util.script.ScriptObject
 
getMethodName() - Method in class org.concord.util.beans.Statement
Returns the name of the method.
getMethodName(boolean) - Method in class org.concord.util.script.HandlerDeclaration
 
getMin() - Method in class org.concord.util.Gauge
Get the minimum value of the gauge.
getMinColor() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getMinimumMaximum(Point, Point) - Method in class org.concord.biologica.ui.PedigreeObject
Get the minimum and maximum positions
getMinimumMaximum(Point, Point) - Method in class org.concord.biologica.ui.PedigreeFamily
Get the minimum and maximum positions for children of this family.
getMinimumNumberChildren() - Method in class org.concord.biologica.ui.PedigreeView
Get the minimum number of children from a breeding.
getMinimumNumberChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the minimum number of children from a breeding.
getMinimumSize() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getMinimumSize() - Method in class org.concord.flash.player.FFlash
 
getMinimumSize() - Method in class org.concord.pedagogica.ui.CCXMLText
 
getModelEvents() - Method in interface org.concord.pedagogica.engine.DomainModel
 
getModelMethods() - Method in interface org.concord.pedagogica.engine.DomainModel
 
getModelType() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getModified() - Method in class org.concord.pedagogica.ui.ActivityView
 
getModify() - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
getMolecularModel() - Method in class org.concord.molecular.ui.MolecularView
 
getMolecules() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getMotherMeiosisModel() - Method in class org.concord.biologica.ui.SexView
Get the mother's meiosis model
getMotherOrFatherView() - Method in class org.concord.biologica.ui.SmallMeiosisView
Get the motherOrFatherView type of this view.
getMotherOrganism() - Method in class org.concord.biologica.ui.SexView
Get the mother organism for this view
getMotherPedigreeOrganism() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the mother PedigreeOrganism
getMotherSmallMeiosisView() - Method in class org.concord.biologica.ui.SexView
 
getMoveable() - Method in class org.concord.collisions.engine.JRigidBox
 
getMovedGamete() - Method in class org.concord.biologica.ui.MeiosisModel
Get the moved gamete
getMovedGameteChromosomeModels() - Method in class org.concord.biologica.ui.MeiosisModel
Get the moved gamete's chromosome models
getMovie() - Method in class org.concord.flash.player.FMovieBuilder
 
getMovieClip(String) - Method in class org.concord.flash.player.FMovie
Retrieves a movie clip based on its path.
getMovieClipByPath(String) - Method in class org.concord.flash.player.FFlash
Gets an movie clip by the specified path.
getMovieHeight() - Method in class org.concord.flash.player.FFlash
Gets the height of the movie as specified in the SWF file.
getMovieWidth() - Method in class org.concord.flash.player.FFlash
Gets the width of the movie as specified in the SWF file.
getMultipleOrganismView() - Method in class org.concord.biologica.ui.AllInOneView
Get the multiple organism view
getMutationSpeciesAllele() - Method in class org.concord.biologica.engine.Gene
Returns the mutation species allele for this gene, if there is one.
getName() - Method in class org.concord.util.beans.FeatureDescriptor
Gets the programmatic name of this feature.
getName() - Method in class org.concord.util.script.ScriptObject
Get the node name;
getName() - Method in class org.concord.util.script.ScriptFile
 
getName() - Method in class org.concord.biologica.engine.World
Return the name of this world.
getName() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the name of this species image column.
getName() - Method in class org.concord.biologica.engine.Environment
Return the name of this environment.
getName() - Method in class org.concord.biologica.engine.SpeciesImage
Return the name of this species image.
getName() - Method in class org.concord.biologica.engine.Species
Return the name of this species.
getName() - Method in class org.concord.biologica.engine.Organism
Return the name of this organism.
getName() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the name of this genotype to phenotype rule.
getName() - Method in class org.concord.biologica.engine.Characteristic
Return the name of this characteristic.
getName() - Method in class org.concord.biologica.engine.BioEngine
Returns the name of the bioengine.
getName() - Method in class org.concord.biologica.engine.Gene
Return the name of this gene.
getName() - Method in class org.concord.biologica.engine.Trait
Return the name of this trait.
getName() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the name of this species image row.
getName() - Method in class org.concord.biologica.engine.Terrain
Return the name of this terrain.
getName() - Method in class org.concord.collisions.engine.JWorldElement
 
getName() - Method in class org.concord.flash.player.FScriptObject
 
getName() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getName() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getName() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getName() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getName() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getName() - Method in class org.concord.pedagogica.ui.NamedTreeNode
 
getName() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
getNameField() - Method in class org.concord.pedagogica.ui.LoginPanel
 
getNames() - Method in class org.concord.util.script.NameStack
 
getNewAllele() - Method in class org.concord.biologica.ui.ChromosomeView
 
getNewValue() - Method in class org.concord.util.beans.PropertyChangeEvent
Sets the new value for the property, expressed as an Object.
getNextItemNumber() - Static method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNode() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNode() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getNodeAccess() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getNodeCenterX() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNodeCenterY() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNodeItems() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNodeList() - Method in class org.concord.pedagogica.ui.ActivityView
 
getNodeList(Vector) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getNodeText(Node) - Method in class org.concord.pedagogica.ui.LogView
 
getNodeType() - Method in class org.concord.biologica.ui.TreeViewNode
Returns node type of this node.
getNodeViewEditor() - Method in class org.concord.pedagogica.ui.ActivityView
 
getNonSexChromosomes() - Method in class org.concord.biologica.engine.Species
Returns an enumeration over the vector of non-sex chromosomes in this species.
getNonSexChromosomes() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of non-sex chromosomes in this organism.
getNthForce(int) - Method in class org.concord.collisions.engine.JWorldElement
Nth force applied to JWorldElement
getNumbAppliedForces() - Method in class org.concord.collisions.engine.JWorldElement
number of applied forces to JWorldElement
getNumbColors() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getNumberFemaleChildren() - Method in class org.concord.biologica.ui.PedigreeView
Get the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
getNumberFemaleChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
getNumberMaleChildren() - Method in class org.concord.biologica.ui.PedigreeView
Get the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
getNumberMaleChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
getNumberOfAtoms() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getNumberOfAtomsPerMolecule() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getNumberOfBends() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getNumberOfBonds() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getNumberOfCharacteristics() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the number of characteristics in this column.
getNumberOfCharacteristics() - Method in class org.concord.biologica.engine.Organism
Return the number of characteristics of this organism.
getNumberOfCharacteristics() - Method in class org.concord.biologica.engine.Trait
Return the number of characteristics of this trait.
getNumberOfCharacteristics() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the number of characteristics in this row.
getNumberOfChildFamilies() - Method in class org.concord.biologica.engine.Organism
Return the number of child families in this organism.
getNumberOfChildren() - Method in class org.concord.biologica.engine.Family
Return the number of children of this family.
getNumberOfChildren() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the number of children for this family.
getNumberOfChromosomes() - Method in class org.concord.biologica.engine.Species
Return the number of sex and non-sex chromosomes in this species.
getNumberOfChromosomes() - Method in class org.concord.biologica.engine.Organism
Get the number of chromosomes, both sex and non-sex.
getNumberOfEnvironments() - Method in class org.concord.biologica.engine.World
Return the number of environments.
getNumberOfFamilies() - Method in class org.concord.biologica.engine.World
Return the number of families.
getNumberOfFamilies() - Method in class org.concord.biologica.ui.PedigreeView
Get the number of pedigreeFamilies in this view.
getNumberOfFamilies() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the number of pedigreeFamilies in this view.
getNumberOfFamilies() - Method in class org.concord.biologica.ui.PedigreeLevel
Get the number of families at this level.
getNumberOfGenes() - Method in class org.concord.biologica.engine.SpeciesChromosome
Return the number of genes in this chromosome.
getNumberOfGenes() - Method in class org.concord.biologica.engine.Species
Return the number of genes in this species.
getNumberOfGenotypeToPhenotypeRules() - Method in class org.concord.biologica.engine.Species
Return the number of genotype to phenotype rules in this species.
getNumberOfIfSpeciesAlleles() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the number of if species alleles of this rule.
getNumberOfMolecules() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getNumberOfNonSexChromosomes() - Method in class org.concord.biologica.engine.Species
Return the number of non-sex chromosomes in this species.
getNumberOfNonSexChromosomes() - Method in class org.concord.biologica.engine.Organism
Return the number of non-sex chromosomes in this organism.
getNumberOfOrganismAllelePairs() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Get the number of organism allele pairs
getNumberOfOrganismAlleles() - Method in class org.concord.biologica.engine.OrganismChromosome
Return the number of organism alleles of this chromosome.
getNumberOfOrganismChromosomePairs() - Method in class org.concord.biologica.engine.Organism
Get the number of organism chromosome pairs, both sex and non-sex.
getNumberOfOrganismImages() - Method in class org.concord.biologica.engine.Organism
Return the number of organism images in this organism.
getNumberOfOrganisms() - Method in class org.concord.biologica.engine.World
Return the number of organisms.
getNumberOfOrganisms() - Method in class org.concord.biologica.ui.PedigreeView
Get the number of pedigreeOrganisms in this view.
getNumberOfOrganisms() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the number of pedigreeOrganisms in this view.
getNumberOfOrganisms() - Method in class org.concord.biologica.ui.PedigreeLevel
Get the total number of organisms at this level.
getNumberOfOrganisms() - Method in class org.concord.biologica.ui.MultipleOrganismView
Get the number of organisms in this view.
getnumberOfPStrandSegments() - Method in class org.concord.biologica.engine.Branch
 
getnumberOfQStrandSegments() - Method in class org.concord.biologica.engine.Branch
 
getNumberOfSelectedObjects() - Method in class org.concord.biologica.ui.SelectionSet
Get the number of selected objects in this view.
getNumberOfSexChromosomes() - Method in class org.concord.biologica.engine.Species
Return the number of sex chromosomes in this species.
getNumberOfSexChromosomes() - Method in class org.concord.biologica.engine.Organism
Return the number of sex chromosomes in this organism.
getNumberOfSpecies() - Method in class org.concord.biologica.engine.World
Return the number of species.
getNumberOfSpeciesAlleles() - Method in class org.concord.biologica.engine.Gene
Return the number of species alleles of this gene.
getNumberOfSpeciesImageColumns() - Method in class org.concord.biologica.engine.SpeciesImage
Get the number of species image columns for this species image.
getNumberOfSpeciesImageRows() - Method in class org.concord.biologica.engine.SpeciesImage
Get the number of species image columns for this species image.
getNumberOfSpeciesImages() - Method in class org.concord.biologica.engine.Species
Get the number of species images for this species.
getNumberOfTerrains() - Method in class org.concord.biologica.engine.World
Return the number of terrains of this world.
getNumberOfTraits() - Method in class org.concord.biologica.engine.Species
Return the number of traits in this species.
getNumberOfValues() - Method in class org.concord.molecular.engine.ConditionValue
 
getNumberOfValues() - Method in class org.concord.molecular.engine.AggregateValue
 
getNumberOfValues() - Method in class org.concord.molecular.engine.AtomicValue
 
getNumberOfVisibleChromosomePairs() - Method in class org.concord.biologica.ui.MeiosisModel
Returns the number of chromosome pairs to be aligned vertically in a cell during Metaphase 1 and Metaphase 2 during meiosis.
getNumberType() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the number / type of this chromosome.
getNumberType() - Method in interface org.concord.biologica.engine.IChromosome
Returns the number / type of this chromosome.
getNumberType() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the number or type of this chromosome.
getNumberType() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the number/type of this chromosome model, zero if no chromosome.
getNumberTypeAsString() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the number / type of this chromosome.
getNumberTypeAsString() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the number / type of this chromosome.
getNumberTypeAsString() - Method in class org.concord.biologica.engine.Branch
 
getNumbForms() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getNumFrames() - Method in class org.concord.flash.player.FMovieClip
 
getObject() - Method in class org.concord.biologica.ui.ObjectPropertiesView
Get the engine object whose properties are shown in this view.
getObject(int) - Method in class org.concord.biologica.engine.ImportContext
Get an object given its old id in the world file.
getObject(String) - Method in class org.concord.flash.player.FFlash
Gets a member object from the root
getObject(String) - Method in class org.concord.pedagogica.engine.NodeAccess
 
getObject(String) - Method in interface org.concord.pedagogica.engine.ActivityAccess
 
getObject(String) - Method in class org.concord.pedagogica.ui.RunActivity
 
getObject(String) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
getObjectPropertiesView() - Method in class org.concord.biologica.ui.AllInOneView
Get the object properties view
getObjectType() - Method in class org.concord.flash.player.FScriptObject
 
getObjectType() - Method in class org.concord.flash.player.FArray
 
getObjectType() - Method in class org.concord.flash.player.FFunction
 
getObjectType() - Method in class org.concord.flash.player.FUndefined
 
getObjectType() - Method in class org.concord.flash.player.FMovieClip
 
getObjectType() - Method in class org.concord.flash.player.builtin.FArray
 
getObstacles() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getObstacles() - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
getOffspringFertilizationModel() - Method in class org.concord.biologica.ui.SexView
Get the fertilization model
getOffspringMode() - Method in class org.concord.biologica.ui.PedigreeView
Get the offspring mode
getOffspringMode() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the offspring mode
getOffspringOrganism() - Method in class org.concord.biologica.ui.FertilizationModel
 
getOffspringOrganism() - Method in class org.concord.biologica.ui.SexView
Get the offspring organism for this view
getOldAllele() - Method in class org.concord.biologica.ui.ChromosomeView
 
getOldValue() - Method in class org.concord.util.beans.PropertyChangeEvent
Gets the old value for the property, expressed as an Object.
getOperand() - Method in class org.concord.util.script.UnaryExpression
 
getOrganism() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the allele's organism.
getOrganism() - Method in class org.concord.biologica.engine.OrganismImage
Return the organism of this object.
getOrganism() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Returns the organism chromosome pair's organism.
getOrganism() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the organism chromosome's organism.
getOrganism() - Method in class org.concord.biologica.engine.OrganismAllelePair
Returns the allele pair's organism.
getOrganism() - Method in class org.concord.biologica.ui.ChromosomeView
Get the shown organism for this view.
getOrganism() - Method in class org.concord.biologica.ui.OrganismAlleleControl
Get the Organism associated with this control
getOrganism() - Method in class org.concord.biologica.ui.PedigreeOrganism
Get the organism for this PedigreeOrganism.
getOrganism() - Method in class org.concord.biologica.ui.StaticOrganismView
Get the organism shown in this view.
getOrganism() - Method in class org.concord.biologica.ui.MeiosisModel
Get the organism for this model, may be null.
getOrganismAllele() - Method in class org.concord.biologica.ui.OrganismAlleleControl
Get the OrganismAllele associated with this control
getOrganismAllele() - Method in class org.concord.biologica.ui.DNAView
Get the shown organism allele for this view.
getOrganismAllelePair() - Method in class org.concord.biologica.ui.DNAView
Get the shown organism allele pair for this view.
getOrganismAllelePairs() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Returns an enumeration over the vector of all organism allele pairs in this organism chromosome pair.
getOrganismAlleles() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns an enumeration over the chromosome's organism alleles.
getOrganismCellDimensions(Organism, int, int, int, boolean) - Method in class org.concord.biologica.ui.OrganismView
Get organism cell dimensions, used when picking.
getOrganismChromosome() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the allele's organism chromosome.
getOrganismChromosomePair() - Method in class org.concord.biologica.engine.OrganismAllelePair
Returns the organism allele pair's chromosome organism pair.
getOrganismChromosomePairs() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of all organism chromosome pairs in this organism.
getOrganismImages() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of organism images in this organism.
getOrganismImageSize() - Method in class org.concord.biologica.ui.PedigreeView
Get the organism image size for this view.
getOrganismImageSize() - Method in class org.concord.biologica.ui.OrganismView
Get the organism image size for this view.
getOrganismLayoutStyle() - Method in class org.concord.biologica.ui.MultipleOrganismView
Get the current organism layout style.
getOrganismPartImage(int[], int, ShortImageDescription, Object, int, int, int[], int[]) - Static method in class org.concord.biologica.datasupport.DataOrganism
 
getOrganismPartImage(ShortImageDescription, Object, int, int, int[], int[]) - Static method in class org.concord.biologica.datasupport.DataOrganism
 
getOrganisms() - Method in class org.concord.biologica.engine.World
Returns an enumeration over the vector of organisms in this world.
getOrganisms() - Method in class org.concord.biologica.ui.PedigreeView
Get the set of pedigreeOrganisms in this view.
getOrganisms() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the set of pedigreeOrganisms in this view.
getOrganisms() - Method in class org.concord.biologica.ui.MultipleOrganismView
Get the set of organisms in this view.
getOrganismViewHeightPercentage() - Method in class org.concord.biologica.ui.SexView
Get the organism view height percentage.
getOrientation() - Method in class org.concord.biologica.ui.ToolView
Get the orientation of the view - horizontal or vertical.
getOutputStream() - Method in class org.concord.util.script.ScriptFile
 
getOwner() - Method in class org.concord.util.beans.XMLDecoder
Gets the owner of this decoder.
getOwner() - Method in class org.concord.util.beans.XMLEncoder
Gets the owner of this encoder.
getOwner() - Method in class org.concord.util.script.ScriptThread
 
getOwner() - Method in class org.concord.collisions.engine.JWorldElement
 
getPackage(String) - Method in class org.concord.util.script.Script
 
getPadding() - Method in class org.concord.pedagogica.ui.TabularView
 
getPairBase(byte, int) - Static method in class org.concord.biologica.engine.Base
Get pair base value in either DNA or RNA.
getPanelToWorldCoordinateTuner() - Method in class org.concord.collisions.engine.JPartWorld
 
getPanelToWorldCoordinateTuner() - Method in class org.concord.collisions.ui.GUIPanel
 
getPanelXfromWorldX(float) - Method in class org.concord.collisions.ui.GUIPanel
Converts x coordinate from world coordinate system to GUIPanel coordinate system
getPanelYfromWorldY(float) - Method in class org.concord.collisions.ui.GUIPanel
Converts y coordinate from world coordinate system to GUIPanel coordinate system
getParameter(String) - Method in class org.concord.pedagogica.ui.ViewerStub
 
getParameterDescriptors() - Method in class org.concord.util.beans.MethodDescriptor
Gets the ParameterDescriptor for each of this MethodDescriptor's method's parameters.
getParameters() - Method in class org.concord.util.script.MethodDeclaration
 
getParameterValues() - Method in class org.concord.util.script.InvocationExpression
 
getParent() - Method in class org.concord.util.script.NameStack
This method is used to pop a stack frame.
getParent() - Method in class org.concord.flash.player.FScriptObject
Retrieves the parent of this object, as specified in the constructor.
getParent() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getParentClip() - Method in class org.concord.flash.player.FComponent
 
getParentFamily() - Method in class org.concord.biologica.engine.Organism
Get the parent family for this organism.
getParentNode() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getParentNode() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getParentNode() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getPart() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getPartByName(String) - Static method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getPath() - Method in class org.concord.util.PathDialog
 
getPath() - Method in class org.concord.util.script.ImportDeclaration
 
getPath() - Method in class org.concord.flash.player.FMovieClip
 
getPath() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getPath() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getPath(boolean) - Method in class org.concord.util.PathDialog
 
getPath(boolean, String) - Method in class org.concord.util.PathDialog
 
getPathList() - Method in class org.concord.pedagogica.engine.LogModel
 
getPause() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getPedigreeObjects() - Method in class org.concord.biologica.ui.PedigreeLevel
Get an enumeration of all the PedigreeObjects in this level
getPedigreeOrganismView() - Method in class org.concord.biologica.ui.PedigreeView
Get the pedigree organism view in this view.
getPedigreeSymbolFirstColor() - Method in class org.concord.biologica.engine.Characteristic
Get the first pedigree symbol color of this characteristic.
getPedigreeSymbolSecondColor() - Method in class org.concord.biologica.engine.Characteristic
Get the second pedigree symbol color of this characteristic.
getPedigreeSymbolType() - Method in class org.concord.biologica.engine.Characteristic
Get the pedigree symbol type of this characteristic.
getPedigreeSymbolTypeAsString() - Method in class org.concord.biologica.engine.Characteristic
Get the pedigree symbol type of this characteristic as a string
getPedigreeView() - Method in class org.concord.biologica.ui.AllInOneView
Get the pedigree view
getPendingTextSymbol() - Method in class org.concord.biologica.engine.OrganismAllele
Get the text symbol that this allele would have if the changes pending on it were to be applied.
getPersistenceDelegate(Class) - Method in class org.concord.util.beans.Encoder
Returns the persistence delegate for the given type.
getPhase(int) - Method in class org.concord.biologica.ui.MeiosisModel
Get the phase of the meiosis at the given step.
getPloidyNumber() - Method in class org.concord.biologica.engine.Species
Returns ploidy number of this species, which may either be 1 (haploid), 2 (diploid) or 3 (haploid and diploid - e.g.
getPloidyNumber() - Method in class org.concord.biologica.engine.Organism
Returns ploidy number of this organism.
getPLStrand() - Method in class org.concord.biologica.engine.Branch
 
getPLStrandColor() - Method in class org.concord.biologica.engine.Branch
 
getPositionChanger() - Method in class org.concord.collisions.engine.JWorldElement
 
getPossibility() - Method in class org.concord.biologica.engine.CrossOver
 
getPotentialEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getPotentialEnergy() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getPotentialEnergy() - Method in class org.concord.molecular.engine.AtomicDataEvent
 
getPreferredSize() - Method in class org.concord.biologica.ui.UIView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.ChromosomeView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.WelcomeView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.StaticOrganismView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.DNAView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.AllInOneView
Return the preferred size of this application
getPreferredSize() - Method in class org.concord.biologica.ui.ObjectPropertiesView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.biologica.ui.ToolView
Return the preferred size of this application
getPreferredSize() - Method in class org.concord.biologica.ui.SexOrganismView
Return the preferred size of this canvas
getPreferredSize() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getPreferredSize() - Method in class org.concord.flash.player.FFlash
 
getPreferredSize() - Method in class org.concord.pedagogica.ui.CCXMLText
 
getPreferredSize() - Method in class org.concord.pedagogica.ui.HTMLViewCustomizer
 
getPreferredSize() - Method in class org.concord.pedagogica.ui.TabularView
 
getPrefixKoeffForUnit(CCUnit, int) - Static method in class org.concord.util.CCUnit
 
getPrefixStringForUnit(CCUnit, int) - Static method in class org.concord.util.CCUnit
 
getPreviousMeiosisChromosomeModel() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Return the previous meiosis chromosome model.
getPrinter() - Method in class org.concord.util.Editor
 
getPrinter() - Method in interface org.concord.util.script.ScriptRuntime
 
getPrinter() - Method in class org.concord.util.script.ECMA
 
getPrintWriter() - Static method in class org.concord.util.Debug
 
getPrintWriter() - Static method in class org.concord.biologica.engine.Debug
 
getPrintWriter2() - Static method in class org.concord.util.Debug
 
getPrintWriter2() - Static method in class org.concord.biologica.engine.Debug
 
getProjections(JWorldElement) - Method in class org.concord.collisions.engine.CCForce
 
getProjectionX() - Method in class org.concord.collisions.engine.CCConstantForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCFrictionForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCConstantForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCImpulseForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCGravityForce
 
getProjectionX(JWorldElement) - Method in class org.concord.collisions.engine.CCBedSpringForce
 
getProjectionY() - Method in class org.concord.collisions.engine.CCConstantForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCFrictionForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCConstantForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCImpulseForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCGravityForce
 
getProjectionY(JWorldElement) - Method in class org.concord.collisions.engine.CCBedSpringForce
 
getPropagationId() - Method in class org.concord.util.beans.PropertyChangeEvent
The "propagationId" field is reserved for future use.
getProperties() - Method in class org.concord.pedagogica.ui.ActivityView
 
getProperty(String) - Method in interface org.concord.util.script.ScriptRuntime
 
getProperty(String) - Method in class org.concord.util.script.ECMA
 
getPropertyChangeEvent() - Method in class org.concord.util.beans.PropertyVetoException
Gets the vetoed PropertyChangeEvent.
getPropertyDescriptors() - Method in class org.concord.util.beans.SimpleBeanInfo
Deny knowledge of properties.
getPropertyDescriptors() - Method in interface org.concord.util.beans.BeanInfo
Gets the beans PropertyDescriptors.
getPropertyDescriptors() - Method in class org.concord.util.script.ScriptObject
 
getPropertyDescriptors() - Method in class org.concord.biologica.engine.BioEngineBeanInfo
Returns descriptions of this bean's properties.
getPropertyDescriptors() - Method in class org.concord.collisions.engine.JDaemonBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.collisions.engine.JWorldElementBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.collisions.engine.JAtomBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.collisions.ui.PassiveElementBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.collisions.ui.PassiveTextBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.collisions.ui.PassiveIconBeanInfo
 
getPropertyDescriptors() - Method in class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
getPropertyEditorClass() - Method in class org.concord.util.beans.PropertyDescriptor
Gets any explicit PropertyEditor Class that has been registered for this property.
getPropertyName() - Method in class org.concord.util.beans.PropertyChangeEvent
Gets the programmatic name of the property that was changed.
getPropertyPanel() - Method in class org.concord.pedagogica.ui.ActivityView
 
getPropertyType() - Method in class org.concord.util.beans.PropertyDescriptor
Gets the Class object for the property.
getPRStrand() - Method in class org.concord.biologica.engine.Branch
 
getPRStrandColor() - Method in class org.concord.biologica.engine.Branch
 
getPStrand() - Method in class org.concord.biologica.engine.OrganismChromosome
 
getPStrandAlleles() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of organism alleles for P strand.
getPStrandColor() - Method in class org.concord.biologica.engine.OrganismChromosome
 
getPStrandColors() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of Colors for P strand.
getPStrandOneAlleles() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of organism alleles for P strand one.
getPStrandOneColors() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Colors for P strand one.
getPStrandTwoAlleles() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of organism alleles for P strand two.
getPStrandTwoColors() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Colors for P strand two.
getPxFromCm(float) - Static method in class org.concord.collisions.engine.JPartWorld
 
getPxUnit() - Static method in class org.concord.collisions.engine.JPartWorld
 
getQLStrand() - Method in class org.concord.biologica.engine.Branch
 
getQLStrandColor() - Method in class org.concord.biologica.engine.Branch
 
getQRStrand() - Method in class org.concord.biologica.engine.Branch
 
getQRStrandColor() - Method in class org.concord.biologica.engine.Branch
 
getQStrand() - Method in class org.concord.biologica.engine.OrganismChromosome
 
getQStrandAlleles() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of organism alleles for Q strand.
getQStrandColor() - Method in class org.concord.biologica.engine.OrganismChromosome
 
getQStrandColors() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of Colors for Q strand.
getQStrandOneAlleles() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of organism alleles for Q strand one.
getQStrandOneColors() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Colors for Q strand one.
getQStrandTwoAlleles() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of organism alleles for Q strand two.
getQStrandTwoColors() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Colors for Q strand two.
getQuantityMeasured(LabBookSession) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
getQuantityMeasured(LabBookSession) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
getQuestion() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestion(int) - Method in class org.concord.pedagogica.ui.Quiz
 
getQuestionClass() - Method in class org.concord.pedagogica.engine.QuestionState
 
getQuestionFont() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionFont(Font) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getQuestionForm() - Method in class org.concord.pedagogica.ui.Question
 
getQuestionID() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getQuestionID() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionID() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getQuestionID() - Method in class org.concord.pedagogica.ui.BlankFill
 
getQuestionID() - Method in class org.concord.pedagogica.ui.EssayFill
 
getQuestionID(String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionPrefix() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getQuestionPrefix() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionPrefix() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getQuestionPrefix() - Method in class org.concord.pedagogica.ui.BlankFill
 
getQuestionPrefix() - Method in class org.concord.pedagogica.ui.EssayFill
 
getQuestions() - Method in class org.concord.pedagogica.ui.Quiz
 
getQuestionState() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getQuestionState() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionState() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getQuestionState() - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
getQuestionState() - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
getQuestionState() - Method in class org.concord.pedagogica.ui.BlankFill
 
getQuestionState() - Method in class org.concord.pedagogica.ui.EssayFill
 
getQuestionState(Object) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionText() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
getQuestionText() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getQuestionText() - Method in class org.concord.pedagogica.ui.Question
 
getQuestionText() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getQuestionText() - Method in class org.concord.pedagogica.ui.BlankFill
 
getQuestionText() - Method in class org.concord.pedagogica.ui.EssayFill
 
getQuestionText(int) - Method in class org.concord.pedagogica.ui.Quiz
 
getR() - Method in class org.concord.collisions.engine.JAtom
 
getRange() - Method in class org.concord.util.Gauge
Returns the range of values shown by this gauge.
getReader() - Method in class org.concord.util.TextInputStream
 
getReader() - Method in class org.concord.util.Editor
 
getReader() - Method in interface org.concord.util.script.ScriptRuntime
 
getReader() - Method in class org.concord.util.script.ECMA
 
getReadMethod() - Method in class org.concord.util.beans.PropertyDescriptor
Gets the method that should be used to read the property value.
getRealLValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getRealMValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getRealTValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getReference() - Method in class org.concord.util.script.AssignmentStatement
 
getRemoveListenerMethod() - Method in class org.concord.util.beans.EventSetDescriptor
Gets the method used to remove event listeners.
getReplaceString() - Method in class org.concord.pedagogica.ui.ActivitySearch
 
getReplaceString() - Method in class org.concord.pedagogica.ui.ActivitySearchResult
 
getRescaleOp(ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
getResource(Object, String) - Static method in class org.concord.biologica.engine.PathStrings
 
getResource(String) - Static method in class org.concord.biologica.engine.PathStrings
 
getResourceAsStream(Object, String) - Static method in class org.concord.biologica.engine.PathStrings
 
getResourceAsStream(String) - Static method in class org.concord.biologica.engine.PathStrings
 
getRHS() - Method in class org.concord.util.script.FactAssignStatement
 
getRightConstraint() - Method in class org.concord.collisions.engine.JWorldElement
 
getRightConstraint() - Method in class org.concord.collisions.engine.JRigidBox
 
getRightConstraint() - Method in class org.concord.collisions.engine.JWall
 
getRightMostChild() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the rightmost child organism.
getRightMostParentX() - Method in class org.concord.biologica.ui.PedigreeObject
Get X position of rightmost parent.
getRightMostParentX() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the X location of the rightmost parent in this family.
getRoot() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getRootDirectory() - Method in interface org.concord.util.script.ScriptRuntime
 
getRootDirectory() - Method in class org.concord.util.script.ECMA
 
getRootEngineObject() - Method in class org.concord.biologica.ui.TreeView
Get the root engine object of this view.
getRootScript() - Method in class org.concord.util.script.Script
 
getRootSources(Vector, LabBookSession) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
getRootSources(Vector, LabBookSession) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
getRow() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
getRowIndex() - Method in class org.concord.biologica.engine.OrganismImage
Return the row index of this organism image in its corresponding species image.
getRunDirectory() - Method in interface org.concord.util.script.ScriptRuntime
 
getRunDirectory() - Method in class org.concord.util.script.ECMA
 
getRunning() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getRuntime() - Method in class org.concord.util.script.Script
 
getRuntime() - Method in class org.concord.pedagogica.engine.Activity
 
getRuntime() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getRuntime(String) - Static method in class org.concord.pedagogica.engine.NodeAccess
 
getRuntimeMethod(String, Object[]) - Method in class org.concord.util.script.Script
 
getScaledLValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScaledMValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScaledTValue(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScaleL() - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScaleM() - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScaleSnapX() - Method in class org.concord.collisions.ui.PassiveGrid
 
getScaleSnapY() - Method in class org.concord.collisions.ui.PassiveGrid
 
getScaleT() - Method in class org.concord.collisions.engine.CCScalingFactors
 
getScope() - Method in class org.concord.util.script.Script
 
getScript() - Method in class org.concord.util.script.ScriptObject
 
getScript() - Method in interface org.concord.util.script.ScriptRuntime
 
getScript() - Method in class org.concord.util.script.ECMA
 
getScript() - Static method in class org.concord.util.script.ScriptThread
 
getScript() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getScriptRuntime() - Method in interface org.concord.util.script.ScriptRuntime
 
getScriptRuntime() - Method in class org.concord.util.script.ECMA
 
getScriptType() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getScriptType() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getScriptType() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getScriptType() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getScroll() - Method in class org.concord.flash.player.FEditField
Returns the current scroll location.
getSearchResult() - Method in class org.concord.pedagogica.ui.ActivityView
 
getSearchString() - Method in class org.concord.pedagogica.ui.ActivitySearch
 
getSecondOrganismAllele() - Method in class org.concord.biologica.engine.OrganismAllelePair
Get the second organism allele of this pair.
getSecondOrganismChromosome() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Get the second organism chromosome of this pair.
getSecurityDomain(Class) - Method in class org.concord.util.script.Script.ScriptSecuritySupport
Return the security context associated with the given class.
getSeed() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the seed value of this algorithmic nucleic acid.
getSelectedAllele() - Method in class org.concord.biologica.ui.ChromosomeView
Get the selected allele.
getSelectedChromosome() - Method in class org.concord.biologica.ui.ChromosomeView
Get the selected chromosome.
getSelectedGamete() - Method in class org.concord.biologica.ui.MeiosisModel
Get the selected gamete
getSelectedObjectAtIndex(int) - Method in class org.concord.biologica.ui.SelectionSet
Get the selected object at the given index in the selection set.
getSelectedObjects() - Method in class org.concord.biologica.ui.SelectionSet
Get the set of selected objects in this view.
getSelectedValue() - Method in class org.concord.pedagogica.ui.ActivitySearch
 
getSelectionColor() - Method in class org.concord.biologica.ui.ChromosomeView
Get the selection color
getSelectionColor() - Method in class org.concord.biologica.ui.OrganismView
Get the selection color
getSelectionColor() - Method in class org.concord.biologica.ui.TreeView
Get the selection color
getSelectionMode() - Method in class org.concord.biologica.ui.SelectionSet
Get the current selection mode.
getSelectionPresenters() - Method in class org.concord.biologica.ui.SelectionSet
Get the selection presenters
getSelectionSet() - Method in interface org.concord.biologica.ui.SelectionPresenter
Get the current selection set.
getSelectionSet() - Method in class org.concord.biologica.ui.ChromosomeView
 
getSelectionSet() - Method in class org.concord.biologica.ui.PedigreeView
Get the current selection set
getSelectionSet() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the current selection set
getSelectionSet() - Method in class org.concord.biologica.ui.AllInOneView
Get the current selection set
getSelectionSet() - Method in class org.concord.biologica.ui.TreeView
Get the current selection set
getSelectionSet() - Method in class org.concord.biologica.ui.MultipleOrganismView
Get the current selection set
getSelectors() - Method in class org.concord.pedagogica.engine.QuestionState
 
getSex() - Method in class org.concord.biologica.engine.Organism
Get the sex of this organism.
getSexAsString() - Method in class org.concord.biologica.engine.Organism
Get the sex of this organism as a string.
getSexChromosomes() - Method in class org.concord.biologica.engine.Species
Returns an enumeration over the vector of sex chromosomes in this species.
getSexChromosomes() - Method in class org.concord.biologica.engine.Organism
Returns an enumeration over the vector of sex chromosomes in this organism.
getSexView() - Method in class org.concord.biologica.ui.AllInOneView
Get the sex view
getSexViewMode() - Method in class org.concord.biologica.ui.SexView
Get the sex view mode.
getShortDescription() - Method in class org.concord.util.beans.FeatureDescriptor
Gets the short description of this feature.
getShortImageDescription(int, int) - Static method in class org.concord.biologica.datasupport.ImageReader
 
getShowAcceleration() - Method in class org.concord.collisions.engine.JWorldElement
 
getShowVelocity() - Method in class org.concord.collisions.engine.JWorldElement
 
getSimulationState() - Method in class org.concord.collisions.engine.JPartWorld
 
getSimulationState() - Method in class org.concord.collisions.ui.GUIPanel
 
getSink() - Method in class org.concord.pedagogica.engine.ActivityArc
 
getSinkPoint() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getSize() - Method in class org.concord.util.script.NameStack
 
getSize() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getSlider() - Method in class org.concord.util.BarGraph
 
getSlider() - Method in class org.concord.util.LineGraph
 
getSmallFertilizationView() - Method in class org.concord.biologica.ui.SexView
 
getSmallHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the small hotspot location.
getSmallMeiosisView() - Method in class org.concord.biologica.ui.BigMeiosisView
Get the small meiosis view.
getSoundFileName() - Method in class org.concord.collisions.engine.CCImpulseForce
 
getSoundOn() - Method in class org.concord.collisions.engine.JPartWorld
 
getSource() - Method in class org.concord.pedagogica.engine.ActivityArc
 
getSource(int) - Method in class org.concord.biologica.engine.SpeciesImage
Return the file of this species image in File form.
getSourcePoint() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getSpanAngle() - Method in class org.concord.biologica.ui.CellArc
Return span angle, using the same definition as is used in java.awt.Graphics.drawArc().
getSpecies() - Method in class org.concord.biologica.engine.World
Returns an enumeration over the vector of species in this world.
getSpecies() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns the chromosome's species.
getSpecies() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the organism allele's species.
getSpecies() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the Species of this object.
getSpecies() - Method in class org.concord.biologica.engine.SpeciesImage
Return the species of this object.
getSpecies() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the species containing this object.
getSpecies() - Method in class org.concord.biologica.engine.Organism
Return the species of this organism, if it is known.
getSpecies() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the species of this genotype to phenotype rule.
getSpecies() - Method in class org.concord.biologica.engine.Characteristic
Get the species containing this object.
getSpecies() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Returns the organism chromosome pair's species.
getSpecies() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns the organism chromosome's species.
getSpecies() - Method in class org.concord.biologica.engine.Gene
Get the species containing this object.
getSpecies() - Method in class org.concord.biologica.engine.Trait
Return the species of this trait.
getSpecies() - Method in class org.concord.biologica.engine.OrganismAllelePair
Returns the organism chromosome pair's species.
getSpecies() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the Species of this object.
getSpecies() - Method in class org.concord.biologica.ui.PedigreeView
Get the current species.
getSpecies() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the current species.
getSpeciesAllele() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the organism allele's species allele.
getSpeciesAlleles() - Method in class org.concord.biologica.engine.Gene
Returns an enumeration over the gene's species alleles.
getSpeciesAlleles() - Method in class org.concord.biologica.engine.ChromosomeSpecification
Returns an enumeration over the species alleles for this specification
getSpeciesAllelesVector() - Method in class org.concord.biologica.engine.Species
Returns a vector of the SpeciesAlleles in this species.
getSpeciesChromosome() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the species chromosome containing this object.
getSpeciesChromosome() - Method in class org.concord.biologica.engine.OrganismChromosome
Get the species chromosome for ths organism chromosome.
getSpeciesChromosome() - Method in class org.concord.biologica.engine.Gene
Get the species chromosome containing this gene.
getSpeciesChromosome() - Method in class org.concord.biologica.engine.ChromosomeSpecification
Returns the species chromosome for this specification.
getSpeciesDirectory() - Static method in class org.concord.biologica.engine.PathStrings
Get the Species Directory, which will end with a file separator
getSpeciesFile(int) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
getSpeciesImage() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return the SpeciesImage of this object.
getSpeciesImage() - Method in class org.concord.biologica.engine.OrganismImage
Return the species image of this object.
getSpeciesImage() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return the SpeciesImage of this object.
getSpeciesImageColumns() - Method in class org.concord.biologica.engine.SpeciesImage
Returns an enumeration over the vector of species image columns in this species image.
getSpeciesImageRowAt(int) - Method in class org.concord.biologica.engine.SpeciesImage
Returns a specific species image row, null if invalid row.
getSpeciesImageRows() - Method in class org.concord.biologica.engine.SpeciesImage
Returns an enumeration over the vector of species image columns in this species image.
getSpeciesImages() - Method in class org.concord.biologica.engine.Species
Returns an enumeration over the vector of species images in this species.
getSpeciesName(int) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
getSpeciesNumber() - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
getSpeciesPulldownVisible() - Method in class org.concord.biologica.ui.AllInOneView
Get species pulldown visible
getSqueezeFactor() - Method in class org.concord.biologica.ui.PedigreeFamily
Accessor for squeeze factor.
getStandalone() - Method in interface org.concord.util.script.ScriptRuntime
 
getStandalone() - Method in class org.concord.util.script.ECMA
 
getStartAngle() - Method in class org.concord.biologica.ui.CellArc
Return start angle
getStartIndexInHolder() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the start index of this nucleic acid in its holder.
getStartIndexInHolder() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the start index of this nucleic acid in its holder.
getStartIndexInHolder() - Method in class org.concord.biologica.engine.NucleicAcid
Returns the start index of this nucleic acid in its holder.
getStartIndexInHolder() - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the start index of this nucleic acid in its holder.
getStartIndexInHolder() - Method in interface org.concord.biologica.engine.INucleicAcid
Returns the start index of this nucleic acid in its holder.
getStartIndexInHolder() - Method in class org.concord.biologica.engine.Gene
Returns the start index of this gene acid in its chromosome.
getStartIndexInHolder() - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the start index of this nucleic acid in its holder.
getState() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getStatement() - Method in class org.concord.util.script.LoopStatement
 
getStatement() - Method in class org.concord.util.script.MethodDeclaration
 
getStep() - Method in class org.concord.biologica.ui.FertilizationModel
Get the current step of the fertilization
getStep() - Method in class org.concord.biologica.ui.MeiosisModel
Get the current step of the meiosis.
getStepTime() - Method in class org.concord.collisions.event.StepEvent
 
getStrand() - Method in class org.concord.biologica.engine.Gene
Get the strand of this gene.
getStrandAlleles(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Alleles for the given strand.
getStrandColors(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of Colors for the given strand
getStride() - Method in class org.concord.flash.player.fill.FLosslessImage
 
getStride() - Method in class org.concord.flash.player.fill.FJPEGImage
 
getStudents() - Method in class org.concord.pedagogica.ui.LoginPanel
 
getStudentsForTitle() - Method in class org.concord.pedagogica.ui.LoginPanel
 
getSummary(LabBookSession) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
getSummary(LabBookSession) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
getSymbol(int) - Method in class org.concord.flash.player.FMovieBuilder
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Returns the default table cell renderer.
getTableInputModel() - Method in class org.concord.pedagogica.ui.TableInputView
Method which returns the associated TableInputModel that e.g.
getTableSize() - Method in class org.concord.pedagogica.ui.TableInputView
 
getTags() - Method in class org.concord.collisions.engine.AtomDragPropertyEditor
 
getTags() - Method in class org.concord.collisions.engine.AtomDragModePropertyEditor
 
getTarget() - Method in class org.concord.util.beans.EventHandler
Returns the object to which this event handler will send a message.
getTarget() - Method in class org.concord.util.beans.Statement
Returns the target of this statement.
getTemperature() - Method in class org.concord.collisions.engine.JWorldElement
 
getTemperature() - Method in class org.concord.collisions.engine.JRigidBox
 
getTemperature() - Method in class org.concord.collisions.engine.JWall
 
getTemperature() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getTerrain(int, int) - Method in class org.concord.biologica.engine.Environment
Get the terrain at the given indexes into the terrain array
getTerrains() - Method in class org.concord.biologica.engine.World
Returns an enumeration over the world's terrains.
getTestDoc() - Static method in class org.concord.pedagogica.ui.CCXMLText
 
getText() - Method in class org.concord.collisions.ui.PassiveText
 
getText() - Method in class org.concord.flash.player.FEditField
 
getText() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getText() - Method in class org.concord.pedagogica.engine.QuestionState
 
getText() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
getText() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getText() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
getText() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getText() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
getText() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getTextArea() - Method in class org.concord.util.EditorInternalFrame
 
getTextIndent() - Method in class org.concord.biologica.ui.PedigreeView
Get the text indent for this view.
getTextIndent() - Method in class org.concord.biologica.ui.OrganismView
Get the text indent for this view.
getTextLineSpacing() - Method in class org.concord.biologica.ui.PedigreeView
Get the text line spacing for this view, the number of pixels between lines of text below an organism.
getTextLineSpacing() - Method in class org.concord.biologica.ui.OrganismView
Get the text line spacing for this view, the number of pixels between lines of text below an organism.
getTextSelection() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getTextSelection() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
getTextSelection() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
getTextSelection() - Method in interface org.concord.pedagogica.ui.ActivityItem
 
getTextSymbol() - Method in class org.concord.biologica.engine.OrganismAllele
Returns the allele's text symbol.
getTextSymbol() - Method in class org.concord.biologica.engine.SpeciesAllele
Returns the allele's text symbol.
getThenCharacteristic() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return the then characteristic of this genotype to phenotype rule.
getToolTipString(int) - Static method in class org.concord.biologica.ui.Tool
Get the tool tip string for the given tool.
getToolTipText() - Method in class org.concord.flash.player.FComponent
Gets the tool tip text set on this component
getTopLeftGameteChromosomeModels() - Method in class org.concord.biologica.ui.MeiosisModel
Return an enumeration of the top left gamete chromosome models.
getTopLeftPoint() - Method in class org.concord.biologica.ui.PedigreeObject
Get the top left point of the pedigree object.
getTopMidPoint() - Method in class org.concord.biologica.ui.PedigreeObject
Get midpoint along top of object .
getTopMostChild() - Method in class org.concord.biologica.ui.PedigreeFamily
Get the topmost child organism.
getTopRightGameteChromosomeModels() - Method in class org.concord.biologica.ui.MeiosisModel
Return an enumeration of the top right gamete chromosome models.
getTotalAtomsEnergy() - Method in class org.concord.collisions.engine.JPartWorld
retrieves total kinetic energy (atoms only) you should call calculateTotalAtomsEnergy immediately before this call
getTotalBoxesEnergy() - Method in class org.concord.collisions.engine.JPartWorld
 
getTotalEnergy() - Method in class org.concord.collisions.engine.JPartWorld
retrieves total kinetic energy you should call calculateTotalWallsEnergy and calculateTotalAtomsEnergy immediately before this call
getTotalWallsEnergy() - Method in class org.concord.collisions.engine.JPartWorld
retrieves total kinetic energy (walls only) you should call calculateTotalWallsEnergy immediately before this call
getTraceColor() - Method in class org.concord.collisions.engine.JAtom
 
getTrait() - Method in class org.concord.biologica.engine.Characteristic
Return the trait of this characteristic.
getTrait() - Method in class org.concord.biologica.ui.PedigreeView
Get the trait for this view.
getTrait() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Get the trait for this view.
getTraits() - Method in class org.concord.biologica.engine.Species
Returns an enumeration over the vector of traits in this species.
getTransform() - Method in class org.concord.flash.player.FComponent
 
getTransformed(AffineTransform) - Method in class org.concord.flash.player.FComponent
Apply the component's transform to the "world transform" that is passed in if there is no transform on the component then return the passed in transform
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.concord.biologica.ui.TreeViewCellRenderer
This is messaged from JTree whenever it needs to get the size of the component or it wants to draw it.
getTreeNode(int, Frame) - Method in class org.concord.flash.util.MovieViewer
 
getTreeNode(TimeLine, Actions[], int, String, String) - Method in class org.concord.flash.util.MovieViewer
 
getTreePaneVisible() - Method in class org.concord.biologica.ui.AllInOneView
Get the tree pane visibility
getTreeView() - Method in class org.concord.biologica.ui.AllInOneView
Get the tree view
getTypeFromCellArc(CellArc) - Method in class org.concord.biologica.ui.BigMeiosisView
 
getTypeName() - Method in class org.concord.util.script.event.EventHandler
 
getUnit(int) - Static method in class org.concord.util.CCUnit
 
getUnit(LabBookSession) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
getUnit(LabBookSession) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
getUpConstraint() - Method in class org.concord.collisions.engine.JWorldElement
 
getUpConstraint() - Method in class org.concord.collisions.engine.JRigidBox
 
getUpConstraint() - Method in class org.concord.collisions.engine.JWall
 
getUtilityButton() - Method in class org.concord.biologica.ui.PedigreeView
 
getValue() - Method in class org.concord.util.BarGraph
 
getValue() - Method in class org.concord.util.Gauge
Get value of gauge sub-bar.
getValue() - Method in class org.concord.util.beans.Expression
If the value property of this instance is not already set, this method dynamically finds the method with the specified methodName on this target with these arguments and calls it.
getValue() - Method in class org.concord.util.script.BooleanLiteral
 
getValue() - Method in class org.concord.util.script.FloatLiteral
 
getValue() - Method in class org.concord.util.script.Quote
 
getValue() - Method in class org.concord.util.script.NullLiteral
 
getValue() - Method in class org.concord.util.script.CharacterLiteral
 
getValue() - Method in class org.concord.util.script.VariableDeclaration
 
getValue() - Method in class org.concord.util.script.IntegerLiteral
 
getValue() - Method in class org.concord.util.script.StringLiteral
 
getValue() - Method in class org.concord.molecular.engine.ConditionValue
 
getValue() - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
getValue(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
getValue(int) - Method in class org.concord.util.BarGraph
Get value of graph element at index.
getValue(int) - Method in class org.concord.util.Gauge
Get value of gauge sub-bar at index.
getValue(int) - Method in class org.concord.molecular.engine.ConditionValue
 
getValue(int) - Method in class org.concord.molecular.engine.AggregateValue
 
getValue(int) - Method in class org.concord.molecular.engine.AtomicValue
 
getValue(int) - Method in class org.concord.molecular.engine.AtomicProperty
 
getValue(int) - Method in class org.concord.molecular.engine.VelocitySquare
 
getValue(int) - Method in class org.concord.molecular.engine.KineticEnergy
 
getValue(int) - Method in class org.concord.molecular.engine.VelocityMagnitude
 
getValue(String) - Method in class org.concord.util.Query
 
getValue(String) - Method in class org.concord.util.beans.FeatureDescriptor
Retrieve a named attribute with this feature.
getValue(String) - Method in interface org.concord.util.script.ScriptRuntime
 
getValue(String) - Method in class org.concord.util.script.ECMA
 
getValueGraph() - Method in class org.concord.molecular.ui.AtomicValueDispatcher
Get the current object that implements ValueGraph
getValues() - Method in class org.concord.util.script.NameStack
 
getValues() - Method in class org.concord.pedagogica.engine.NodeAccess
 
getValueString() - Method in class org.concord.biologica.engine.ElementContext
Return a String that contains the contents of the text buffer
getVariable() - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
getVariable(String) - Method in class org.concord.flash.player.StackFrame4
 
getVariables() - Method in class org.concord.pedagogica.engine.NodeAccess
 
getVector() - Method in class org.concord.molecular.engine.IndexList
 
getVelColor() - Method in class org.concord.collisions.engine.JAtom
 
getVelocityDraggable(char) - Method in class org.concord.collisions.engine.JAtom
 
getVelScale() - Static method in class org.concord.collisions.engine.JWorldElement
 
getVelXArrowEnd() - Method in class org.concord.collisions.engine.JAtom
 
getVelYArrowEnd() - Method in class org.concord.collisions.engine.JAtom
 
getViewEvents() - Method in interface org.concord.pedagogica.engine.DomainView
 
getViewMethods() - Method in interface org.concord.pedagogica.engine.DomainView
 
getViewObject(String) - Method in class org.concord.pedagogica.engine.ActivityNode
 
getViewText() - Method in class org.concord.pedagogica.engine.ActivityScript
 
getVisiblePropertyChangeEvent(int) - Static method in class org.concord.biologica.ui.Tool
Get the visible property change event for the given tool.
getVisitor() - Method in class org.concord.collisions.event.AreaEvent
 
getVx() - Method in class org.concord.collisions.engine.JWorldElement
 
getVx() - Method in class org.concord.collisions.ui.PassiveElement
 
getVx() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getVy() - Method in class org.concord.collisions.engine.JWorldElement
 
getVy() - Method in class org.concord.collisions.ui.PassiveElement
 
getVy() - Method in class org.concord.collisions.ui.DataCrossPanel
 
getWabaGraph() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
getWaitingThread() - Method in class org.concord.util.script.Script
 
getWallByName(String) - Method in class org.concord.collisions.engine.JPartWorld
 
getWalls() - Method in class org.concord.collisions.engine.JPartWorld
 
getWalls() - Method in class org.concord.collisions.engine.JRigidBox
 
getWallTemperatureMode() - Method in class org.concord.collisions.engine.JWall
 
getWatchableElement() - Method in class org.concord.collisions.ui.GUIPanel
 
getWatchMode() - Method in class org.concord.collisions.ui.GUIPanel
 
getWeight() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the weight of this allele.
getWhen() - Method in class org.concord.collisions.event.AreaEvent
 
getWhen() - Method in class org.concord.collisions.event.CollisionsEvent
 
getWhichVelocity() - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
getWidth() - Method in class org.concord.biologica.engine.Environment
Get the width of the environment
getWidth() - Method in class org.concord.biologica.ui.PedigreeObject
Get the width
getWidth() - Method in class org.concord.biologica.ui.FilledCircle
Return width
getWidth() - Method in class org.concord.biologica.ui.PedigreeLevel
Get our width.
getWidth() - Method in class org.concord.biologica.ui.CellArc
Return width
getWidth() - Method in class org.concord.collisions.engine.JDaemon
Get the width of the daemon
getWidth() - Method in class org.concord.collisions.event.AreaEvent
 
getWidth() - Method in class org.concord.flash.player.fill.FImage
 
getWidth() - Method in class org.concord.flash.player.fill.FLosslessImage
 
getWidth() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getWorld() - Method in class org.concord.biologica.engine.EngineObject
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.World
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.SpeciesChromosome
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.OrganismAllele
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Returns the world containing this nucleic acid.
getWorld() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Environment
Return the world containing this environment.
getWorld() - Method in class org.concord.biologica.engine.SpeciesImage
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Species
Return the world containing this species.
getWorld() - Method in class org.concord.biologica.engine.NucleicAcid
Returns the world containing this nucleic acid.
getWorld() - Method in class org.concord.biologica.engine.SpeciesAllele
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Organism
Return the world containing this organism.
getWorld() - Method in class org.concord.biologica.engine.Family
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.OrganismImage
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Characteristic
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.OrganismChromosome
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Gene
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Trait
Get the world containing this object.
getWorld() - Method in interface org.concord.biologica.engine.INucleicAcidHolder
Returns the world containing this holder
getWorld() - Method in class org.concord.biologica.engine.OrganismAllelePair
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the world containing this object.
getWorld() - Method in class org.concord.biologica.engine.Terrain
Return the world containing this terrain.
getWorld() - Method in class org.concord.biologica.engine.RawNucleicAcid
Returns the world containing this nucleic acid.
getWorldElementByName(int, String) - Method in class org.concord.collisions.engine.JPartWorld
 
getWorldModel() - Method in class org.concord.collisions.engine.JWorldElement
 
getWorldModel() - Method in class org.concord.collisions.engine.CCForce
 
getWorldModel() - Method in class org.concord.collisions.ui.GUIPanel
 
getWorldsDirectory() - Static method in class org.concord.biologica.engine.PathStrings
Get the Worlds Directory, which will end with a file separator
getWorldTime() - Method in class org.concord.collisions.event.StepEvent
 
getWorldToPanelCoordinateTuner() - Method in class org.concord.collisions.engine.JPartWorld
 
getWorldToPanelCoordinateTuner() - Method in class org.concord.collisions.ui.GUIPanel
 
getWorldXfromPanelX(float) - Method in class org.concord.collisions.ui.GUIPanel
Converts x coordinate from GUIPanel coordinate system to world coordinate system
getWorldYfromPanelY(float) - Method in class org.concord.collisions.ui.GUIPanel
Converts y coordinate from GUIPanel coordinate system to world coordinate system
getWriteMethod() - Method in class org.concord.util.beans.PropertyDescriptor
Gets the method that should be used to write the property value.
getWriter() - Method in class org.concord.util.TextOutputStream
 
getWSize() - Method in class org.concord.biologica.datasupport.SpecieFileDesc
 
getX() - Method in class org.concord.collisions.engine.JWorldElement
 
getX() - Method in class org.concord.collisions.engine.CCPoint
 
getX() - Method in class org.concord.collisions.engine.JRigidBox
 
getX() - Method in class org.concord.collisions.engine.JWall
 
getX() - Method in class org.concord.collisions.engine.JDaemon
Get the x position of the daemon
getX() - Method in class org.concord.collisions.engine.JAtom
 
getX() - Method in class org.concord.collisions.event.AreaEvent
 
getX() - Method in class org.concord.collisions.event.CollisionsEvent
 
getX() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getX(CCUnit) - Method in class org.concord.collisions.engine.JWorldElement
 
getX1() - Method in class org.concord.biologica.ui.CellLine
Return x1
getX1() - Method in class org.concord.biologica.ui.SpindleLine
Return x1
getX2() - Method in class org.concord.biologica.ui.CellLine
Return x2
getX2() - Method in class org.concord.biologica.ui.SpindleLine
Return x2
getXacceleration() - Method in class org.concord.collisions.engine.JWorldElement
X projection of acceleration cause by applied forces
getXacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCDefaultForceCalculator
 
getXacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
getXacceleration(JWorldElement) - Method in interface org.concord.collisions.engine.CCForceCalculator
 
getXacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCFrictionForceCalculator
 
getXCentromereAtStep(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the X centromere location as an int at the given meiosis step (NOT the array index!!).
getXCentromereAtStep(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the X centromere location as an int at the given fertilization step (NOT the array index!!).
getXLargeHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the xLarge hotspot location.
getXLeft() - Method in class org.concord.biologica.ui.FilledCircle
Return xLeft
getXLeft() - Method in class org.concord.biologica.ui.CellArc
Return xLeft
getXLocation() - Method in class org.concord.biologica.ui.PedigreeObject
Get the X location
getXMLParser() - Method in class org.concord.biologica.engine.ElementContext
Return the parser
getXNeighbors() - Method in class org.concord.collisions.engine.JWorldElement
 
getXNeighbors() - Method in class org.concord.collisions.engine.JAtom
 
getXPotentialEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getXPotentialEnergy() - Method in class org.concord.collisions.engine.JRigidBox
 
getXPotentialEnergy() - Method in class org.concord.collisions.engine.JWall
 
getXPotentialEnergy() - Method in class org.concord.collisions.engine.JDaemon
 
getXPotentialEnergy() - Method in class org.concord.collisions.engine.JAtom
 
getXPStrandOnePoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for x coordinates of P strand one at the given meiosis step.
getXPStrandPoints(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of int's for x coordinates of P strand at the given fertilization step.
getXPStrandTwoPoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for x coordinates of P strand two at the given meiosis step.
getXQStrandOnePoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for x coordinates of Q strand one at the given meiosis step.
getXQStrandPoints(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of int's for x coordinates of Q strand at the given fertilization step.
getXQStrandTwoPoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for x coordinates of Q strand two at the given meiosis step.
getXSmallHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the xSmall hotspot location.
getXTemperature() - Method in class org.concord.collisions.engine.JWorldElement
 
getXTemperature() - Method in class org.concord.collisions.engine.JRigidBox
 
getXTemperature() - Method in class org.concord.collisions.engine.JWall
 
getXTemperature() - Method in class org.concord.collisions.engine.JImpulseDaemon
 
getXTemperature() - Method in class org.concord.collisions.engine.JAtom
 
getXTemperature() - Method in class org.concord.collisions.engine.JBooster
 
getXTemporaryOffset() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the X temporary offset of this chromosome.
getXTemporaryOffset() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the X temporary offset of this chromosome.
getXXSmallHotspot() - Method in class org.concord.biologica.engine.SpeciesImageRow
Get the xxSmall hotspot location.
getY() - Method in class org.concord.collisions.engine.JWorldElement
 
getY() - Method in class org.concord.collisions.engine.CCPoint
 
getY() - Method in class org.concord.collisions.engine.JRigidBox
 
getY() - Method in class org.concord.collisions.engine.JWall
 
getY() - Method in class org.concord.collisions.engine.JDaemon
Get the y position of the daemon
getY() - Method in class org.concord.collisions.engine.JAtom
 
getY() - Method in class org.concord.collisions.event.AreaEvent
 
getY() - Method in class org.concord.collisions.event.CollisionsEvent
 
getY() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
getY(CCUnit) - Method in class org.concord.collisions.engine.JWorldElement
 
getY1() - Method in class org.concord.biologica.ui.CellLine
Return y1
getY1() - Method in class org.concord.biologica.ui.SpindleLine
Return y1
getY2() - Method in class org.concord.biologica.ui.CellLine
Return y2
getY2() - Method in class org.concord.biologica.ui.SpindleLine
Return y2
getYacceleration() - Method in class org.concord.collisions.engine.JWorldElement
Y projection of acceleration cause by applied forces
getYacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCDefaultForceCalculator
 
getYacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
getYacceleration(JWorldElement) - Method in interface org.concord.collisions.engine.CCForceCalculator
 
getYacceleration(JWorldElement) - Method in class org.concord.collisions.engine.CCFrictionForceCalculator
 
getYCentromereAtStep(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the Y centromere location as an int at the given meiosis step (NOT the array index!!).
getYCentromereAtStep(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the Y centromere location as an int at the given fertilization step (NOT the array index!!).
getYLocation() - Method in class org.concord.biologica.ui.PedigreeObject
Get the Y location
getYNeighbors() - Method in class org.concord.collisions.engine.JWorldElement
 
getYNeighbors() - Method in class org.concord.collisions.engine.JAtom
 
getYPotentialEnergy() - Method in class org.concord.collisions.engine.JWorldElement
 
getYPotentialEnergy() - Method in class org.concord.collisions.engine.JRigidBox
 
getYPotentialEnergy() - Method in class org.concord.collisions.engine.JWall
 
getYPotentialEnergy() - Method in class org.concord.collisions.engine.JDaemon
 
getYPotentialEnergy() - Method in class org.concord.collisions.engine.JAtom
 
getYPStrandOnePoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for y coordinates of P strand one at the given meiosis step.
getYPStrandPoints(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of int's for y coordinates of P strand at the given meiosis step.
getYPStrandTwoPoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for y coordinates of P strand two at the given meiosis step.
getYQStrandOnePoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for y coordinates of Q strand one at the given meiosis step.
getYQStrandPoints(int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the array of int's for y coordinates of Q strand at the given fertilization step.
getYQStrandTwoPoints(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the array of int's for y coordinates of Q strand two at the given meiosis step.
getYTemperature() - Method in class org.concord.collisions.engine.JWorldElement
 
getYTemperature() - Method in class org.concord.collisions.engine.JRigidBox
 
getYTemperature() - Method in class org.concord.collisions.engine.JWall
 
getYTemperature() - Method in class org.concord.collisions.engine.JImpulseDaemon
 
getYTemperature() - Method in class org.concord.collisions.engine.JAtom
 
getYTemperature() - Method in class org.concord.collisions.engine.JBooster
 
getYTemporaryOffset() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get the Y temporary offset of this chromosome.
getYTemporaryOffset() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Get the Y temporary offset of this chromosome.
getYTop() - Method in class org.concord.biologica.ui.FilledCircle
Return yTop
getYTop() - Method in class org.concord.biologica.ui.CellArc
Return yTop
getZipFile() - Method in class org.concord.util.script.ScriptFile
 
GifFileFilter - class org.concord.biologica.ui.GifFileFilter.
 
GifFileFilter() - Constructor for class org.concord.biologica.ui.GifFileFilter
 
GLN - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Glutamine
globalHandlers - Static variable in class org.concord.util.script.ListenStatement
 
globals - Variable in class org.concord.util.script.NameStack
 
globals - Variable in class org.concord.util.script.Script
 
GlossaryFrame - class org.concord.biologica.ui.GlossaryFrame.
 
GlossaryFrame() - Constructor for class org.concord.biologica.ui.GlossaryFrame
 
GlossaryFrame(String) - Constructor for class org.concord.biologica.ui.GlossaryFrame
 
GlossaryFrame(String, boolean) - Constructor for class org.concord.biologica.ui.GlossaryFrame
 
glossaryHTML - Variable in class org.concord.pedagogica.ui.HelpView
 
GLU - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Glutamic acid
GLUTAMIC_ACID - Static variable in class org.concord.biologica.engine.AminoAcid
Glutamic acid
GLUTAMINE - Static variable in class org.concord.biologica.engine.AminoAcid
Glutamine
GLY - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Glycine
GLYCINE - Static variable in class org.concord.biologica.engine.AminoAcid
Glycine
GOTO - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
gotoAndPlay(int) - Method in class org.concord.flash.player.FMovieClip
Go to the specified frame and start playing
gotoAndPlay(String) - Method in class org.concord.flash.player.FMovieClip
Go to the specified frame and start playing
gotoAndStop(int) - Method in class org.concord.flash.player.FMovieClip
Go to the specified frame and stop playing
gotoAndStop(String) - Method in class org.concord.flash.player.FMovieClip
Go to the specified frame and stop playing
goToAnimationStep(int) - Method in class org.concord.biologica.ui.BigFertilizationView
Go to a particular step in the animation and stop there.
goToAnimationStep(int) - Method in class org.concord.biologica.ui.SmallMeiosisView
Go to a particular step in the animation and stop there.
goToAnimationStep(int) - Method in class org.concord.biologica.ui.SmallFertilizationView
Go to a particular step in the animation and stop there.
goToAnimationStep(int) - Method in class org.concord.biologica.ui.BigMeiosisView
Go to a particular step in the animation and stop there.
gravityX - Variable in class org.concord.collisions.engine.JPartWorld
 
gravityY - Variable in class org.concord.collisions.engine.JPartWorld
 
gridColor - Variable in class org.concord.util.LineGraph
 
gridSize - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
gridSizeMenu - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
group - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
GTExpression - class org.concord.util.script.GTExpression.
The GTExpression class implements the semantic node for "greater than".
GTExpression() - Constructor for class org.concord.util.script.GTExpression
 
GUANINE - Static variable in class org.concord.biologica.engine.Base
A pyrimidine which links with cytosine in DNA and RNA.
GUIElementsFrame - class org.concord.collisions.ui.GUIElementsFrame.
 
GUIElementsFrame() - Constructor for class org.concord.collisions.ui.GUIElementsFrame
 
GUIPanel - class org.concord.collisions.ui.GUIPanel.
GUI front end for JPartWorld
GUIPanel() - Constructor for class org.concord.collisions.ui.GUIPanel
GUIPanel constructor creates instance of GUIPanel
GUITestIngrid - class org.concord.collisions.ui.GUITestIngrid.
 
GUITestIngrid() - Constructor for class org.concord.collisions.ui.GUITestIngrid
 

H

halfThickness - Variable in class org.concord.collisions.engine.JRigidBox
wall's thickness/2 default value is 5
halfThickness - Variable in class org.concord.collisions.engine.JWall
wall's thickness/2 default value is 5
handleBreakpointHit(Context) - Method in class org.concord.util.script.Script
 
handleCompilationDone(Context, DebuggableScript, StringBuffer) - Method in class org.concord.util.script.Script
 
handleDocEvent(DocumentEvent) - Method in class org.concord.util.TextReader
 
handleEvent(String, EventObject) - Method in class org.concord.util.script.event.EventHandler
 
handleExceptionThrown(Context, Object) - Method in class org.concord.util.script.Script
 
handler - Variable in class org.concord.util.script.HandlerDeclaration
 
handler - Variable in class org.concord.pedagogica.engine.Activity
 
handler - Variable in class org.concord.pedagogica.ui.ActivityView
 
HANDLER_PACKAGE - Static variable in class org.concord.util.script.ScriptClassLoader
 
HANDLER_SUFFIX - Static variable in class org.concord.util.script.ScriptClassLoader
 
handlerClassTable - Static variable in class org.concord.util.script.ScriptClassLoader
 
handlerDeclaration - Variable in class org.concord.util.script.ListenStatement
 
HandlerDeclaration - class org.concord.util.script.HandlerDeclaration.
The HandlerDeclaration class holds the state asscociated with the definition of a script event handler.
HandlerDeclaration(Script) - Constructor for class org.concord.util.script.HandlerDeclaration
 
handlerName - Variable in class org.concord.util.script.ListenStatement
 
handlerName - Variable in class org.concord.util.script.HandlerDeclaration
 
handlerPrefix - Static variable in class org.concord.util.script.ScriptClassLoader
 
hasAlpha(ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
hasBeenHere - Variable in class org.concord.util.LogProcess
 
hasCharacteristics(String[], String[]) - Method in class org.concord.biologica.engine.Organism
 
hasCollided() - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon has collided with any element
hasCollidedWith(JWorldElement) - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon has collided with a given element
hasCollidedWithAt(JWorldElement, int) - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon has collided with a given element
hasIllegalStr(String) - Static method in class org.concord.pedagogica.ui.LoginPanel
 
hasMoreElements() - Method in class org.concord.util.Enumerator
 
hasX - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
hasY - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
hcells - Variable in class org.concord.biologica.datasupport.ShortImageDescription
 
header(int, long, int, int, float, int) - Method in class org.concord.flash.player.FMovieBuilder
SWFHeader interface.
height - Variable in class org.concord.util.LineGraph
 
height - Variable in class org.concord.biologica.ui.PedigreeObject
The height of the pedigree object as drawn
height - Variable in class org.concord.collisions.event.AreaEvent
 
height - Variable in class org.concord.flash.player.fill.FImage
 
HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
Height changed.
HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
helpHTML - Variable in class org.concord.pedagogica.ui.HelpView
 
helpScroll - Variable in class org.concord.pedagogica.ui.HelpView
 
HelpView - class org.concord.pedagogica.ui.HelpView.
 
HelpView.LocalHyperlinkAdapter - class org.concord.pedagogica.ui.HelpView.LocalHyperlinkAdapter.
 
HelpView.LocalHyperlinkAdapter(HelpView) - Constructor for class org.concord.pedagogica.ui.HelpView.LocalHyperlinkAdapter
 
HelpView() - Constructor for class org.concord.pedagogica.ui.HelpView
 
hexCharCode(char) - Method in class org.concord.util.Query
 
hideCM() - Method in class org.concord.collisions.ui.GUIPanel
hide Center of Mass point
hideMaxVelMenu() - Method in class org.concord.collisions.ui.DataCrossPanel
 
hideSwitchAlignmentButtons() - Method in class org.concord.biologica.ui.BigMeiosisView
Hide switch alignment buttons
highlightColor - Variable in class org.concord.biologica.ui.OrganismView
Highlight color for a particular view
HIS - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Histidine
HISTIDINE - Static variable in class org.concord.biologica.engine.AminoAcid
Histidine
HIT_AREA - Static variable in class org.concord.flash.player.FButton
 
HOLDER_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
HOLDER_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
HORIZONTAL_WALL - Static variable in class org.concord.collisions.engine.JRigidBox
 
HORIZONTAL_WALL - Static variable in class org.concord.collisions.engine.JWall
 
HOTSPOT_COLOR - Static variable in class org.concord.biologica.engine.EngineProp
Hotspot color changed.
HOTSPOT_COLOR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
HOTSPOT_COLOR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
HOTSPOT_IMAGE_TYPE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
HOTSPOT_RADIUS - Static variable in class org.concord.biologica.engine.EngineProp
Hotspot radius changed.
HOTSPOT_RADIUS_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
HOTSPOT_RADIUS_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
hotspotOrganism - Variable in class org.concord.biologica.ui.OrganismView
Transient hotspot organism.
hotspotOrganismImage - Variable in class org.concord.biologica.ui.OrganismView
Transient hotspot organism image.
howManyParticleInRect(int, float, float, float, float) - Method in class org.concord.collisions.engine.JPartWorld
retrieves amount of particles of given type existed inside of rectangle with given coordinates
HSBtoRGB(float, float, float) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
hsize - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
HSL2RGB(int, int, int, int[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
HSV2RGB(int, int, int, int[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
htmlText2 - Variable in class org.concord.pedagogica.ui.LoginPanel
 
htmlText3 - Variable in class org.concord.pedagogica.ui.LoginPanel
 
htmlView - Variable in class org.concord.pedagogica.ui.LoginPanel
 
HTMLView - class org.concord.pedagogica.ui.HTMLView.
 
HTMLView() - Constructor for class org.concord.pedagogica.ui.HTMLView
 
HTMLView(String) - Constructor for class org.concord.pedagogica.ui.HTMLView
 
HTMLView(String, String) - Constructor for class org.concord.pedagogica.ui.HTMLView
 
htmlView2 - Variable in class org.concord.pedagogica.ui.LoginPanel
 
HTMLViewBeanInfo - class org.concord.pedagogica.ui.HTMLViewBeanInfo.
 
HTMLViewBeanInfo() - Constructor for class org.concord.pedagogica.ui.HTMLViewBeanInfo
 
HTMLViewCustomizer - class org.concord.pedagogica.ui.HTMLViewCustomizer.
 
HTMLViewCustomizer() - Constructor for class org.concord.pedagogica.ui.HTMLViewCustomizer
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
hyperlinkUpdate(HyperlinkEvent) - Method in class org.concord.pedagogica.ui.HelpView.LocalHyperlinkAdapter
 

I

IChromosome - interface org.concord.biologica.engine.IChromosome.
This interface represents a chromosome which all chromosomes implement.
ICON_COLOR_16x16 - Static variable in interface org.concord.util.beans.BeanInfo
Constant to indicate a 16 x 16 color icon.
ICON_COLOR_32x32 - Static variable in interface org.concord.util.beans.BeanInfo
Constant to indicate a 32 x 32 color icon.
ICON_MONO_16x16 - Static variable in interface org.concord.util.beans.BeanInfo
Constant to indicate a 16 x 16 monochrome icon.
ICON_MONO_32x32 - Static variable in interface org.concord.util.beans.BeanInfo
Constant to indicate a 32 x 32 monochrome icon.
id - Variable in class org.concord.biologica.engine.EngineObject
Identifier for engine object, used when saving and restoring the object to and from a file.
id - Variable in class org.concord.collisions.event.StepEvent
 
id - Variable in class org.concord.collisions.event.DaemonEvent
 
id - Variable in class org.concord.collisions.event.CollisionsEvent
 
id - Variable in class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
id - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
id - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
ID - Static variable in class org.concord.biologica.engine.EngineProp
ID simple property name.
ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IDLE - Static variable in class org.concord.flash.player.FButton
 
IF_SPECIES_ALLELE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
An "if species allele" was added to a genotype to phenotype rule.
IF_SPECIES_ALLELE_IDS_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IF_SPECIES_ALLELE_IDS_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IF_SPECIES_ALLELE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
An "if species allele" was removed from a genotype to phenotype rule.
ifExpression - Variable in class org.concord.util.script.IfThenElseStatement
 
ifStatement - Variable in class org.concord.util.script.IfThenElseStatement
 
IfThenElseStatement - class org.concord.util.script.IfThenElseStatement.
The IfThenElseStatement implements conventional if-then-else semantics.
IfThenElseStatement() - Constructor for class org.concord.util.script.IfThenElseStatement
 
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.World
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.OrganismAllele
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Environment
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImage
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Species
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesAllele
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Organism
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Family
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.OrganismImage
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Characteristic
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.OrganismChromosome
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Gene
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.ElementContext
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Trait
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.OrganismAllelePair
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.SpeciesImageRow
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.Terrain
Receive notification of ignorable white space character data.
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
ignorableWhitespace(char[], int, int) - Method in class org.concord.biologica.engine.RawNucleicAcid
Receive notification of ignorable white space character data.
IGNORE_ALL_BEANINFO - Static variable in class org.concord.util.beans.Introspector
 
IGNORE_IMMEDIATE_BEANINFO - Static variable in class org.concord.util.beans.Introspector
 
ILE - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Isoleucine
IMAGE_DATA_SOURCE_SUPPORT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_DATA_SOURCE_SUPPORT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_ID - Static variable in class org.concord.biologica.engine.EngineProp
Phenotype image ID changed.
IMAGE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_NUMBER - Static variable in class org.concord.biologica.engine.EngineProp
Image number of a chromosome, used in chromosome view.
IMAGE_NUMBER_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_NUMBER_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_TYPE - Static variable in class org.concord.biologica.engine.EngineProp
Image type property changed.
IMAGE_TYPE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IMAGE_TYPE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
imageData - Variable in class org.concord.flash.player.fill.FImage
 
imageDescriptions - Static variable in class org.concord.biologica.datasupport.ImageReader
 
ImageReader - class org.concord.biologica.datasupport.ImageReader.
 
ImageReader() - Constructor for class org.concord.biologica.datasupport.ImageReader
 
images - Variable in class org.concord.biologica.datasupport.ShortImageDescription
 
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.ChromosomeView
ImageObserver method
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.OrganismView
ImageObserver method
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.StaticOrganismView
ImageObserver method
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.DNAView
ImageObserver method
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.ObjectPropertiesView
ImageObserver method
imageUpdate(Image, int, int, int, int, int) - Method in class org.concord.biologica.ui.SexOrganismView
ImageObserver method
ImportContext - class org.concord.biologica.engine.ImportContext.
This class represents a context for a set of objects being imported into an active BioLogica process.
ImportContext() - Constructor for class org.concord.biologica.engine.ImportContext
Creates a new ImportContext.
ImportDeclaration - class org.concord.util.script.ImportDeclaration.
 
ImportDeclaration(Script) - Constructor for class org.concord.util.script.ImportDeclaration
 
importFileChooser - Variable in class org.concord.pedagogica.ui.ActivityView
 
importFilter - Variable in class org.concord.pedagogica.ui.ActivityView
 
importItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
imports - Variable in class org.concord.util.script.NameStack
 
imports - Variable in class org.concord.util.script.Script
 
IN_DNA - Static variable in class org.concord.biologica.engine.Base
Used in various methods to indicate a base or some nucleic acid is in DNA.
IN_DNA_OR_RNA - Static variable in class org.concord.biologica.engine.Base
Used in various methods to indicate a base or some nucleic acid is in DNA or RNA.
IN_DNA_OR_RNA - Static variable in class org.concord.biologica.engine.EngineProp
In DNA or RNA simple property name.
IN_DNA_OR_RNA_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
IN_DNA_OR_RNA_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
IN_DNA_STRING - Static variable in class org.concord.biologica.engine.Base
 
IN_RNA - Static variable in class org.concord.biologica.engine.Base
Used in various methods to indicate a base or some nucleic acid is in RNA.
IN_RNA_STRING - Static variable in class org.concord.biologica.engine.Base
 
inArcs - Variable in class org.concord.pedagogica.engine.ActivityNode
 
INCLUDE - Static variable in class org.concord.util.Query
 
include(String) - Method in class org.concord.util.Query
 
incrementStep() - Method in class org.concord.biologica.ui.FertilizationModel
Increment the current step of the fertilization
incrementStep() - Method in class org.concord.biologica.ui.MeiosisModel
Increment the current step of the meiosis
indent - Static variable in class org.concord.util.script.NameStack
 
index - Variable in class org.concord.collisions.engine.JWorldElement
 
index - Variable in class org.concord.flash.player.FMovieBuilder.GlyphBuilder
 
IndexedPropertyDescriptor - class org.concord.util.beans.IndexedPropertyDescriptor.
An IndexedPropertyDescriptor describes a property that acts like an array and has an indexed read and/or indexed write method to access specific elements of the array.
IndexedPropertyDescriptor(String, Class) - Constructor for class org.concord.util.beans.IndexedPropertyDescriptor
This constructor constructs an IndexedPropertyDescriptor for a property that follows the standard Java conventions by having getFoo and setFoo accessor methods, for both indexed access and array access.
IndexedPropertyDescriptor(String, Class, String, String, String, String) - Constructor for class org.concord.util.beans.IndexedPropertyDescriptor
This constructor takes the name of a simple property, and method names for reading and writing the property, both indexed and non-indexed.
IndexedPropertyDescriptor(String, Method, Method, Method, Method) - Constructor for class org.concord.util.beans.IndexedPropertyDescriptor
This constructor takes the name of a simple property, and Method objects for reading and writing the property.
IndexExpression - class org.concord.util.script.IndexExpression.
 
IndexExpression(Script) - Constructor for class org.concord.util.script.IndexExpression
 
indexInteraction - Variable in class org.concord.util.LogProcess
 
IndexList - class org.concord.molecular.engine.IndexList.
 
IndexList() - Constructor for class org.concord.molecular.engine.IndexList
 
indexMap - Variable in class org.concord.util.BarGraph
 
indices - Variable in class org.concord.molecular.engine.ConditionValue
 
INFO - Static variable in class org.concord.util.Debug
 
INFO - Static variable in class org.concord.biologica.engine.Debug
 
INFO - Static variable in class org.concord.biologica.engine.EngineStrings
 
IngridProblem - class org.concord.collisions.ui.IngridProblem.
 
IngridProblem() - Constructor for class org.concord.collisions.ui.IngridProblem
 
init() - Method in class org.concord.pedagogica.ui.LoginPanel
 
init(NameStack, boolean) - Method in class org.concord.util.script.NameStack
 
init(ViewerAppletEvent) - Method in interface org.concord.pedagogica.ui.event.ViewerAppletListener
 
initElement() - Method in class org.concord.collisions.engine.JWorldElement
 
initElement() - Method in class org.concord.collisions.engine.JRigidBox
 
initElement() - Method in class org.concord.collisions.engine.JWall
 
initElement() - Method in class org.concord.collisions.engine.JDaemon
 
initElement() - Method in class org.concord.collisions.engine.JAtom
 
initElements() - Method in class org.concord.collisions.engine.JPartWorld
 
initFilters() - Static method in class org.concord.biologica.datasupport.ImageReader
 
initialize() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
initialize() - Method in class org.concord.pedagogica.engine.ActivityScript
 
initialize() - Method in class org.concord.pedagogica.engine.Activity
 
initialize() - Method in class org.concord.pedagogica.engine.LogModel
 
initialize() - Method in class org.concord.pedagogica.ui.TableInputView
Method that: provides the table with resizing capability and listens for a mouse press for table cell selection.
initialize() - Method in class org.concord.pedagogica.ui.VariableDialog
 
initialize(Class, Object, Object, Encoder) - Method in class org.concord.util.beans.PersistenceDelegate
Produce a series of statements with side effects on newInstance so that the new instance becomes equivalent to oldInstance.
initialize(Class, Object, Object, Encoder) - Method in class org.concord.util.beans.DefaultPersistenceDelegate
This default implementation of the initialize method assumes all state held in objects of this type is exposed via the matching pairs of "setter" and "getter" methods in the order they are returned by the Introspector.
initialize(File) - Method in class org.concord.biologica.ui.PracticeView
 
initialize(File) - Method in class org.concord.biologica.ui.ChromosomePracticeView
 
initialize(File) - Method in class org.concord.biologica.ui.PedigreePracticeView
 
initialize(File) - Method in class org.concord.biologica.ui.MutationsPracticeView
 
initialize(File) - Method in class org.concord.biologica.ui.MeiosisPracticeView
 
initialize(String) - Method in class org.concord.pedagogica.ui.ClassTree
 
initialize(String, String[], boolean) - Method in class org.concord.pedagogica.ui.Question
 
initializeFrames(TimeLine) - Method in class org.concord.flash.player.FMovieClip
Initializes the frames in the movie clip with the data from clip
initializeFromProperties(AtomPropertiesEditor) - Method in class org.concord.molecular.ui.MolecularView
 
initializeImageSource(String) - Method in class org.concord.biologica.engine.SpeciesImage
 
initializeLevel(int) - Method in class org.concord.pedagogica.ui.LogView
 
initializeLogWriters() - Method in class org.concord.pedagogica.engine.Logging
 
initializer - Variable in class org.concord.pedagogica.engine.ActivityNode
 
initializer - Variable in class org.concord.pedagogica.engine.Activity
 
initializer - Variable in class org.concord.pedagogica.engine.ActivityArc
 
initImageDownloading(int, Component) - Method in class org.concord.biologica.engine.SpeciesImage
 
initLoadImages() - Method in class org.concord.biologica.engine.World
 
initLoadImages(String) - Method in class org.concord.biologica.engine.World
 
initQuiz() - Method in class org.concord.pedagogica.ui.Quiz
 
initWabaSystem(int, int) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
INPUT_ARGUMENT_ILLEGAL - Static variable in class org.concord.biologica.engine.EngineStrings
 
INPUT_DEBUG_LOG_LEVEL_ILLEGAL - Static variable in class org.concord.biologica.engine.EngineStrings
 
inputWaitThread - Variable in class org.concord.util.TextReader
 
insert(int, int) - Method in class org.concord.molecular.engine.IndexList
 
insertUpdate(DocumentEvent) - Method in class org.concord.util.TextReader
 
insertUpdate(DocumentEvent) - Method in class org.concord.util.EditorInternalFrame
 
instanceOf(Class, Object) - Method in interface org.concord.util.script.ScriptRuntime
 
instanceOf(Class, Object) - Method in class org.concord.util.script.ECMA
 
instances - Variable in class org.concord.flash.player.FMovieBuilder
 
instantiate(Object, Encoder) - Method in class org.concord.util.beans.PersistenceDelegate
Returns an expression whose value is oldInstance.
instantiate(Object, Encoder) - Method in class org.concord.util.beans.DefaultPersistenceDelegate
This default implementation of the instantiate method returns an expression containing the predefined method name "new" which denotes a call to a constructor with the arguments as specified in the DefaultPersistenceDelegate's constructor.
instructorName - Variable in class org.concord.pedagogica.engine.Logging
 
IntegerLiteral - class org.concord.util.script.IntegerLiteral.
This node represents an integer value in the semantic tree.
IntegerLiteral(String) - Constructor for class org.concord.util.script.IntegerLiteral
 
INTENTIONALLY_THROWING_EXCEPTION - Static variable in class org.concord.biologica.engine.EngineStrings
 
InternalEngineException - exception org.concord.biologica.engine.InternalEngineException.
Exception indicating that an internal exception occurred within BioLogica's engine.
InternalEngineException(String) - Constructor for class org.concord.biologica.engine.InternalEngineException
Creates a new exception.
InternalException - exception org.concord.util.InternalException.
Exception indicating that an internal exception occurred within BioScope.
InternalException(String) - Constructor for class org.concord.util.InternalException
Creates a new exception.
interpret() - Method in class org.concord.util.script.ScriptObject
This does nothing.
interpret() - Method in class org.concord.util.script.Expression
 
interpret() - Method in class org.concord.util.script.BinaryExpression
The binary expression interpret checks if both operands are expressions, and then applies the more derived binOp method.
interpret() - Method in class org.concord.util.script.BooleanLiteral
 
interpret() - Method in class org.concord.util.script.FloatLiteral
 
interpret() - Method in class org.concord.util.script.Statement
 
interpret() - Method in class org.concord.util.script.UnaryExpression
 
interpret() - Method in class org.concord.util.script.InvocationExpression
 
interpret() - Method in class org.concord.util.script.ExpressionStatement
 
interpret() - Method in class org.concord.util.script.ListenStatement
 
interpret() - Method in class org.concord.util.script.SequenceLiteral
 
interpret() - Method in class org.concord.util.script.ArrayLiteral
 
interpret() - Method in class org.concord.util.script.LoopStatement
 
interpret() - Method in class org.concord.util.script.BlockStatement
 
interpret() - Method in class org.concord.util.script.SkipStatement
 
interpret() - Method in class org.concord.util.script.NullLiteral
 
interpret() - Method in class org.concord.util.script.ImportDeclaration
 
interpret() - Method in class org.concord.util.script.AssignmentStatement
 
interpret() - Method in class org.concord.util.script.CharacterLiteral
 
interpret() - Method in class org.concord.util.script.IndexExpression
 
interpret() - Method in class org.concord.util.script.Script
 
interpret() - Method in class org.concord.util.script.IfThenElseStatement
The interpret method implements conventional if-then-else-semantics.
interpret() - Method in class org.concord.util.script.VariableDeclaration
 
interpret() - Method in class org.concord.util.script.FinishStatement
 
interpret() - Method in class org.concord.util.script.ObjectExpression
 
interpret() - Method in class org.concord.util.script.IntegerLiteral
 
interpret() - Method in class org.concord.util.script.ReturnStatement
 
interpret() - Method in class org.concord.util.script.StringLiteral
 
interpret() - Method in class org.concord.util.script.ExtendsDeclaration
 
interpret() - Method in class org.concord.util.script.ReferenceExpression
 
interpret() - Method in class org.concord.util.script.NameExpression
 
interpret(Object) - Method in class org.concord.util.script.Expression
 
interpret(Object) - Method in class org.concord.util.script.InvocationExpression
 
interpret(Object) - Method in class org.concord.util.script.IndexExpression
 
interpret(Object) - Method in class org.concord.util.script.ReferenceExpression
 
interval - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
interval - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
IntrospectionException - exception org.concord.util.beans.IntrospectionException.
Thrown when an exception happens during Introspection.
IntrospectionException(String) - Constructor for class org.concord.util.beans.IntrospectionException
Constructs an IntrospectionException with a detailed message.
Introspector - class org.concord.util.beans.Introspector.
The Introspector class provides a standard way for tools to learn about the properties, events, and methods supported by a target Java Bean.
introTest() - Static method in class org.concord.collisions.ui.GUIElementsFrame
 
introTest() - Static method in class org.concord.collisions.ui.GUITestIngrid
 
INucleicAcid - interface org.concord.biologica.engine.INucleicAcid.
This interface presents the API for a nucleic acid, either a full strand of DNA or RNA or just a segment of one.
INucleicAcidHolder - interface org.concord.biologica.engine.INucleicAcidHolder.
This interface presents the API for a holder of nucleic acid.
INVISIBLE_IMAGE_TYPE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
InvocationExpression - class org.concord.util.script.InvocationExpression.
 
InvocationExpression(Script) - Constructor for class org.concord.util.script.InvocationExpression
 
invoke(Object, Method, Object[]) - Method in class org.concord.util.beans.EventHandler
Extract the appropriate property value from the event and pass it to the action associated with this EventHandler.
invokeCachedConstructor(String, Object[]) - Method in class org.concord.util.script.InvocationExpression
 
invokeCachedMethod(Object, String, Object[]) - Method in class org.concord.util.script.InvocationExpression
 
io - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
IOEXCEPTION_WHILE_READING_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
isActive() - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon is active
isActive() - Method in class org.concord.collisions.engine.CCConstantForce
 
isActive() - Method in class org.concord.collisions.engine.CCImpulseForce
 
isActive() - Method in class org.concord.pedagogica.ui.ViewerStub
 
isActiveCollision(JWorldElement) - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon has collided with a given element and the collision is still active
isActivity() - Method in class org.concord.pedagogica.engine.ActivityNode
 
isActivity() - Method in class org.concord.pedagogica.engine.Activity
 
isActivity() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
isAlignmentControlsVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Get alignment controls visibility
isAlignmentControlsVisible() - Method in class org.concord.biologica.ui.SexView
Get alignment controls visibility in big meiosis view
isAlive() - Method in class org.concord.collisions.engine.JDaemon
Determine if the daemon is alive
isAllelesAlterable() - Method in class org.concord.biologica.engine.Organism
Get whether this organism's alleles are visible.
isAllelesVisible() - Method in class org.concord.biologica.engine.Organism
Get whether this organism's alleles are visible.
isAnimationSliderVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check animation slider visibility.
isAnimationSliderVisible() - Method in class org.concord.biologica.ui.SmallMeiosisView
Check animation slider visibility.
isAnimationSliderVisible() - Method in class org.concord.biologica.ui.SmallFertilizationView
Check animation slider visibility.
isAnimationSliderVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check animation slider visibility.
isAnswerTextVisible() - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
isAnswerTextVisible() - Method in class org.concord.pedagogica.ui.EssayFill
 
isArrayMember(Object[], Object) - Method in class org.concord.pedagogica.ui.LogView
 
isAutomaticLocked() - Method in class org.concord.biologica.engine.EngineObject
Is the object automatic locked? Ignores other components of the locked state.
isAutomaticStart() - Method in class org.concord.collisions.engine.JDaemon
Determine if it is an automatic daemon
isBedSpringMode() - Method in class org.concord.collisions.engine.JPartWorld
 
isBound() - Method in class org.concord.util.beans.PropertyDescriptor
Updates to "bound" properties will cause a "PropertyChange" event to get fired when the property is changed.
isCellChanged(int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
isCellEditable(int, int) - Method in class org.concord.pedagogica.ui.TableInputView
 
isCellSelectable(int, int) - Method in class org.concord.pedagogica.ui.TableInputView
 
isCellSelectable(int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
isCellSelected(int, int) - Method in class org.concord.pedagogica.ui.TableInputView
 
isCellSelected(int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
isCharacteristicsTextVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the characteristics text visible?
isCharacteristicsTextVisible() - Method in class org.concord.biologica.ui.OrganismView
Is the characteristics text visible?
isChild(Organism) - Method in class org.concord.biologica.engine.Family
 
isChromosomesSelectable(boolean) - Method in class org.concord.biologica.ui.ChromosomeView
 
isChromosomeToolEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is the chromosome tool enabled?
isChromosomeToolVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the chromosome tool visible?
isCollisionSensitive() - Method in class org.concord.collisions.engine.JWorldElement
 
isCollisionSensitive() - Method in class org.concord.collisions.engine.JBooster
 
isConstrained() - Method in class org.concord.util.beans.PropertyDescriptor
Attempted updates to "Constrained" properties will cause a "VetoableChange" event to get fired when the property is changed.
isConstraintsWasSet() - Method in class org.concord.collisions.engine.JWorldElement
 
isConstructor - Variable in class org.concord.util.script.InvocationExpression
 
isControllable() - Method in class org.concord.collisions.engine.JWorldElement
 
isCrossoverControlsVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Get crossover controls visibility
isCrossoverControlsVisible() - Method in class org.concord.biologica.ui.SexView
Get crossover controls visibility in big meiosis view
isCrossOverEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is cross over enabled?
isCrossOverHappened() - Method in class org.concord.biologica.ui.MeiosisModel
 
isCrossOverTurnOn() - Method in class org.concord.biologica.ui.PedigreeView
Is the Cross over turn on?
isCrossOverVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the cross over check box visibled?
isCrossToolEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is the cross tool enabled?
isCrossToolVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the cross tool visible?
isDataSourceExist(int) - Method in class org.concord.biologica.engine.SpeciesImage
 
isDebugging(Object, String) - Static method in class org.concord.util.Debug
 
isDebugging(String) - Static method in class org.concord.util.Debug
 
isDeleted() - Method in class org.concord.biologica.engine.EngineObject
Get whether or not this object is deleted.
isDirty() - Method in class org.concord.biologica.engine.World
Return the dirty state of this engine.
isDisconnected() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
isDNAAlterable() - Method in class org.concord.biologica.engine.Organism
Get whether this organism's DNA is alterable.
isDNAVisible() - Method in class org.concord.biologica.engine.Organism
Get whether this organism's DNA is visible.
isDoAACollisions() - Method in class org.concord.collisions.engine.JPartWorld
 
isDoAACollisions() - Method in class org.concord.collisions.ui.GUIPanel
 
isDoAWCollisions() - Method in class org.concord.collisions.engine.JPartWorld
 
isDoAWCollisions() - Method in class org.concord.collisions.ui.GUIPanel
 
isDoCollisions() - Method in class org.concord.collisions.engine.JPartWorld
 
isDoTrace() - Method in class org.concord.collisions.engine.JAtom
 
isDraggable() - Method in class org.concord.collisions.engine.JWorldElement
 
isDraggable() - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
isDraggable() - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
isDraggable() - Method in class org.concord.collisions.ui.PassiveElement
 
isDraggable() - Method in interface org.concord.collisions.ui.CCDraggable
 
isDrawForce() - Method in class org.concord.collisions.engine.CCBedSpringForce
 
isEditable() - Method in class org.concord.util.BarGraph
Returns editable state.
isEditable() - Method in class org.concord.collisions.ui.DataCrossPanel
 
isElementInside(JWorldElement) - Method in class org.concord.collisions.ui.GUIPanel
 
isEmpty() - Method in class org.concord.biologica.ui.PedigreeLevel
Is this level empty? True of there are no PedigreeObjects
isEmpty() - Method in class org.concord.biologica.ui.PedigreeFamily
Is this family empty? True if there are no children.
isEnabled() - Method in class org.concord.collisions.engine.JWorldElement
Determine if the JWorldElement is enabled.
isExpert() - Method in class org.concord.util.beans.FeatureDescriptor
The "expert" flag is used to distinguish between those features that are intended for expert users from those that are intended for normal users.
isFatal() - Method in class org.concord.biologica.engine.Characteristic
Return the fatality of this characteristic.
isFertilizationManuallyDisabled() - Method in class org.concord.biologica.ui.BigFertilizationView
Get whether or not fertilization is manually disabled.
isFertilizationManuallyDisabled() - Method in class org.concord.biologica.ui.SmallFertilizationView
Get whether or not fertilization is manually disabled.
isFertilizationManuallyDisabled() - Method in class org.concord.biologica.ui.SexView
Get whether or not fertilization is manually disabled.
isFlashing() - Method in class org.concord.collisions.engine.JWorldElement
 
isFocusTraversable() - Method in class org.concord.collisions.ui.DataCrossPanel
 
isFocusTraversable() - Method in class org.concord.collisions.ui.GUIPanel
Returns the value of a flag that indicates whether this component can be traversed using Tab or Shift-Tab keyboard focus traversal.
isFrameRateDrawn() - Method in class org.concord.flash.player.FFlash
 
isGameteMoveButtonEnabled() - Method in class org.concord.biologica.ui.SexView
Get whether or not the replay button is enabled.
isGlobal() - Method in class org.concord.util.script.VariableDeclaration
 
isGoToEndButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check go to end button visibility.
isGoToEndButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check go to end button visibility.
isGoToStartButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check go to start button visibility.
isGoToStartButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check go to start button visibility.
isHidden() - Method in class org.concord.util.beans.FeatureDescriptor
The "hidden" flag is used to identify features that are intended only for tool use, and which should not be exposed to humans.
isIdentity(ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
isImageVisible() - Static method in class org.concord.biologica.engine.SpeciesImage
 
isInDefaultEventSet() - Method in class org.concord.util.beans.EventSetDescriptor
Reports if an event set is in the "default" set.
isLeaf() - Method in class org.concord.biologica.ui.TreeViewNode
Returns if this node is a leaf node (has no children) or not.
isLocked() - Method in class org.concord.biologica.engine.EngineObject
Get locked state as a boolean.
isLocked() - Method in class org.concord.biologica.ui.TreeViewNode
Return the locked state of this node.
isLockSymbolVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the lock symbol visible?
isLockSymbolVisible() - Method in class org.concord.biologica.ui.OrganismView
Is the lock symbol visible?
isLooping() - Method in class org.concord.collisions.engine.JDaemon
Determine if it is a looping daemon
isMagnifyButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check magnify button visibility.
isMagnifyButtonVisible() - Method in class org.concord.biologica.ui.SmallMeiosisView
Check magnify button visibility.
isMagnifyButtonVisible() - Method in class org.concord.biologica.ui.SmallFertilizationView
Check magnify button visibility.
isMagnifyButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check magnify button visibility.
isManualLocked() - Method in class org.concord.biologica.engine.EngineObject
Is the object manual locked? Ignores other components of the locked state.
isModified() - Method in class org.concord.util.Editor
 
isModified() - Method in class org.concord.util.EditorInternalFrame
 
isModified() - Method in class org.concord.flash.player.FComponent
 
isModified() - Method in interface org.concord.pedagogica.engine.QuestionForm
 
isModified() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
isModified() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
isModified() - Method in class org.concord.pedagogica.ui.BlankFill
 
isModified() - Method in class org.concord.pedagogica.ui.EssayFill
 
isMove - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
isMoveable() - Method in class org.concord.collisions.engine.JWorldElement
 
isMoveable() - Method in class org.concord.collisions.engine.JWall
 
isMoveable() - Method in class org.concord.collisions.ui.PassiveElement
 
isMutationAllele() - Method in class org.concord.biologica.engine.OrganismAllele
Is this allele an instance of the mutation allele for its gene?
isMutationAllele() - Method in class org.concord.biologica.engine.SpeciesAllele
Is this allele the mutation allele for its gene?
isNameSuperVisible() - Method in class org.concord.biologica.engine.Organism
Get whether this organism's name is super visible, meaning that the name should be shown even when a view isn't showing names in general.
isNameTextVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the name text visible?
isNameTextVisible() - Method in class org.concord.biologica.ui.OrganismView
Is the name text visible?
isNear(int, int, Point, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
isNearSinkLocation(int, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
isNearSourceLocation(int, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
isNumberArray - Variable in class org.concord.util.script.ArrayLiteral
 
isOffspringModePulldownEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is the offspring mode pulldown enabled?
isOffspringModePulldownVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the offspring mode pulldown visible?
ISOLEUCINE - Static variable in class org.concord.biologica.engine.AminoAcid
Isoleucine
isOnHotspot(int, int, int) - Method in class org.concord.biologica.engine.SpeciesImageRow
Return whether the given coordinates are on the hotspot for this image row
isOnlyLiveChildren() - Method in class org.concord.biologica.ui.PedigreeView
Is the Only Live Children flag true?
isOnlyLiveChildren() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Is the Only Live Children flag true?
isOrganismImagesVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the organism images visible?
isOrganismImagesVisible() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Is the organism images visible?
isParentCrossOver() - Method in class org.concord.biologica.engine.Organism
 
isPartialMatch() - Static method in class org.concord.util.Debug
 
isPlayBackwardFastToggleButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check play backward fast toggle button visibility.
isPlayBackwardFastToggleButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check play backward fast toggle button visibility.
isPlayBackwardToggleButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check play backward toggle button visibility.
isPlayBackwardToggleButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check play backward toggle button visibility.
isplayForwardFastToggleButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check play forward fast toggle button visibility.
isplayForwardFastToggleButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check play forward fast toggle button visibility.
isPlayForwardToggleButtonVisible() - Method in class org.concord.biologica.ui.SmallMeiosisView
Check play forward toggle button visibility.
isPlayForwardToggleButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check play forward toggle button visibility.
isPlaying() - Method in class org.concord.flash.player.FMovieClip
 
isPointInside(float, float) - Method in class org.concord.collisions.ui.PassiveElement
 
isPointInside(Point) - Method in class org.concord.collisions.ui.PassiveElement
 
isPointInside(Point) - Method in class org.concord.collisions.ui.PassiveOval
 
isPointInside(Point) - Method in class org.concord.collisions.ui.PassiveLine
 
isPointOnTheBoxesWalls(float, float) - Method in class org.concord.collisions.engine.JRigidBox
 
isPointOnTheWall(float, float) - Method in class org.concord.collisions.engine.JWall
check whether or not point with coordinates x,y belong to wall
isPreferred() - Method in class org.concord.util.beans.FeatureDescriptor
The "preferred" flag is used to identify features that are particularly important for presenting to humans.
isPressedState() - Method in class org.concord.collisions.engine.JWorldElement
 
isQuestionTextVisible() - Method in class org.concord.pedagogica.ui.CustomQuestion
 
isQuestionTextVisible() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
isQuestionTextVisible() - Method in class org.concord.pedagogica.ui.BlankFill
 
isQuestionTextVisible() - Method in class org.concord.pedagogica.ui.EssayFill
 
isReplayButtonEnabled() - Method in class org.concord.biologica.ui.SexView
Get whether or not the replay button is enabled.
isReplayButtonVisible() - Method in class org.concord.biologica.ui.SexView
Get whether or not the replay button is visible.
isReplicated() - Method in class org.concord.biologica.ui.MeiosisModel
Returns whether the current step of meiosis represents a step in which chromosome are replicated.
isResetAutomatic() - Method in class org.concord.biologica.ui.SexView
Get whether or not reset is automatic when an offspring is created.
isResetButtonEnabled() - Method in class org.concord.biologica.ui.SexView
Get whether or not the reset button is enabled.
isResetButtonVisible() - Method in class org.concord.biologica.ui.SexView
Get whether or not the reset button is visible.
isResetDeleteOffspringOrganism() - Method in class org.concord.biologica.ui.SexView
Get whether or not reset should automatically delete an offspring organism.
isRigidBoxOK() - Method in class org.concord.collisions.engine.JRigidBox
 
isRunning() - Method in class org.concord.collisions.engine.JPartWorld
isRunning
isRunning() - Method in class org.concord.collisions.ui.GUIPanel
isRunning
isSelectable() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
isSelected() - Method in class org.concord.biologica.ui.TreeViewNode
Return the selected state of this node
isSelected() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
isSelectionToolEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is the selection tool enabled?
isSelectionToolVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the selection tool visible?
isSexChromosome() - Method in class org.concord.biologica.engine.SpeciesChromosome
Returns whether the chromosome is a sex chromosome.
isSexChromosome() - Method in interface org.concord.biologica.engine.IChromosome
Returns whether the chromosome is a sex chromosome.
isSexChromosome() - Method in class org.concord.biologica.engine.OrganismChromosome
Returns whether the chromosome is a sex chromosome.
isSexSpecies(Species) - Method in class org.concord.biologica.ui.MutationsPracticeView
 
isSexTextVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the sex text visible?
isSexTextVisible() - Method in class org.concord.biologica.ui.OrganismView
Is the sex text visible?
isShortImageDescriptionInCache(int, int) - Static method in class org.concord.biologica.datasupport.ImageReader
 
isShowAsTextInOrganismView() - Method in class org.concord.biologica.engine.Trait
Get whether this trait should be shown as text in the organism view.
isShowingNegative() - Method in class org.concord.util.LineGraph
 
isSingleSelect(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
isSkippingFrames() - Method in class org.concord.flash.player.FFlash
If SkippingFrames is true then the movie skips frames when the actual frame rate drops below the specified frame rate.
isSkippingFrames() - Method in class org.concord.flash.player.FMovie
If SkippingFrames is true then the movie skips frames when the actual frame rate drops below the specified frame rate.
isSnipToolEnabled() - Method in class org.concord.biologica.ui.PedigreeView
Is the snip tool enabled?
isSnipToolVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the snip tool visible?
isSpeciesTextVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the species text visible?
isSpeciesTextVisible() - Method in class org.concord.biologica.ui.OrganismView
Is the species text visible?
isStepBackwardButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check step backward button visibility.
isStepBackwardButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check step backward button visibility.
isStepForwardButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check step forward button visibility.
isStepForwardButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check step forward button visibility.
isStopToggleButtonVisible() - Method in class org.concord.biologica.ui.BigFertilizationView
Check stop toggle visibility.
isStopToggleButtonVisible() - Method in class org.concord.biologica.ui.SmallMeiosisView
Check stop toggle visibility.
isStopToggleButtonVisible() - Method in class org.concord.biologica.ui.SmallFertilizationView
Check stop toggle visibility.
isStopToggleButtonVisible() - Method in class org.concord.biologica.ui.BigMeiosisView
Check stop toggle visibility.
isStopWhenFertilizationStarts() - Method in class org.concord.biologica.ui.SexView
Get whether or not fertilization should stop immediately when it starts.
isStopWhenMeiosisStarts() - Method in class org.concord.biologica.ui.SexView
Get whether or not meiosiis should stop immediately when it starts.
isSuspendingCallers() - Static method in class org.concord.util.script.Script
 
isTimed() - Method in class org.concord.collisions.engine.JDaemon
 
isTimedAverage() - Method in class org.concord.molecular.engine.ConditionValue
 
isToolEnabled(int) - Method in class org.concord.biologica.ui.ToolView
Is the tool enabled?
isToolVisible(int) - Method in class org.concord.biologica.ui.ToolView
Is the tool visible?
isTracePossible() - Method in class org.concord.collisions.ui.GUIPanel
 
isTraitPulldownVisible() - Method in class org.concord.biologica.ui.PedigreeView
Is the trait pulldown visible?
isTransformed() - Method in class org.concord.flash.player.FComponent
Detects whether this component has been transformed, that is one of set_x, set_y, set_xscale, set_yscale, set_rotate, has been called which changes the original placement.
isTranslatedTransforms(AffineTransform, AffineTransform) - Static method in class org.concord.flash.player.FUtil
 
isUnicast() - Method in class org.concord.util.beans.EventSetDescriptor
Normally event sources are multicast.
isUnitCompatible(CCUnit, CCUnit) - Static method in class org.concord.util.CCUnit
 
isUnitCompatible(int, int) - Static method in class org.concord.util.CCUnit
 
isValidAminoAcid(byte) - Static method in class org.concord.biologica.engine.AminoAcid
Determines if an amino acid value is valid.
isValidBase(byte, int) - Static method in class org.concord.biologica.engine.Base
Determines if a base value is valid.
isValidToDoFertilization() - Method in class org.concord.biologica.ui.FertilizationModel
 
isValueChanged() - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
isViewBefore() - Method in interface org.concord.util.script.ScriptRuntime
 
isViewBefore() - Method in class org.concord.util.script.ECMA
 
isVisible() - Method in class org.concord.biologica.engine.SpeciesChromosome
Get whether this chromosome is visible.
isVisible() - Method in class org.concord.biologica.engine.SpeciesAllele
Is this allele visible?
isVisible() - Method in class org.concord.biologica.engine.Organism
Get whether this organism is visible.
isVisible() - Method in class org.concord.biologica.engine.OrganismChromosome
Get the visibility of this chromosome.
isVisible() - Method in class org.concord.biologica.engine.Gene
Get whether this gene is visible.
isVisible() - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Get whether this model is visible (true) or not visible (false).
isVisible() - Method in class org.concord.collisions.engine.JWorldElement
Determine if the JWorldElement is visible.
isWabaSystemReady() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
isWhen - Variable in class org.concord.util.script.NameStack
 
isZipFile() - Method in class org.concord.util.script.ScriptFile
 
itemChanged(ActivityItemEvent) - Method in class org.concord.pedagogica.PedAgogica
 
itemChanged(ActivityItemEvent) - Method in interface org.concord.pedagogica.ui.event.ActivityItemListener
 
itemError(ActivityItem) - Method in interface org.concord.pedagogica.ui.ActivityItemErrorHandler
 
itemError(ActivityItem) - Method in class org.concord.pedagogica.ui.ActivityView
 
itemNameField - Variable in class org.concord.pedagogica.ui.ActivityView
 
itemNameLabel - Variable in class org.concord.pedagogica.ui.ActivityView
 
itemNumber - Static variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
itemPlacement - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
itemStateChanged(ItemEvent) - Method in class org.concord.biologica.ui.PedigreeView
Handle combo box item changed events.
itemStateChanged(ItemEvent) - Method in class org.concord.biologica.ui.OrganismAlleleControl
Handle combo box item changed events.
itemStateChanged(ItemEvent) - Method in class org.concord.biologica.ui.AllInOneView
Handle combo box item changed events.
itemStateChanged(ItemEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle combo box item changed events.
itemTable - Variable in class org.concord.pedagogica.ui.ActivityView
 
iteratorList - Variable in class org.concord.pedagogica.ui.LogView
 

J

JAtom - class org.concord.collisions.engine.JAtom.
one of implementation of JWorldElement abstract class
JAtom.AtomDraggable - class org.concord.collisions.engine.JAtom.AtomDraggable.
 
JAtom.VelocityDraggable - class org.concord.collisions.engine.JAtom.VelocityDraggable.
 
JAtom() - Constructor for class org.concord.collisions.engine.JAtom
 
JAtomBeanInfo - class org.concord.collisions.engine.JAtomBeanInfo.
 
JAtomBeanInfo() - Constructor for class org.concord.collisions.engine.JAtomBeanInfo
 
JAVA_HOME - Static variable in class org.concord.util.PathDialog
 
javaCommand - Variable in class org.concord.pedagogica.ui.ActivityView
 
javaHome - Variable in class org.concord.util.PathDialog
 
javaHome - Variable in class org.concord.pedagogica.ui.ActivityView
 
javaHome - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
javaHomeButton - Variable in class org.concord.util.PathDialog
 
javaVersion - Variable in class org.concord.pedagogica.ui.ActivityView
 
JBooster - class org.concord.collisions.engine.JBooster.
Booster element in the world
JBooster() - Constructor for class org.concord.collisions.engine.JBooster
 
JDaemon - class org.concord.collisions.engine.JDaemon.
Daemon elements in the world
JDaemon() - Constructor for class org.concord.collisions.engine.JDaemon
 
JDaemonBeanInfo - class org.concord.collisions.engine.JDaemonBeanInfo.
 
JDaemonBeanInfo() - Constructor for class org.concord.collisions.engine.JDaemonBeanInfo
 
JImpulseDaemon - class org.concord.collisions.engine.JImpulseDaemon.
Impulse daemon element in the world
JImpulseDaemon() - Constructor for class org.concord.collisions.engine.JImpulseDaemon
 
join(String) - Method in class org.concord.flash.player.builtin.FArray
 
JPartWorld - class org.concord.collisions.engine.JPartWorld.
main class for kinetic engine contains methods for calculating positions/velocity of particles many methods are duplicated in GUIPanel class
JPartWorld.Distance2Line - class org.concord.collisions.engine.JPartWorld.Distance2Line.
 
JPartWorld.Distance2Line(float, float, float, boolean) - Constructor for class org.concord.collisions.engine.JPartWorld.Distance2Line
 
JPartWorld(float, float) - Constructor for class org.concord.collisions.engine.JPartWorld
JPartWorld constructor user shouldn't create world directly GUIPanel constructor will create it for you
JPropertyFilter - class org.concord.collisions.engine.JPropertyFilter.
 
JRigidBox - class org.concord.collisions.engine.JRigidBox.
one of implementation of JWorldElement abstract class
JWall - class org.concord.collisions.engine.JWall.
one of implementation of JWorldElement abstract class
JWall() - Constructor for class org.concord.collisions.engine.JWall
 
JWorldElement - class org.concord.collisions.engine.JWorldElement.
 
JWorldElement() - Constructor for class org.concord.collisions.engine.JWorldElement
 
JWorldElementBeanInfo - class org.concord.collisions.engine.JWorldElementBeanInfo.
 
JWorldElementBeanInfo() - Constructor for class org.concord.collisions.engine.JWorldElementBeanInfo
 
JWorldElementFilter - class org.concord.collisions.engine.JWorldElementFilter.
Filter of JWorldElements in the world

K

keConstant - Variable in class org.concord.molecular.ui.MolecularView
 
keFactor - Variable in class org.concord.molecular.ui.MolecularView
 
kelvin - Variable in class org.concord.util.CCUnit
 
keyHandler - Variable in class org.concord.pedagogica.PedAgogica
 
keyPressed(KeyEvent) - Method in class org.concord.biologica.ui.DNAView
Handle key pressed event
keyPressed(KeyEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
keyReleased(KeyEvent) - Method in class org.concord.biologica.ui.DNAView
Handle key released event
keyReleased(KeyEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
keyTyped(KeyEvent) - Method in class org.concord.biologica.ui.DNAView
Handle key typed event
keyTyped(KeyEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
kg - Variable in class org.concord.util.CCUnit
 
kineticEnergy - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
KineticEnergy - class org.concord.molecular.engine.KineticEnergy.
 
KineticEnergy() - Constructor for class org.concord.molecular.engine.KineticEnergy
 
koeffA - Variable in class org.concord.util.CCUnit
 
koeffB - Variable in class org.concord.util.CCUnit
 
kx - Variable in class org.concord.collisions.engine.CCSpring
 
ky - Variable in class org.concord.collisions.engine.CCSpring
 

L

label - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
LAMINAR_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForce
 
LAMINAR_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForceCalculator
 
LARGE_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
Large hotspot location.
LARGE_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
Large image column width of a Species object.
LARGE_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
Large image row height of a Species object.
LARGE_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
LARGE_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
lastError - Variable in class org.concord.pedagogica.engine.ActivityScript
 
lastError - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
lastError - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
lastSelectedValue - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
lastTime - Variable in class org.concord.util.LogProcess
 
lastX - Variable in class org.concord.pedagogica.ui.ActivityView
 
lastX - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
lastY - Variable in class org.concord.pedagogica.ui.ActivityView
 
lastY - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
LEExpression - class org.concord.util.script.LEExpression.
The LEExpression class implements the semantic node for "less or equal".
LEExpression() - Constructor for class org.concord.util.script.LEExpression
 
LEFT_BOTTOM_ORIGIN - Static variable in class org.concord.collisions.ui.PassiveIcon
 
LEFT_DAUGHTER_CELL_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
LEFT_TOP_ORIGIN - Static variable in class org.concord.collisions.ui.PassiveIcon
 
left(float, float, JComponent) - Method in class org.concord.collisions.engine.JRigidBox
shift wall left
left(float, float, JComponent) - Method in class org.concord.collisions.engine.JWall
shift wall left
LENGTH_IN_BASES - Static variable in class org.concord.biologica.engine.EngineProp
Length in bases simple property name.
LENGTH_IN_BASES_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
LENGTH_IN_BASES_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
LEU - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Leucine
LEUCINE - Static variable in class org.concord.biologica.engine.AminoAcid
Leucine
lhs - Variable in class org.concord.util.script.FactAssignStatement
 
line(int, int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
LineGraph - class org.concord.util.LineGraph.
Plot a function of time.
LineGraph() - Constructor for class org.concord.util.LineGraph
 
lineLabel - Variable in class org.concord.pedagogica.PedAgogica
 
lineStatus - Variable in class org.concord.pedagogica.PedAgogica
 
list - Variable in class org.concord.molecular.engine.IndexList
 
list() - Method in class org.concord.pedagogica.engine.LogModel
 
listButtonPanel - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
listen - Variable in class org.concord.util.script.ListenStatement
 
LISTENER_SUFFIX - Static variable in class org.concord.util.script.ScriptClassLoader
 
listeners - Variable in class org.concord.molecular.engine.ConditionValue
 
listeners - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
listeners - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
listeners - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
listeners - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
listeners - Variable in class org.concord.pedagogica.ui.ActivityView
 
listeners - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
ListenStatement - class org.concord.util.script.ListenStatement.
 
ListenStatement(Script) - Constructor for class org.concord.util.script.ListenStatement
 
listLevel(Vector, int) - Method in class org.concord.pedagogica.engine.LogModel
 
listPanel - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
listScroll - Variable in class org.concord.util.PathDialog
 
listScroll - Variable in class org.concord.pedagogica.ui.VariableDialog
 
LN10 - Static variable in class org.concord.flash.player.builtin.FMath
 
LN2 - Static variable in class org.concord.flash.player.builtin.FMath
 
LOAD_ACTIVITY - Static variable in class org.concord.pedagogica.ui.ActivityView
 
load(File) - Method in class org.concord.pedagogica.engine.Activity
 
load(File) - Method in class org.concord.pedagogica.ui.ActivityView
 
load(String) - Method in class org.concord.util.EditorInternalFrame
 
load(String, String) - Method in class org.concord.util.EditorInternalFrame
 
load(ZipFile) - Method in class org.concord.pedagogica.engine.ActivityScript
 
load(ZipFile) - Method in class org.concord.pedagogica.engine.Activity
 
load(ZipFile) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
load(ZipFile) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
load(ZipFile, String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
loadButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
loadClass(String, boolean) - Method in class org.concord.util.script.ScriptClassLoader
 
loadComponents - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
loaded(MovieClipEvent) - Method in interface org.concord.flash.player.event.MovieClipListener
 
loader - Variable in class org.concord.util.script.Script
 
loader - Variable in class org.concord.pedagogica.ui.ActivityView
 
loadFileChooser - Variable in class org.concord.pedagogica.ui.ActivityView
 
loadImage(String) - Method in class org.concord.util.beans.SimpleBeanInfo
This is a utility method to help in loading icon images.
loadModel(String) - Method in class org.concord.molecular.ui.MolecularView
Load a previously saved AtomicModel.
loadResourceData(ZipFile) - Method in class org.concord.pedagogica.ui.ActivityView
 
loadScript(String, Object[]) - Method in interface org.concord.util.script.ScriptRuntime
 
loadScript(String, Object[]) - Method in class org.concord.util.script.ECMA
 
loadScript(String, String) - Method in interface org.concord.util.script.ScriptRuntime
 
loadScript(String, String) - Method in class org.concord.util.script.ECMA
 
loadStringData(ZipFile) - Method in class org.concord.pedagogica.engine.NodeAccess
 
loadView(ActivityNode) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
loadView(ActivityNode, boolean) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
locals - Variable in class org.concord.util.script.BlockStatement
 
locator - Variable in class org.concord.biologica.engine.BioLogicaSpecies
 
LOCK_SYMBOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The flag indicating whether a view should draw the lock symbol when an organism is locked has changed.
locked - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Locked state
LOCKED_STATE - Static variable in class org.concord.biologica.engine.EngineProp
Locked state of the object.
LOCKED_STATE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
LOCKED_STATE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
lockedCharacteristicIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked characteristic
lockedEnvironmentIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked environment
lockedGeneIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked gene
lockedOrganismIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked organism
lockedRuleIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked rule
lockedSpeciesAlleleIcon1 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked allele
lockedSpeciesAlleleIcon2 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
lockedSpeciesAlleleIcon3 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
lockedSpeciesAlleleIcon4 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
lockedSpeciesAlleleIcon5 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
lockedSpeciesChromosomeIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked species chromosome
lockedSpeciesIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked species.
lockedSpeciesImageColumnIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked species image column
lockedSpeciesImageIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked species image
lockedSpeciesImageRowIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked species image row
lockedState - Variable in class org.concord.biologica.engine.EngineObject
Current locked state of this object - see above LOCKED statics.
lockedTerrainIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked terrain
lockedTraitIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked trait
lockedWorldIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is a locked world.
lockSymbolVisible - Variable in class org.concord.biologica.ui.OrganismView
Lock symbol visible boolean flag
LOG_EXTENSION - Static variable in class org.concord.pedagogica.engine.Logging
 
log(double) - Method in class org.concord.flash.player.builtin.FMath
 
log(int, String) - Method in class org.concord.pedagogica.engine.Logging
 
log(int, String, Object) - Static method in class org.concord.util.Debug
Log a debug string to the system output if the passed in log level is LOWER than or equal to the current log level OR if the Debug log level is greater than INFO, the level passed in is INFO or less or equal to the current Debug log level.
log(int, String, Object) - Static method in class org.concord.biologica.engine.Debug
Log a debug string to the system output if the passed in log level is LOWER than or equal to the current log level OR if the Debug log level is greater than INFO, the level passed in is INFO or less or equal to the current Debug log level.
log10(double) - Method in class org.concord.util.BarGraph
 
log10(double) - Method in class org.concord.util.LineGraph
 
LOG10E - Static variable in class org.concord.flash.player.builtin.FMath
 
LOG2E - Static variable in class org.concord.flash.player.builtin.FMath
 
logAction(int, String) - Method in class org.concord.pedagogica.engine.Logging
 
LogConfigure - class org.concord.util.LogConfigure.
 
LogConfigure() - Constructor for class org.concord.util.LogConfigure
Creates new form frame
logDir - Variable in class org.concord.pedagogica.engine.Logging
 
logDirectory - Variable in class org.concord.pedagogica.engine.LogModel
 
logDirPath - Variable in class org.concord.pedagogica.engine.LogModel
 
logFiles - Variable in class org.concord.pedagogica.engine.Logging
 
logging - Variable in class org.concord.pedagogica.engine.Activity
 
logging - Variable in class org.concord.pedagogica.ui.RunActivity
 
Logging - class org.concord.pedagogica.engine.Logging.
 
Logging() - Constructor for class org.concord.pedagogica.engine.Logging
 
Logging(Activity) - Constructor for class org.concord.pedagogica.engine.Logging
 
Logging(String, String) - Constructor for class org.concord.pedagogica.engine.Logging
 
loggingEnabled - Variable in class org.concord.pedagogica.ui.LoginPanel
 
logImmediate(String) - Method in class org.concord.pedagogica.engine.Logging
 
login - Variable in class org.concord.pedagogica.ui.LoginPanel
 
loginButton - Variable in class org.concord.pedagogica.ui.LoginPanel
 
loginHTML - Variable in class org.concord.pedagogica.ui.LoginPanel
 
loginLabel - Variable in class org.concord.pedagogica.ui.LoginPanel
 
LoginPanel - class org.concord.pedagogica.ui.LoginPanel.
 
LoginPanel() - Constructor for class org.concord.pedagogica.ui.LoginPanel
 
logList - Variable in class org.concord.pedagogica.ui.LogView
 
LogModel - class org.concord.pedagogica.engine.LogModel.
 
LogModel() - Constructor for class org.concord.pedagogica.engine.LogModel
 
LogModel(String) - Constructor for class org.concord.pedagogica.engine.LogModel
 
logObservation(int, String) - Method in class org.concord.pedagogica.engine.Logging
 
logPath - Variable in class org.concord.pedagogica.engine.LogModel
 
LogProcess - class org.concord.util.LogProcess.
 
LogProcess(String, String, String, String) - Constructor for class org.concord.util.LogProcess
 
logQuestion(int, QuestionForm) - Method in class org.concord.pedagogica.engine.Logging
 
logScroll - Variable in class org.concord.pedagogica.ui.LogView
 
logTransition(int, ActivityNode, ActivityNode) - Method in class org.concord.pedagogica.engine.Logging
 
LogView - class org.concord.pedagogica.ui.LogView.
 
LogView() - Constructor for class org.concord.pedagogica.ui.LogView
 
logWriters - Variable in class org.concord.pedagogica.engine.Logging
 
LONG_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
LONGER_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
LONGEST_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
Chromosome image numbers.
lookup(String) - Method in class org.concord.util.script.NameStack
Find a variable value in the stack frame.
lookup(String, boolean) - Method in class org.concord.util.script.NameStack
 
lookupHandler(String) - Method in class org.concord.util.script.event.EventHandler
 
LoopStatement - class org.concord.util.script.LoopStatement.
 
LoopStatement() - Constructor for class org.concord.util.script.LoopStatement
 
LTExpression - class org.concord.util.script.LTExpression.
The LTExpression class implements the semantic node for "less than".
LTExpression() - Constructor for class org.concord.util.script.LTExpression
 
LYS - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Lysine
LYSINE - Static variable in class org.concord.biologica.engine.AminoAcid
Lysine

M

main(String[]) - Static method in class org.concord.util.BarGraph
 
main(String[]) - Static method in class org.concord.util.LogConfigure
 
main(String[]) - Static method in class org.concord.util.Gauge
 
main(String[]) - Static method in class org.concord.util.Query
 
main(String[]) - Static method in class org.concord.util.NetworkTime
 
main(String[]) - Static method in class org.concord.util.Transfer
 
main(String[]) - Static method in class org.concord.util.Crypt
 
main(String[]) - Static method in class org.concord.util.LogProcess
 
main(String[]) - Static method in class org.concord.util.Editor
 
main(String[]) - Static method in class org.concord.util.LineGraph
 
main(String[]) - Static method in class org.concord.util.script.ECMA
This the the main method.
main(String[]) - Static method in class org.concord.biologica.test.TestWindow
Main process method.
main(String[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
main(String[]) - Static method in class org.concord.biologica.ui.BioLogicaFrame
 
main(String[]) - Static method in class org.concord.biologica.ui.GlossaryFrame
 
main(String[]) - Static method in class org.concord.collisions.ui.GUIElementsFrame
 
main(String[]) - Static method in class org.concord.collisions.ui.GUITestIngrid
 
main(String[]) - Static method in class org.concord.collisions.ui.IngridProblem
 
main(String[]) - Static method in class org.concord.flash.player.FFlash
 
main(String[]) - Static method in class org.concord.flash.util.DumpSWF
First arg is the name of the input SWF file
main(String[]) - Static method in class org.concord.flash.util.MovieViewer
 
main(String[]) - Static method in class org.concord.pedagogica.PedAgogica
 
main(String[]) - Static method in class org.concord.pedagogica.engine.LogModel
 
main(String[]) - Static method in class org.concord.pedagogica.ui.LoginPanel
 
main(String[]) - Static method in class org.concord.pedagogica.ui.ActivityView
 
main(String[]) - Static method in class org.concord.pedagogica.ui.TableInputView
 
main(String[]) - Static method in class org.concord.pedagogica.ui.RunActivity
 
main(String[]) - Static method in class org.concord.pedagogica.ui.HelpView
 
main(String[]) - Static method in class org.concord.pedagogica.ui.ClassTree
 
main(String[]) - Static method in class org.concord.pedagogica.ui.Quiz
 
main(String[]) - Static method in class org.concord.pedagogica.ui.LogView
 
main(String[]) - Static method in class org.concord.pedagogica.ui.NodeViewEditor
 
main(String[]) - Static method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
mainPanel - Variable in class org.concord.pedagogica.PedAgogica
 
majorTickLength - Variable in class org.concord.util.Gauge
 
majorTicks - Variable in class org.concord.util.Gauge
 
majorTickValue - Variable in class org.concord.util.Gauge
 
MALE - Static variable in class org.concord.biologica.engine.Organism
Sex values
MALE_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.FertilizationChromosomeModel
 
MALE_ONLY - Static variable in class org.concord.biologica.engine.Species
 
MALE_ONLY_STRING - Static variable in class org.concord.biologica.engine.Species
 
MALE_PARENT_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
MALE_PARENT_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
MALE_STRING - Static variable in class org.concord.biologica.engine.Organism
 
manageCollision(JWorldElement) - Method in class org.concord.collisions.engine.JPartWorld
 
manageCollision(JWorldElement) - Method in class org.concord.collisions.engine.JDaemon
Abstract method This method is called by JPartWorld when the daemon collides with an element
manageCollision(JWorldElement) - Method in class org.concord.collisions.engine.JImpulseDaemon
This method is called by JPartWorld when the booster collides with an element
manageCollision(JWorldElement) - Method in class org.concord.collisions.engine.JBooster
This method is called by JPartWorld when the booster collides with an element
manageNoCollision(JWorldElement) - Method in class org.concord.collisions.engine.JDaemon
 
manageNoCollision(JWorldElement) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
manageNoCollision(JWorldElement) - Method in class org.concord.collisions.engine.JBooster
 
manageVelocity(CCCoordinateTuner, int, int) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
MANUAL_AND_AUTOMATIC_LOCKED - Static variable in class org.concord.biologica.engine.EngineObject
Manual and automatic locked value.
MANUAL_AND_AUTOMATIC_LOCKED_STRING - Static variable in class org.concord.biologica.engine.EngineObject
 
MANUAL_LOCKED - Static variable in class org.concord.biologica.engine.EngineObject
Manual locked value.
MANUAL_LOCKED_STRING - Static variable in class org.concord.biologica.engine.EngineObject
 
mapElementNameToID(String) - Static method in class org.concord.biologica.engine.Elements
Map the given element name to an element id, returning that id.
mark(int) - Method in class org.concord.util.script.ScriptFileInputStream
 
markSupported() - Method in class org.concord.util.script.ScriptFileInputStream
 
mass - Variable in class org.concord.collisions.engine.JWorldElement
 
mass1 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
mass1 - Variable in class org.concord.molecular.ui.MolecularView
 
mass2 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
mass2 - Variable in class org.concord.molecular.ui.MolecularView
 
mass3 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
mass3 - Variable in class org.concord.molecular.ui.MolecularView
 
mass4 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
mass4 - Variable in class org.concord.molecular.ui.MolecularView
 
matchBases(byte[]) - Method in class org.concord.biologica.engine.SpeciesAllele
Do the input bases match the bases of this allele?
matchPrefix(String) - Method in class org.concord.util.PathDialog
 
matrix - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
max - Variable in class org.concord.util.Gauge
 
max - Variable in class org.concord.molecular.engine.ConditionValue
 
MAX_SEARCH - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
max(double, double) - Method in class org.concord.flash.player.builtin.FMath
 
MAXIMUM_NUMBER_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The maximum number of children from a breeding has changed.
maxString - Variable in class org.concord.util.Gauge
 
maxX - Variable in class org.concord.pedagogica.ui.ActivityView
 
maxY - Variable in class org.concord.pedagogica.ui.ActivityView
 
MEAN - Static variable in class org.concord.molecular.engine.ConditionValue
 
mean(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
MEDIUM_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
MEDIUM_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
Medium hotspot location.
MEDIUM_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
Medium image column width of a Species object.
MEDIUM_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
Medium image row height of a Species object.
MEDIUM_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
MEDIUM_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
MEIOSIS_CHROMOSOME_SELECTED - Static variable in class org.concord.biologica.ui.UIProp
 
MEIOSIS_FATHER_STARTED_AND_STOPPED - Static variable in class org.concord.biologica.ui.UIProp
The father meiosis has started and was stopped.
MEIOSIS_FATHER_STEP - Static variable in class org.concord.biologica.ui.UIProp
The father meiosis step of the sex view has changed.
MEIOSIS_MODEL - Static variable in class org.concord.biologica.ui.UIProp
The meiosis model has changed.
MEIOSIS_MOTHER_STARTED_AND_STOPPED - Static variable in class org.concord.biologica.ui.UIProp
Meiosis of the mother has started and was stopped.
MEIOSIS_MOTHER_STEP - Static variable in class org.concord.biologica.ui.UIProp
The mother meiosis step of the sex view has changed.
MEIOSIS_STARTED - Static variable in class org.concord.biologica.ui.UIProp
Meiosis has started.
MEIOSIS_STEP - Static variable in class org.concord.biologica.ui.UIProp
The meiosis step of a subview (mother or father) has changed.
MeiosisChromosomeModel - class org.concord.biologica.ui.MeiosisChromosomeModel.
MeiosisChromosomeModel contains the data describing the meiosis state for a given chromosome.
MeiosisChromosomeModel(MeiosisModel, OrganismChromosome, int, MeiosisChromosomeModel, int, Rectangle, int, Color) - Constructor for class org.concord.biologica.ui.MeiosisChromosomeModel
Creates a new instance of MeiosisChromosomeModel with the given chromosome, meiosis model, type and previous chromosome model.
MeiosisModel - class org.concord.biologica.ui.MeiosisModel.
MeiosisModel contains the data describing the meiosis process state for a given organism.
MeiosisModel() - Constructor for class org.concord.biologica.ui.MeiosisModel
Creates a new instance of MeiosisModel with no organism.
meiosisPracticeView - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
MeiosisPracticeView - class org.concord.biologica.ui.MeiosisPracticeView.
 
MeiosisPracticeView(JFrame) - Constructor for class org.concord.biologica.ui.MeiosisPracticeView
 
members - Variable in class org.concord.util.script.NameStack
 
members - Variable in class org.concord.util.script.Script
 
members - Variable in class org.concord.flash.player.FScriptObject
 
menuCanceled(MenuEvent) - Method in class org.concord.biologica.ui.AllInOneView
 
menuDeselected(MenuEvent) - Method in class org.concord.biologica.ui.AllInOneView
 
menuSelected(MenuEvent) - Method in class org.concord.biologica.ui.AllInOneView
React to menu events
messageID - Variable in class org.concord.collisions.engine.CCTimer
messageID you can check source of ActionEvent and if it's instance of org.concord.collisions.engine.CCTimer, you can ask messageID field
MET - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Methionine
meter - Variable in class org.concord.util.CCUnit
 
METHIONINE - Static variable in class org.concord.biologica.engine.AminoAcid
Methionine
method - Variable in class org.concord.util.script.InvocationExpression
 
method - Variable in class org.concord.pedagogica.engine.DomainMethod
 
MethodDeclaration - class org.concord.util.script.MethodDeclaration.
The MethodDeclaration class holds the state asscociated with the definition of a script method.
MethodDeclaration() - Constructor for class org.concord.util.script.MethodDeclaration
 
MethodDeclaration(Script) - Constructor for class org.concord.util.script.MethodDeclaration
 
MethodDescriptor - class org.concord.util.beans.MethodDescriptor.
A MethodDescriptor describes a particular method that a Java Bean supports for external access from other components.
MethodDescriptor(Method) - Constructor for class org.concord.util.beans.MethodDescriptor
Constructs a MethodDescriptor from a Method.
MethodDescriptor(Method, ParameterDescriptor[]) - Constructor for class org.concord.util.beans.MethodDescriptor
Constructs a MethodDescriptor from a Method providing descriptive information for each of the method's parameters.
methods - Variable in class org.concord.util.script.Script
 
methodTemplate - Static variable in class org.concord.util.script.ScriptClassLoader
 
methodUseCount - Variable in class org.concord.util.script.InvocationExpression
 
min - Variable in class org.concord.util.Gauge
 
min - Variable in class org.concord.molecular.engine.ConditionValue
 
MIN_PREFERRED_HEIGHT - Static variable in class org.concord.biologica.ui.ChromosomeView
 
min(double, double) - Method in class org.concord.flash.player.builtin.FMath
 
minDistance - Static variable in class org.concord.collisions.engine.JDaemon
 
MINIMUM_NUMBER_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The minimum number of children from a breeding has changed.
MINMAX_NUMBER_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The minimum and/or maximum number of children from a breeding has changed.
minorTickLength - Variable in class org.concord.util.Gauge
 
minorTicks - Variable in class org.concord.util.Gauge
 
minorTickValue - Variable in class org.concord.util.Gauge
 
minString - Variable in class org.concord.util.Gauge
 
MinusExpression - class org.concord.util.script.MinusExpression.
The MinusExpression class implements the semantic node for minus.
MinusExpression() - Constructor for class org.concord.util.script.MinusExpression
 
minX - Variable in class org.concord.pedagogica.ui.ActivityView
 
minY - Variable in class org.concord.pedagogica.ui.ActivityView
 
mixColorTransform(ColorTransform, ColorTransform) - Static method in class org.concord.flash.player.FUtil
 
mml - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
model - Variable in class org.concord.molecular.ui.MolecularView
 
model - Variable in class org.concord.pedagogica.ui.LogView
 
MODEL_UPDATE - Static variable in class org.concord.molecular.engine.DefaultAtomicModel
 
modelType - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
modified - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
modified - Variable in class org.concord.pedagogica.ui.ActivityView
 
modifyButton - Variable in class org.concord.util.PathDialog
 
modifyButton - Variable in class org.concord.pedagogica.ui.VariableDialog
 
modifyDialog - Variable in class org.concord.pedagogica.ui.VariableDialog
 
modifyHandler - Variable in class org.concord.pedagogica.PedAgogica
 
modifyPathDialog - Variable in class org.concord.util.PathDialog
 
ModifyValueDialog - class org.concord.pedagogica.ui.ModifyValueDialog.
 
ModifyValueDialog(JFrame, String) - Constructor for class org.concord.pedagogica.ui.ModifyValueDialog
 
ModulusExpression - class org.concord.util.script.ModulusExpression.
The ModulusExpression class implements the modulus binary operation.
ModulusExpression() - Constructor for class org.concord.util.script.ModulusExpression
 
mole - Variable in class org.concord.util.CCUnit
 
MolecularView - class org.concord.molecular.ui.MolecularView.
 
MolecularView() - Constructor for class org.concord.molecular.ui.MolecularView
Constructor for the MolecularView.
molecules - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
MOTHER_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
The mother organism shown in a view has changed from one organism to another.
MOTHER_VIEW - Static variable in class org.concord.biologica.ui.SmallMeiosisView
 
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse click events
mouseClicked(MouseEvent) - Method in class org.concord.flash.player.FButton
 
mouseClicked(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseClicked(MouseEvent) - Method in class org.concord.flash.player.FSprite
 
mouseClicked(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseClicked(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse dragged event
mouseDragged(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseDragged(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseDragged(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse entered event
mouseEntered(MouseEvent) - Method in class org.concord.flash.player.FButton
 
mouseEntered(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseEntered(MouseEvent) - Method in class org.concord.flash.player.FSprite
 
mouseEntered(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseEntered(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse exited event
mouseExited(MouseEvent) - Method in class org.concord.flash.player.FButton
 
mouseExited(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseExited(MouseEvent) - Method in class org.concord.flash.player.FSprite
 
mouseExited(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseExited(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse moved event
mouseMoved(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseMoved(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseMoved(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse pressed event.
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse pressed event
mousePressed(MouseEvent) - Method in class org.concord.flash.player.FButton
 
mousePressed(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mousePressed(MouseEvent) - Method in class org.concord.flash.player.FSprite
 
mousePressed(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mousePressed(MouseEvent) - Method in class org.concord.pedagogica.ui.TableInputView
Event handler that
mousePressed(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle mouse released event.
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.DNAView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle mouse released event
mouseReleased(MouseEvent) - Method in class org.concord.flash.player.FButton
 
mouseReleased(MouseEvent) - Method in class org.concord.flash.player.FMouseSupport
 
mouseReleased(MouseEvent) - Method in class org.concord.flash.player.FSprite
 
mouseReleased(MouseEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
mouseReleased(MouseEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
MOVABLE - Static variable in class org.concord.biologica.ui.UIProp
The view's movable state has changed.
move(float) - Method in class org.concord.collisions.ui.PassiveElement
 
move(float) - Method in class org.concord.collisions.ui.PassiveLine
 
move(int, int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
moveable - Variable in class org.concord.collisions.ui.PassiveElement
 
MOVED_FATHER_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The moved father gamete in a sex view has changed.
MOVED_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The moved gamete in a meiosis model has changed.
MOVED_MOTHER_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The moved mother gamete in a sex view has changed.
moveGamete() - Method in class org.concord.biologica.ui.MeiosisModel
Move the gamete currently selected into fertilization.
moveGenotypeToPhenotypeRuleAfter(GenotypeToPhenotypeRule, GenotypeToPhenotypeRule) - Method in class org.concord.biologica.engine.Species
Move the given genotype to phenotype rule immediately after the second rule.
moveGenotypeToPhenotypeRuleDown(GenotypeToPhenotypeRule) - Method in class org.concord.biologica.engine.Species
Move the given genotype to phenotype rule down one position in the list of rules for this species.
moveGenotypeToPhenotypeRuleUp(GenotypeToPhenotypeRule) - Method in class org.concord.biologica.engine.Species
Move the given genotype to phenotype rule up one position in the list of rules for this species.
moveSelectedItems(int, int) - Method in class org.concord.pedagogica.ui.ActivityView
 
moveTo(int, int, Atom[]) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
movie - Variable in class org.concord.flash.player.FComponent
 
movie - Variable in class org.concord.flash.player.FMovieBuilder
 
MovieClipEvent - class org.concord.flash.player.event.MovieClipEvent.
 
MovieClipEvent(Object, int, int) - Constructor for class org.concord.flash.player.event.MovieClipEvent
 
MovieClipListener - interface org.concord.flash.player.event.MovieClipListener.
 
MovieViewer - class org.concord.flash.util.MovieViewer.
 
MovieViewer.ElementObj - class org.concord.flash.util.MovieViewer.ElementObj.
 
MovieViewer.ElementObj(MovieViewer) - Constructor for class org.concord.flash.util.MovieViewer.ElementObj
 
MovieViewer.ElementObj(MovieViewer, Shape.Element, int) - Constructor for class org.concord.flash.util.MovieViewer.ElementObj
 
MovieViewer(String, Movie) - Constructor for class org.concord.flash.util.MovieViewer
 
MULTIPLE_SELECTION - Static variable in class org.concord.pedagogica.ui.ClassTree
 
MultipleChoice - class org.concord.pedagogica.ui.MultipleChoice.
 
MultipleChoice() - Constructor for class org.concord.pedagogica.ui.MultipleChoice
 
MultipleChoice(String, String[]) - Constructor for class org.concord.pedagogica.ui.MultipleChoice
This constructs a multiple choice question.
MultipleOrganismView - class org.concord.biologica.ui.MultipleOrganismView.
The multiple organism view of BioLogica.
MultipleOrganismView() - Constructor for class org.concord.biologica.ui.MultipleOrganismView
Creates a multiple organism view.
multipleSelected(ActivityItemEvent) - Method in class org.concord.pedagogica.PedAgogica
 
multipleSelected(ActivityItemEvent) - Method in interface org.concord.pedagogica.ui.event.ActivityItemListener
 
MultiplyExpression - class org.concord.util.script.MultiplyExpression.
The MultiplyExpression class implements the semantic node for multiply.
MultiplyExpression() - Constructor for class org.concord.util.script.MultiplyExpression
 
mutatesTo(Object, Object) - Method in class org.concord.util.beans.PersistenceDelegate
Returns true if an equivalent copy of oldInstance may be created by applying a series of statements to newInstance.
mutatesTo(Object, Object) - Method in class org.concord.util.beans.DefaultPersistenceDelegate
If the number of arguments in the specified constructor is non-zero and the class of oldInstance explicitly declares an "equals" method this method returns the value of oldInstance.equals(newInstance).
MUTATION_ALLELE - Static variable in class org.concord.biologica.engine.EngineProp
Mutation allele of its gene? New and old values are Boolean.
MUTATION_ALLELE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
MUTATION_ALLELE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
mutationsPracticeView - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
MutationsPracticeView - class org.concord.biologica.ui.MutationsPracticeView.
 
MutationsPracticeView(JFrame) - Constructor for class org.concord.biologica.ui.MutationsPracticeView
 

N

name - Variable in class org.concord.util.CCUnit
 
name - Variable in class org.concord.util.script.ScriptObject
This is the name of this particular script node.
name - Variable in class org.concord.biologica.engine.BioEngine
The name of this object.
name - Variable in class org.concord.collisions.engine.JWorldElement
 
name - Variable in class org.concord.flash.player.FScriptObject
 
name - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
name - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
name - Variable in class org.concord.pedagogica.engine.ActivityScript
 
name - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
name - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
name - Variable in class org.concord.pedagogica.ui.NamedTreeNode
 
NAME - Static variable in class org.concord.biologica.engine.EngineProp
Name simple property name.
NAME_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
NAME_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
NAME_SUPER_VISIBLE - Static variable in class org.concord.biologica.engine.EngineProp
Name super visible flag.
NAME_SUPER_VISIBLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
NAME_SUPER_VISIBLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
NAME_TEXT_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The flag indicating whether a view should draw the text for an organism's name under the organism has changed.
NamedTreeNode - class org.concord.pedagogica.ui.NamedTreeNode.
 
NamedTreeNode() - Constructor for class org.concord.pedagogica.ui.NamedTreeNode
 
NameExpression - class org.concord.util.script.NameExpression.
 
NameExpression() - Constructor for class org.concord.util.script.NameExpression
 
nameField - Variable in class org.concord.pedagogica.ui.LoginPanel
 
nameLabel - Variable in class org.concord.pedagogica.ui.LoginPanel
 
names - Variable in class org.concord.util.script.NameStack
 
names - Variable in class org.concord.biologica.engine.BioLogicaSpecies
 
NameStack - class org.concord.util.script.NameStack.
The NameStack class implements a stack frame mechanism for the script interpreter.
NameStack() - Constructor for class org.concord.util.script.NameStack
 
NameStack(boolean) - Constructor for class org.concord.util.script.NameStack
 
NameStack(NameStack) - Constructor for class org.concord.util.script.NameStack
 
nameTextVisible - Variable in class org.concord.biologica.ui.OrganismView
Name text visible boolean flag.
needAngle - Variable in class org.concord.collisions.engine.CCSpring
 
needX - Variable in class org.concord.collisions.engine.CCSpring
 
NEExpression - class org.concord.util.script.NEExpression.
The NEExpression class implements the semantic node for "not equal".
NEExpression() - Constructor for class org.concord.util.script.NEExpression
 
negate - Variable in class org.concord.molecular.engine.ConditionValue
 
NegateExpression - class org.concord.util.script.NegateExpression.
 
NegateExpression() - Constructor for class org.concord.util.script.NegateExpression
 
NetworkTime - class org.concord.util.NetworkTime.
 
NetworkTime(String) - Constructor for class org.concord.util.NetworkTime
 
NEW_ACTIVITY - Static variable in class org.concord.pedagogica.ui.ActivityView
 
newButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
newButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
newDocument() - Method in class org.concord.util.Editor
 
newElement(String, int) - Method in class org.concord.biologica.engine.ElementContext
New element is starting in an existing element context.
NewExpression - class org.concord.util.script.NewExpression.
 
NewExpression() - Constructor for class org.concord.util.script.NewExpression
 
newMovie - Variable in class org.concord.flash.player.FMovieBuilder
 
newPlacement - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
newPlacement() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
NEWTONIUM - Static variable in class org.concord.molecular.ui.MolecularView
 
NEXT_HIGHEST_AUTOSOME_NUMBER - Static variable in interface org.concord.biologica.engine.IChromosome
Next highest autosome number.
next() - Method in class org.concord.pedagogica.engine.ActivityNode
 
nextElement() - Method in class org.concord.util.Enumerator
 
nextFrame() - Method in class org.concord.flash.player.FMovieClip
Move to the next frame Usually called by the timer
nextStep - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
nextStep() - Method in class org.concord.collisions.engine.JPartWorld
nextStep shouldn't be called directly calculates next simulation's step
nextStep() - Method in class org.concord.collisions.engine.BedSpringWorld
 
nextStep() - Method in class org.concord.collisions.ui.GUIPanel
nextStep shouldn't be called directly calculates next simulation's step
nil - Static variable in class org.concord.util.script.ScriptObject
 
Nil - class org.concord.util.script.Nil.
 
Nil() - Constructor for class org.concord.util.script.Nil
 
NO_CELL - Static variable in class org.concord.biologica.engine.OrganismImage
Indicates image should not draw anything, as there was no cell in the speciesImage which should be drawn for this organism.
NO_GAMETE - Static variable in class org.concord.biologica.ui.MeiosisModel
Gamete identifiers
NO_INTERVAL - Static variable in class org.concord.molecular.engine.ConditionValue
 
NO_SEX - Static variable in class org.concord.biologica.engine.Organism
 
NO_SEX_STRING - Static variable in class org.concord.biologica.engine.Organism
 
NO_TOOL - Static variable in class org.concord.biologica.ui.Tool
 
node - Variable in class org.concord.util.script.NameStack
 
node - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
node - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
nodeAccess - Variable in class org.concord.pedagogica.engine.ActivityScript
 
NodeAccess - class org.concord.pedagogica.engine.NodeAccess.
 
NodeAccess() - Constructor for class org.concord.pedagogica.engine.NodeAccess
 
nodeButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
nodeChanged(TreeViewNode) - Method in class org.concord.biologica.ui.TreeView
Notification that a node in this tree has changed.
nodeName - Variable in class org.concord.pedagogica.engine.ActivityNode
 
nodeObjectDeleted(TreeViewNode) - Method in class org.concord.biologica.ui.TreeView
Notification that the engine object corresponding to a node in this tree has been deleted.
nodes - Variable in class org.concord.pedagogica.engine.Activity
 
nodeSelected(ActivityItemEvent) - Method in class org.concord.pedagogica.PedAgogica
 
nodeSelected(ActivityItemEvent) - Method in interface org.concord.pedagogica.ui.event.ActivityItemListener
 
nodeSelectedStateChanged(TreeViewNode, boolean, boolean) - Method in class org.concord.biologica.ui.TreeView
Notification that a node's selected state in this tree changed.
nodeStack - Variable in class org.concord.pedagogica.engine.Activity
 
nodeStack - Variable in class org.concord.pedagogica.engine.NodeAccess
 
nodeStack - Variable in class org.concord.pedagogica.ui.ActivityView
 
nodeStack - Variable in class org.concord.pedagogica.ui.RunActivity
 
nodeTable - Variable in class org.concord.pedagogica.engine.Activity
 
nodeTable - Variable in class org.concord.pedagogica.engine.NodeAccess
 
nodeTable - Variable in class org.concord.pedagogica.ui.ClassTree
 
nodeThread - Variable in class org.concord.pedagogica.engine.ActivityNode
 
nodeView - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
NodeViewEditor - class org.concord.pedagogica.ui.NodeViewEditor.
 
NodeViewEditor() - Constructor for class org.concord.pedagogica.ui.NodeViewEditor
 
nodeViewList - Variable in class org.concord.pedagogica.ui.ActivityView
 
noFocusBorder - Static variable in class org.concord.pedagogica.ui.CCTableCellRenderer
 
NONE - Static variable in class org.concord.util.Debug
Constants used for the log level and in calls to log().
NONE - Static variable in class org.concord.biologica.engine.Debug
Constants used for the log level and in calls to log().
noOthers - Variable in class org.concord.util.LogProcess
 
NORMAL_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForce
 
NORMAL_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForceCalculator
 
NORMAL_IMAGE_TYPE - Static variable in class org.concord.biologica.engine.SpeciesImage
Possible image types:
normalizePosition() - Method in class org.concord.pedagogica.ui.ActivityView
 
NOSCRIPT - Static variable in class org.concord.util.script.InvocationExpression
 
NOT_BIOLOGICA_SPECIES_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
NOT_BIOLOGICA_WORLD_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
NOT_SAVED - Static variable in class org.concord.biologica.engine.EngineStrings
 
NotBioLogicaFileException - exception org.concord.biologica.engine.NotBioLogicaFileException.
Exception indicating that an attempt was made to use a file which is not a BioLogica file as a BioLogica file.
NotBioLogicaFileException(String) - Constructor for class org.concord.biologica.engine.NotBioLogicaFileException
Creates a new exception.
NotExpression - class org.concord.util.script.NotExpression.
 
NotExpression() - Constructor for class org.concord.util.script.NotExpression
 
notifyActionListeners() - Method in class org.concord.pedagogica.ui.TableInputView
 
notifyActivityItemListeners(Object, boolean) - Method in class org.concord.pedagogica.ui.ActivityView
 
notifyAreaListener() - Method in class org.concord.collisions.engine.JWorldElement
 
notifyAreaListener() - Method in class org.concord.collisions.engine.JAtom
 
notifyChangeListeners() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
notifyCollisionsListeners(JWorldElement, int, int, int) - Method in class org.concord.collisions.engine.JPartWorld
 
notifyConditionListeners(ConditionEvent) - Method in class org.concord.molecular.engine.ConditionValue
 
notifying - Variable in class org.concord.molecular.engine.ConditionValue
 
notifyPropertyListeners(PropertyChangeEvent) - Method in class org.concord.collisions.engine.JWorldElement
 
notifySelected(boolean, boolean) - Method in class org.concord.biologica.engine.EngineObject
Notify listeners that the selected state of this object has changed.
notifyWaitingThread() - Method in class org.concord.util.script.Script
 
nPart - Variable in class org.concord.collisions.engine.VelDistFraction
 
NUCLEIC_ACID_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
An INucleicAcid object was added.
NUCLEIC_ACID_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
NUCLEIC_ACID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
NUCLEIC_ACID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
NUCLEIC_ACID_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
An INucleicAcid object was removed.
NucleicAcid - class org.concord.biologica.engine.NucleicAcid.
This class represents a container nucleic acid, which is little more than a collection of other nucleic acids, some of which are alleles, some algorithmic sequences, some containers, etc.
NucleicAcid(INucleicAcidHolder, int, byte[], int) - Constructor for class org.concord.biologica.engine.NucleicAcid
Creates a new nucleic acid from the given base values.
NucleicAcid(INucleicAcidHolder, int, Vector, int) - Constructor for class org.concord.biologica.engine.NucleicAcid
Creates a new nucleic acid from the given vector of nucleic acids, which is handy when the vector is created during meiosis.
NULL_ID - Static variable in class org.concord.biologica.engine.EngineObject
Null ID value.
NullLiteral - class org.concord.util.script.NullLiteral.
This node represents the null value in the semantic tree.
NullLiteral() - Constructor for class org.concord.util.script.NullLiteral
 
NUMBER_FEMALE_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The number of female children to create in a family when the pedigree view is in OFFSPRING_MODE_MALE_FEMALE mode.
NUMBER_MALE_CHILDREN - Static variable in class org.concord.biologica.ui.UIProp
The number of male children to create in a family when the pedigree view is in OFFSPRING_MODE_MALE_FEMALE mode.
NUMBER_OF_COLUMNS - Static variable in class org.concord.biologica.engine.EngineProp
The number of columns in a SpeciesImage.
NUMBER_OF_ROWS - Static variable in class org.concord.biologica.engine.EngineProp
The number of rows in a SpeciesImage.
NUMBER_OF_TOOLS - Static variable in class org.concord.biologica.ui.Tool
 
NUMBER_P_STRAND_SEGMENTS_LONG_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_LONGER_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_LONGEST_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
Number of segments in P and Q strands of each type of chromosome image.
NUMBER_P_STRAND_SEGMENTS_MEDIUM_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_SHORT_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_SHORTER_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_SHORTEST_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_P_STRAND_SEGMENTS_TINY_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_LONG_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_LONGER_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_LONGEST_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_MEDIUM_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_SHORT_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_SHORTER_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_SHORTEST_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_Q_STRAND_SEGMENTS_TINY_CHROMOSOME - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
NUMBER_TYPE - Static variable in class org.concord.biologica.engine.EngineProp
Chromosome number type.
NUMBER_TYPE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
NUMBER_TYPE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
numberOfActions - Variable in class org.concord.util.LogProcess
 
numberOfAnswers - Variable in class org.concord.util.LogProcess
 
numberOfAtoms - Variable in class org.concord.molecular.engine.AtomicValue
 
numberOfAtoms - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
numberOfAtomsPerMolecules - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
numberOfBars - Variable in class org.concord.util.Gauge
 
numberOfBends - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
numberOfBonds - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
numberOfGauges - Variable in class org.concord.util.BarGraph
 
numberOfMolecules - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
numberOfQuestions - Variable in class org.concord.util.LogProcess
 
numberOfWords - Variable in class org.concord.util.LogProcess
 

O

OBJECT - Static variable in class org.concord.biologica.ui.UIProp
The object shown in a view has changed from one object to another This event is typically fired by a view which contains a single engine object of any type (e.g.
OBJECT_DELETED - Static variable in class org.concord.biologica.engine.EngineStrings
 
OBJECT_ILLEGAL_AFTER_STREAM_READ - Static variable in class org.concord.biologica.engine.EngineStrings
 
OBJECT_LOCKED - Static variable in class org.concord.biologica.engine.EngineStrings
 
ObjectDeletedException - exception org.concord.util.ObjectDeletedException.
Exception indicating that the object has been "deleted" and is awaiting garbage collection.
ObjectDeletedException - exception org.concord.biologica.engine.ObjectDeletedException.
Exception indicating that the object has been "deleted" and is awaiting garbage collection.
ObjectDeletedException(String) - Constructor for class org.concord.util.ObjectDeletedException
Creates a new exception.
ObjectDeletedException(String) - Constructor for class org.concord.biologica.engine.ObjectDeletedException
Creates a new exception.
ObjectExpression - class org.concord.util.script.ObjectExpression.
 
ObjectExpression() - Constructor for class org.concord.util.script.ObjectExpression
 
ObjectLockedException - exception org.concord.biologica.engine.ObjectLockedException.
Exception indicating that the object has been "locked" and may not be modified.
ObjectLockedException(String) - Constructor for class org.concord.biologica.engine.ObjectLockedException
Creates a new exception.
ObjectPropertiesView - class org.concord.biologica.ui.ObjectPropertiesView.
The object properties view of BioLogica.
ObjectPropertiesView() - Constructor for class org.concord.biologica.ui.ObjectPropertiesView
Creates an object property view.
obstacles - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
obstacles - Variable in class org.concord.molecular.engine.DefaultMolecularModel
 
OFFSPRING_MODE - Static variable in class org.concord.biologica.ui.UIProp
The pedigree view offspring mode has changed.
OFFSPRING_MODE_FIXED - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_FIXED_STRING - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_MALE_FEMALE - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_MALE_FEMALE_STRING - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_MIN_MAX - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_MIN_MAX_STRING - Static variable in class org.concord.biologica.ui.PedigreeView
 
OFFSPRING_MODE_PULLDOWN_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The enabled state of the offspring mode pulldown has changed.
OFFSPRING_MODE_PULLDOWN_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the offspring mode pulldown has changed.
OFFSPRING_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
The offspring organism shown in a view has changed from one organism to another.
okButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
oldBars - Variable in class org.concord.util.Gauge
 
oldGauges - Static variable in class org.concord.util.BarGraph
 
onExit() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
onFatherGameteChanged() - Method in class org.concord.biologica.ui.FertilizationModel
React to the father selected gamete changing
onMotherGameteChanged() - Method in class org.concord.biologica.ui.FertilizationModel
React to the mother selected gamete changing
onStart() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
openButton - Variable in class org.concord.pedagogica.ui.LogView
 
openDocument() - Method in class org.concord.util.Editor
 
openFile(String, String) - Method in class org.concord.util.Editor
 
openLogDirectory - Variable in class org.concord.pedagogica.ui.LogView
 
operand - Variable in class org.concord.util.script.UnaryExpression
 
operatorString() - Method in class org.concord.util.script.BinaryExpression
 
operatorString() - Method in class org.concord.util.script.NEExpression
 
operatorString() - Method in class org.concord.util.script.OrExpression
 
operatorString() - Method in class org.concord.util.script.UnaryExpression
 
operatorString() - Method in class org.concord.util.script.NotExpression
 
operatorString() - Method in class org.concord.util.script.BitAndExpression
 
operatorString() - Method in class org.concord.util.script.AndExpression
 
operatorString() - Method in class org.concord.util.script.ModulusExpression
 
operatorString() - Method in class org.concord.util.script.NegateExpression
 
operatorString() - Method in class org.concord.util.script.BitOrExpression
 
operatorString() - Method in class org.concord.util.script.LEExpression
 
operatorString() - Method in class org.concord.util.script.MinusExpression
 
operatorString() - Method in class org.concord.util.script.BitXorExpression
 
operatorString() - Method in class org.concord.util.script.EQExpression
 
operatorString() - Method in class org.concord.util.script.GEExpression
 
operatorString() - Method in class org.concord.util.script.PlusExpression
 
operatorString() - Method in class org.concord.util.script.MultiplyExpression
 
operatorString() - Method in class org.concord.util.script.LTExpression
 
operatorString() - Method in class org.concord.util.script.GTExpression
 
operatorString() - Method in class org.concord.util.script.DivideExpression
 
operatorString() - Method in class org.concord.util.script.BitNotExpression
 
ops - Variable in class org.concord.util.script.BinaryExpression
 
OrExpression - class org.concord.util.script.OrExpression.
 
OrExpression() - Constructor for class org.concord.util.script.OrExpression
 
org.concord.biologica.datasupport - package org.concord.biologica.datasupport
 
org.concord.biologica.engine - package org.concord.biologica.engine
 
org.concord.biologica.test - package org.concord.biologica.test
 
org.concord.biologica.ui - package org.concord.biologica.ui
 
org.concord.collisions.engine - package org.concord.collisions.engine
 
org.concord.collisions.event - package org.concord.collisions.event
 
org.concord.collisions.ui - package org.concord.collisions.ui
 
org.concord.flash.player - package org.concord.flash.player
 
org.concord.flash.player.builtin - package org.concord.flash.player.builtin
 
org.concord.flash.player.event - package org.concord.flash.player.event
 
org.concord.flash.player.fill - package org.concord.flash.player.fill
 
org.concord.flash.util - package org.concord.flash.util
 
org.concord.molecular.engine - package org.concord.molecular.engine
 
org.concord.molecular.ui - package org.concord.molecular.ui
 
org.concord.pedagogica - package org.concord.pedagogica
 
org.concord.pedagogica.engine - package org.concord.pedagogica.engine
 
org.concord.pedagogica.graph - package org.concord.pedagogica.graph
 
org.concord.pedagogica.ui - package org.concord.pedagogica.ui
 
org.concord.pedagogica.ui.event - package org.concord.pedagogica.ui.event
 
org.concord.util - package org.concord.util
 
org.concord.util.beans - package org.concord.util.beans
 
org.concord.util.event - package org.concord.util.event
 
org.concord.util.script - package org.concord.util.script
 
org.concord.util.script.event - package org.concord.util.script.event
 
Organism - class org.concord.biologica.engine.Organism.
This class represents an organism.
ORGANISM - Static variable in class org.concord.biologica.engine.EngineStrings
 
ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
The organism shown in a view has changed from one organism to another.
ORGANISM_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
An Organism object was added.
ORGANISM_ADDED_TO_VIEW - Static variable in class org.concord.biologica.ui.UIProp
An Organism object has been added to a view.
ORGANISM_ALLELE - Static variable in class org.concord.biologica.engine.EngineStrings
 
ORGANISM_ALLELE - Static variable in class org.concord.biologica.ui.UIProp
The OrganismAllele object has been changed in a view, most likely in the DNA View.
ORGANISM_ALLELE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
An OrganismAllele object was added to an OrganismChromosome.
ORGANISM_ALLELE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ORGANISM_ALLELE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ORGANISM_ALLELE_PAIR - Static variable in class org.concord.biologica.ui.UIProp
The OrganismAllelePair object has been changed in a view, most likely in the DNA View.
ORGANISM_ALLELE_PAIR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_PAIR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_PAIR_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_PAIR_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ALLELE_PAIR_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ORGANISM_ALLELE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
An OrganismAllele object was removed from an OrganismChromosome.
ORGANISM_CHROMOSOME_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Organism chromosome added.
ORGANISM_CHROMOSOME_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ORGANISM_CHROMOSOME_PAIR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_PAIR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_PAIR_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_PAIR_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_CHROMOSOME_PAIR_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ORGANISM_CHROMOSOME_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Organism chromosome removed.
ORGANISM_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ORGANISM_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_GENOTYPE_AND_NOT_PHENOTYPE - Static variable in class org.concord.biologica.engine.EngineProp
The genotype of an organism has changed but the phenotype did not change.
ORGANISM_GENOTYPE_AND_PHENOTYPE - Static variable in class org.concord.biologica.engine.EngineProp
The genotype and phenotype of an organism have changed.
ORGANISM_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_IMAGE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Organism image added.
ORGANISM_IMAGE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ORGANISM_IMAGE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_IMAGE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_IMAGE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_IMAGE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
ORGANISM_IMAGE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Organism image removed.
ORGANISM_IMAGE_SIZE - Static variable in class org.concord.biologica.ui.UIProp
The organism image size for a view has changed.
ORGANISM_IMAGES_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The organism images visibility in the pedigree view has changed.
ORGANISM_LAYOUT_STYLE - Static variable in class org.concord.biologica.ui.UIProp
Organism layout style, used in MultipleOrganismView.
ORGANISM_LAYOUT_STYLE_LEFT_TO_RIGHT_NO_WRAP - Static variable in class org.concord.biologica.ui.MultipleOrganismView
An alternative organism layout style for this view - left to right with no wrap (e.g.
ORGANISM_LAYOUT_STYLE_LEFT_TO_RIGHT_WRAP - Static variable in class org.concord.biologica.ui.MultipleOrganismView
Default organism layout style for this view - left to right and wrap (e.g.
ORGANISM_LAYOUT_STYLE_TOP_TO_BOTTOM_NO_WRAP - Static variable in class org.concord.biologica.ui.MultipleOrganismView
An alternative organism layout style for this view - top to bottom with no wrap (e.g.
ORGANISM_LAYOUT_STYLE_TOP_TO_BOTTOM_WRAP - Static variable in class org.concord.biologica.ui.MultipleOrganismView
An alternative organism layout style for this view - top to bottom and wrap (e.g.
ORGANISM_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
ORGANISM_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
An Organism object was removed.
ORGANISM_REMOVED_FROM_VIEW - Static variable in class org.concord.biologica.ui.UIProp
An Organism object has been removed from a view and deselected.
ORGANISM_VIEW_HEIGHT_PERCENTAGE - Static variable in class org.concord.biologica.ui.UIProp
The percentage of a sex view devoted to organism views.
Organism(Organism, Organism, String) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism from 2 parents, randomly choosing the parent chromosome from which to copy alleles for each child chromosome.
Organism(Organism, Organism, String, boolean) - Constructor for class org.concord.biologica.engine.Organism
 
Organism(Organism, Organism, String, int) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism from 2 parents, randomly choosing the parent chromosome from which to copy alleles for each child chromosome.
Organism(Organism, Organism, String, int, boolean) - Constructor for class org.concord.biologica.engine.Organism
 
Organism(World, int, String, Species) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism of the specified sex, randomly choosing the alleles of the chromosomes.
Organism(World, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Organism
Create a new organism and start handling XML parsing events to set the properties of this object.
Organism(World, String, int, Species) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism in the given world from a species definition, randomly choosing the sex and genetic makeup of the organism.
Organism(World, String, Species, int, String) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism of the specified species using the given allele string to create the correct alleles.
Organism(World, String, Species, Organism, Organism, Vector) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism of the specified species using the given ChromosomeSpecification objects to create the correct alleles.
Organism(World, String, Species, Vector) - Constructor for class org.concord.biologica.engine.Organism
Creates a new organism of the specified species using the given ChromosomeSpecification objects to create the correct alleles.
OrganismAllele - class org.concord.biologica.engine.OrganismAllele.
This class represents an organism allele - an allele within one organism.
OrganismAllele(OrganismChromosome, OrganismAllele) - Constructor for class org.concord.biologica.engine.OrganismAllele
Create a new organism allele given an organism chromosome and an organism allele to copy.
OrganismAllele(OrganismChromosome, SpeciesAllele) - Constructor for class org.concord.biologica.engine.OrganismAllele
Create a new organism allele given an organism chromosome parent and the species allele to use.
OrganismAllele(OrganismChromosome, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.OrganismAllele
Create a new organism allele and start handling XML parsing events to set the properties of this object.
OrganismAlleleControl - class org.concord.biologica.ui.OrganismAlleleControl.
This class represents an organism allele combobox in BioLogica.
OrganismAlleleControl(ChromosomeView) - Constructor for class org.concord.biologica.ui.OrganismAlleleControl
Creates an AlleleComboBox given a ChromosomeView
organismAlleleControlChanged(OrganismAlleleControl, OrganismAllele, String) - Method in class org.concord.biologica.ui.ChromosomeView
Handle combo box item changed events.
OrganismAllelePair - class org.concord.biologica.engine.OrganismAllelePair.
This class represents a pair of organism alleles or, in the case of sex chromosomes, it can represent a single allele on a single chromosome.
OrganismAllelePair(OrganismChromosomePair, OrganismAllele, OrganismAllele) - Constructor for class org.concord.biologica.engine.OrganismAllelePair
Create a new organism allele pair from the two given organism alleles.
OrganismAllelePair(OrganismChromosomePair, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.OrganismAllelePair
Create a new organism allele pair and start handling XML parsing events to set the properties of this object.
OrganismChromosome - class org.concord.biologica.engine.OrganismChromosome.
This class represents an organism chromosome - a chromosome which has a length and some organism alleles.
OrganismChromosome(Organism, ChromosomeSpecification) - Constructor for class org.concord.biologica.engine.OrganismChromosome
Create a new organism chromosome from a chromosome specification, choosing alleles based on the chromosome specification.
OrganismChromosome(Organism, OrganismChromosome) - Constructor for class org.concord.biologica.engine.OrganismChromosome
Create a new organism chromosome with another organism chromosome as a model.
OrganismChromosome(Organism, SpeciesChromosome) - Constructor for class org.concord.biologica.engine.OrganismChromosome
Create a new organism chromosome from a species chromosome, randomly choosing alleles from the genes of the species chromosome.
OrganismChromosome(Organism, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.OrganismChromosome
Create a new organism chromosome and start handling XML parsing events to set the properties of this object.
OrganismChromosomePair - class org.concord.biologica.engine.OrganismChromosomePair.
This class represents a pair of organism chromosomes, either a pair of autosomes or a pair of sex chromosomes.
OrganismChromosomePair(Organism, OrganismChromosome, OrganismChromosome) - Constructor for class org.concord.biologica.engine.OrganismChromosomePair
Create a new organism chromosome pair from the two given organism chromosomes.
OrganismChromosomePair(Organism, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.OrganismChromosomePair
Create a new organism chromosome pair and start handling XML parsing events to set the properties of this object.
OrganismImage - class org.concord.biologica.engine.OrganismImage.
This class represents a portion of the image used to draw an organism.
OrganismImage(Organism, SpeciesImage) - Constructor for class org.concord.biologica.engine.OrganismImage
Creates a new organism image given an organism and a species image.
OrganismImage(Organism, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.OrganismImage
Create a new organism image and start handling XML parsing events to set the properties of this object.
organismImageDirty - Variable in class org.concord.biologica.engine.OrganismImage
 
organismImageSize - Variable in class org.concord.biologica.ui.OrganismView
Organism image size, used when drawing organisms.
OrganismView - class org.concord.biologica.ui.OrganismView.
The basic organism view of BioLogica, used to hold all the code that is common to all views that draw organisms in a phenotypical manner.
OrganismView() - Constructor for class org.concord.biologica.ui.OrganismView
Creates an organism view.
ORIG_CELL_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
Types of chromosome models
OS_NAME - Static variable in class org.concord.util.PathDialog
 
outArcs - Variable in class org.concord.pedagogica.engine.ActivityNode
 
OUTDOWN - Static variable in class org.concord.flash.player.FButton
 
output - Variable in class org.concord.util.LogProcess
 
OVER_STATE - Static variable in class org.concord.flash.player.FButton
 
OVERDOWN - Static variable in class org.concord.flash.player.FButton
 
OVERUP - Static variable in class org.concord.flash.player.FButton
 
owner - Variable in class org.concord.util.script.ScriptThread
 

P

P_STRAND_ONE - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
Types of chromosome model strands
P_STRAND_TWO - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
pacifier - Static variable in class org.concord.pedagogica.ui.RunActivity
 
packageDirectory(String, char) - Method in class org.concord.util.script.ScriptClassLoader
 
pad - Variable in class org.concord.pedagogica.ui.TabularView
 
pageSet(ActionEvent) - Method in class org.concord.pedagogica.ui.HTMLView
 
paint(BufferedImage, AffineTransform, ColorTransform) - Method in class org.concord.flash.player.FComponent
 
paint(BufferedImage, AffineTransform, ColorTransform) - Method in class org.concord.flash.player.FSprite
 
paint(Graphics) - Method in class org.concord.collisions.engine.JWorldElement
 
paint(Graphics) - Method in class org.concord.collisions.engine.JRigidBox
 
paint(Graphics) - Method in class org.concord.collisions.engine.JWall
 
paint(Graphics) - Method in class org.concord.collisions.engine.JDaemon
 
paint(Graphics) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
paint(Graphics) - Method in class org.concord.collisions.engine.JAtom
 
paint(Graphics) - Method in class org.concord.collisions.engine.JBooster
 
paint(Graphics) - Method in class org.concord.collisions.ui.PassiveElement
 
paint(Graphics) - Method in class org.concord.collisions.ui.PassiveText
 
paint(Graphics) - Method in class org.concord.collisions.ui.PassiveLine
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCForce
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCFrictionForce
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCConstantForce
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCImpulseForce
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCGravityForce
 
paint(Graphics, JWorldElement) - Method in class org.concord.collisions.engine.CCBedSpringForce
 
paint(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeObject
Paint the object with the given Graphics object on the given PedigreeOrganismView.
paint(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeOrganism
Paint the object with the given Graphics object on the given PedigreeOrganismView.
paint(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeFamily
Paint the Families and Organisms with the given Graphics object on the given PedigreeOrganismView.
paintAllele(Graphics, OrganismAllele, OrganismAllele, int, int) - Method in class org.concord.biologica.ui.DNAView
Paint a single allele
paintAlleleList(Graphics, CellArc) - Method in class org.concord.biologica.ui.BigMeiosisView
 
paintAtom(Graphics) - Method in class org.concord.collisions.engine.JAtom
 
paintBackground(Graphics, Rectangle) - Method in class org.concord.biologica.ui.UIView
Paint the background of this view using the given Graphics and bounds rectangle.
paintBase(Graphics, byte, int, int, boolean, boolean) - Method in class org.concord.biologica.ui.DNAView
Paint a single base pair
paintBorder(Component, Graphics, int, int, int, int) - Method in class org.concord.pedagogica.ui.CellBorder
 
paintBottom(Component, Graphics, int, int, int, int) - Method in class org.concord.pedagogica.ui.CellBorder
 
paintComponent(Graphics) - Method in class org.concord.util.BarGraph
 
paintComponent(Graphics) - Method in class org.concord.util.Gauge
 
paintComponent(Graphics) - Method in class org.concord.util.LineGraph
 
paintComponent(Graphics) - Method in class org.concord.biologica.ui.ChromosomeView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.PedigreeView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.BigFertilizationView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.WelcomeView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.StaticOrganismView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.SmallMeiosisView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.DNAView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.SmallFertilizationView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.MultipleOrganismView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.SexOrganismView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.biologica.ui.BigMeiosisView
 
paintComponent(Graphics) - Method in class org.concord.biologica.ui.SexView
Draw the graphics in this view.
paintComponent(Graphics) - Method in class org.concord.collisions.ui.DataCrossPanel
 
paintComponent(Graphics) - Method in class org.concord.collisions.ui.GUIPanel
shouldn't be called directly
paintComponent(Graphics) - Method in class org.concord.flash.player.FFlash
 
paintComponent(Graphics) - Method in class org.concord.pedagogica.ui.CCXMLText
 
paintComponent(Graphics) - Method in class org.concord.pedagogica.ui.ActivityView
 
paintComponent(Graphics) - Method in class org.concord.pedagogica.ui.TableInputView
 
paintComponent(Graphics) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
paintConnections(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeObject
Paint the connections.
paintConnections(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeLevel
Paint the level's connections given PedigreeOrganismView.
paintConnections(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeFamily
Paint the connections with the given Graphics object on the given PedigreeOrganismView.
paintForce(Graphics, float, float, JWorldElement) - Method in class org.concord.collisions.engine.CCConstantForce
 
paintForces(Graphics) - Method in class org.concord.collisions.engine.JAtom
 
paintForces(Graphics, JPartWorld) - Method in class org.concord.collisions.engine.CCDefaultForceCalculator
 
paintForces(Graphics, JPartWorld) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
paintForces(Graphics, JPartWorld) - Method in interface org.concord.collisions.engine.CCForceCalculator
 
paintLines(Graphics, Color) - Method in class org.concord.biologica.ui.OrganismAlleleControl
Tell organism allele control to paint its lines.
paintLines(Graphics, Color, int, int, int) - Method in class org.concord.biologica.ui.OrganismAlleleControl
 
paintOrganisms(Graphics, PedigreeOrganismView, Trait, int, SelectionSet, SelectionSet) - Method in class org.concord.biologica.ui.PedigreeLevel
Paint the level's PedigreeOrganisms given PedigreeOrganismView.
paintRight(Component, Graphics, int, int, int, int) - Method in class org.concord.pedagogica.ui.CellBorder
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveElement
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveText
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveIcon
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveOval
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveGrid
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveLine
 
paintSpecific(Graphics) - Method in class org.concord.collisions.ui.PassiveRect
 
paintTrace(Graphics) - Method in class org.concord.collisions.engine.JAtom
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JRigidBox
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JWall
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JDaemon
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JAtom
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
panelInfoSupport() - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
panelInfoSupport() - Method in class org.concord.collisions.ui.PassiveElement
 
panelInfoSupport() - Method in interface org.concord.collisions.ui.CCDraggable
 
ParameterDescriptor - class org.concord.util.beans.ParameterDescriptor.
The ParameterDescriptor class allows bean implementors to provide additional information on each of their parameters, beyond the low level type information provided by the java.lang.reflect.Method class.
ParameterDescriptor() - Constructor for class org.concord.util.beans.ParameterDescriptor
Public default constructor.
parameters - Variable in class org.concord.util.script.MethodDeclaration
 
parent - Variable in class org.concord.flash.player.FScriptObject
 
parent - Variable in class org.concord.pedagogica.engine.ActivityScript
 
PARENT_FAMILY - Static variable in class org.concord.biologica.engine.EngineProp
The parent family of this organism has changed.
parentNode - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
parentNode - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
parse(String) - Method in class org.concord.util.Query
 
parse(String, Reader, NameStack) - Method in class org.concord.util.script.ECMA
 
parseAlleleString(int, String) - Method in class org.concord.biologica.engine.Species
Parse an allele string to create a ChromosomeSpecification
parseError(ActivityScript) - Method in interface org.concord.pedagogica.engine.ActivityErrorHandler
 
parseError(ActivityScript) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
parseError(ActivityScript) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
parseError(Throwable, int, int, int, int) - Method in interface org.concord.util.script.ScriptError
 
parseError(Throwable, int, int, int, int) - Method in class org.concord.pedagogica.engine.ActivityScript
 
parseFile(ScriptFile, NameStack) - Method in interface org.concord.util.script.ScriptRuntime
 
parseFile(ScriptFile, NameStack) - Method in class org.concord.util.script.ECMA
 
parseInput(ActivityScript) - Method in class org.concord.pedagogica.engine.NodeAccess
 
parseInput(InputStream) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
parseInput(InputStream) - Method in class org.concord.pedagogica.engine.Activity
 
parseInput(InputStream) - Method in class org.concord.pedagogica.engine.NodeAccess
 
parseInput(InputStream) - Method in class org.concord.pedagogica.ui.ActivityView
 
parser - Variable in class org.concord.util.LogProcess
 
parser - Variable in class org.concord.pedagogica.ui.LogView
 
parseText(String, String, NameStack) - Method in interface org.concord.util.script.ScriptRuntime
 
parseText(String, String, NameStack) - Method in class org.concord.util.script.ECMA
 
PART_BODIES - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_COUNT - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_DEAD - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_FIRE - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
part_fract - Variable in class org.concord.collisions.engine.VelDistFraction
 
PART_HEADS - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_INVISIBLE - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_PLATES - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_SCALES - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_UNKNOWN - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PART_WINGS - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
partNames - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
PassiveElement - class org.concord.collisions.ui.PassiveElement.
 
PassiveElement() - Constructor for class org.concord.collisions.ui.PassiveElement
 
PassiveElementBeanInfo - class org.concord.collisions.ui.PassiveElementBeanInfo.
 
PassiveElementBeanInfo() - Constructor for class org.concord.collisions.ui.PassiveElementBeanInfo
 
PassiveGrid - class org.concord.collisions.ui.PassiveGrid.
 
PassiveGrid(int, int, int, int) - Constructor for class org.concord.collisions.ui.PassiveGrid
 
PassiveIcon - class org.concord.collisions.ui.PassiveIcon.
 
PassiveIcon(String) - Constructor for class org.concord.collisions.ui.PassiveIcon
 
PassiveIconBeanInfo - class org.concord.collisions.ui.PassiveIconBeanInfo.
 
PassiveIconBeanInfo() - Constructor for class org.concord.collisions.ui.PassiveIconBeanInfo
 
PassiveLine - class org.concord.collisions.ui.PassiveLine.
 
PassiveLine(int, int, int, int, int) - Constructor for class org.concord.collisions.ui.PassiveLine
 
PassiveLine(int, int, int, int, int, int) - Constructor for class org.concord.collisions.ui.PassiveLine
 
PassiveOval - class org.concord.collisions.ui.PassiveOval.
 
PassiveOval() - Constructor for class org.concord.collisions.ui.PassiveOval
 
PassiveRect - class org.concord.collisions.ui.PassiveRect.
 
PassiveRect() - Constructor for class org.concord.collisions.ui.PassiveRect
 
PassiveText - class org.concord.collisions.ui.PassiveText.
 
PassiveText(String) - Constructor for class org.concord.collisions.ui.PassiveText
 
PassiveTextBeanInfo - class org.concord.collisions.ui.PassiveTextBeanInfo.
 
PassiveTextBeanInfo() - Constructor for class org.concord.collisions.ui.PassiveTextBeanInfo
 
PASTE - Static variable in class org.concord.pedagogica.ui.ActivityView
 
pasteButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
pasteEdit() - Method in class org.concord.util.Editor
 
pasteItems() - Method in class org.concord.pedagogica.ui.ActivityView
 
PathDialog - class org.concord.util.PathDialog.
 
PathDialog(JFrame) - Constructor for class org.concord.util.PathDialog
 
pathList - Variable in class org.concord.util.PathDialog
 
pathList - Variable in class org.concord.pedagogica.engine.LogModel
 
pathList - Variable in class org.concord.pedagogica.ui.LogView
 
paths - Variable in class org.concord.util.PathDialog
 
PathStrings - class org.concord.biologica.engine.PathStrings.
PathStrings is a class containing static references to path strings used in various parts of BioLogica, including the engine.
PathStrings() - Constructor for class org.concord.biologica.engine.PathStrings
 
PAULINGIUM - Static variable in class org.concord.molecular.ui.MolecularView
 
pause - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
paused - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
PedAgogica - class org.concord.pedagogica.PedAgogica.
This class represents the main class for starting up PedAgogica.
PedAgogica() - Constructor for class org.concord.pedagogica.PedAgogica
 
PedAgogica(String) - Constructor for class org.concord.pedagogica.PedAgogica
 
PEDIGREE - Static variable in class org.concord.biologica.ui.Tool
 
PEDIGREE_NAME - Static variable in class org.concord.biologica.ui.Tool
 
PEDIGREE_SYMBOL_FIRST_COLOR - Static variable in class org.concord.biologica.engine.EngineProp
The first color used by a characteristic in drawing its symbol in a pedigree view.
PEDIGREE_SYMBOL_FIRST_COLOR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_SYMBOL_FIRST_COLOR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_SYMBOL_FORWARD_SLASH - Static variable in class org.concord.biologica.engine.Characteristic
 
PEDIGREE_SYMBOL_FORWARD_SLASH_STRING - Static variable in class org.concord.biologica.engine.Characteristic
 
PEDIGREE_SYMBOL_SECOND_COLOR - Static variable in class org.concord.biologica.engine.EngineProp
The second color used by a characteristic in drawing its symbol in a pedigree view.
PEDIGREE_SYMBOL_SECOND_COLOR_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_SYMBOL_SECOND_COLOR_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_SYMBOL_SOLID_COLOR - Static variable in class org.concord.biologica.engine.Characteristic
Pedigree symbol type values, used to determine how to draw pedigree symbols.
PEDIGREE_SYMBOL_SOLID_COLOR_STRING - Static variable in class org.concord.biologica.engine.Characteristic
 
PEDIGREE_SYMBOL_TYPE - Static variable in class org.concord.biologica.engine.EngineProp
The symbol type used by a characteristic in drawing its symbol in a pedigree view.
PEDIGREE_SYMBOL_TYPE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_SYMBOL_TYPE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
PEDIGREE_TOOL_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the pedigree tool has enabled.
PEDIGREE_TOOL_PICK_ON_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
Pedigree tool was used to pick on an organism.
PEDIGREE_TOOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the pedigree tool has changed.
PedigreeFamily - class org.concord.biologica.ui.PedigreeFamily.
An object that manages the state for a family in the pedigree view.
PedigreeFamily(PedigreeOrganismView, Family, PedigreeOrganism, PedigreeOrganism, Vector) - Constructor for class org.concord.biologica.ui.PedigreeFamily
Creates a new pedigree family
PedigreeLevel - class org.concord.biologica.ui.PedigreeLevel.
An object that manages the contents and layout of a generation in the pedigree view.
PedigreeLevel() - Constructor for class org.concord.biologica.ui.PedigreeLevel
Creates a new pedigree level.
PedigreeObject - class org.concord.biologica.ui.PedigreeObject.
An object that manages the state for a graphical object shown in the pedigree view.
PedigreeObject() - Constructor for class org.concord.biologica.ui.PedigreeObject
Default constructor
PedigreeOrganism - class org.concord.biologica.ui.PedigreeOrganism.
An object that manages the state for an organism in the pedigree view.
PedigreeOrganism(Organism, int, int, int, int) - Constructor for class org.concord.biologica.ui.PedigreeOrganism
Creates a new pedigree organism.
PedigreeOrganismView - class org.concord.biologica.ui.PedigreeOrganismView.
The pedigree organism view of BioLogica.
PedigreeOrganismView() - Constructor for class org.concord.biologica.ui.PedigreeOrganismView
Creates a pedigree organism view.
pedigreePracticeView - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
PedigreePracticeView - class org.concord.biologica.ui.PedigreePracticeView.
 
PedigreePracticeView(JFrame) - Constructor for class org.concord.biologica.ui.PedigreePracticeView
 
pedigreeToolCursor - Static variable in class org.concord.biologica.ui.Tool
 
pedigreeToolImageIcon - Static variable in class org.concord.biologica.ui.Tool
 
PedigreeView - class org.concord.biologica.ui.PedigreeView.
The pedigree view of BioLogica.
PedigreeView() - Constructor for class org.concord.biologica.ui.PedigreeView
Creates a pedigree view.
peek() - Method in class org.concord.flash.player.StackFrame4
 
peek() - Method in class org.concord.flash.player.StackFrame5
 
pendingsImages - Static variable in class org.concord.flash.player.FMovieBuilder
 
PersistenceDelegate - class org.concord.util.beans.PersistenceDelegate.
The PersistenceDelegate class takes the responsibility for expressing the state of an instance of a given class in terms of the methods in the class's public API.
PersistenceDelegate() - Constructor for class org.concord.util.beans.PersistenceDelegate
 
PHE - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Phenylalanine
PHENYLALANINE - Static variable in class org.concord.biologica.engine.AminoAcid
Phenylalanine
PI - Static variable in class org.concord.flash.player.builtin.FMath
 
pick(int, int) - Method in class org.concord.biologica.ui.OrganismAlleleControl
Is this control at the x,y coordinates specified?
pick(int, int) - Method in class org.concord.biologica.ui.PedigreeObject
Pick this object, determining if the given x,y location is on the object.
pickForSnip(int, int) - Method in class org.concord.biologica.ui.PedigreeFamily
Pick this object, determining if the given x,y location is on the object.
placeChildren() - Method in class org.concord.biologica.ui.PedigreeObject
Place children.
placeChildren() - Method in class org.concord.biologica.ui.PedigreeFamily
Loop through the children and set their relative placement
placeConnections() - Method in class org.concord.biologica.ui.PedigreeObject
Place the connections.
placeConnections() - Method in class org.concord.biologica.ui.PedigreeLevel
Place the connections at this level.
placeConnections() - Method in class org.concord.biologica.ui.PedigreeFamily
Place the connections.
placeFamilies(Dimension) - Method in class org.concord.biologica.ui.PedigreeLevel
Place all the families at this level.
placement - Variable in class org.concord.pedagogica.engine.NodeAccess
 
placement - Variable in class org.concord.pedagogica.ui.RunActivity
 
platform - Static variable in class org.concord.pedagogica.ui.CustomQuestion
 
platform - Variable in class org.concord.pedagogica.ui.ActivityView
 
play() - Method in class org.concord.flash.player.FFlash
Starts playing the movie
play() - Method in class org.concord.flash.player.FMovieClip
Start playing at the next frame
play() - Method in class org.concord.flash.player.FMovie
 
playAnimationBackward() - Method in class org.concord.biologica.ui.BigFertilizationView
Play animation backward
playAnimationBackward() - Method in class org.concord.biologica.ui.BigMeiosisView
Play animation backward
playAnimationBackwardFast() - Method in class org.concord.biologica.ui.BigFertilizationView
Play animation backward fast
playAnimationBackwardFast() - Method in class org.concord.biologica.ui.BigMeiosisView
Play animation backward fast
playAnimationForward() - Method in class org.concord.biologica.ui.BigFertilizationView
Play animation forward
playAnimationForward() - Method in class org.concord.biologica.ui.SmallMeiosisView
Play animation forward
playAnimationForward() - Method in class org.concord.biologica.ui.SmallFertilizationView
Play animation forward
playAnimationForward() - Method in class org.concord.biologica.ui.BigMeiosisView
Play animation forward
playAnimationForwardFast() - Method in class org.concord.biologica.ui.BigFertilizationView
Play animation forward fast
playAnimationForwardFast() - Method in class org.concord.biologica.ui.BigMeiosisView
Play animation forward fast
playChannel(int) - Method in class org.concord.collisions.engine.JPartWorld
play default note on given channel
playChannel(int, int) - Method in class org.concord.collisions.engine.JPartWorld
play default note on given channel
playCrossoverAnimation() - Method in class org.concord.biologica.ui.BigMeiosisView
Play the crossover animation
PLOIDY_NUMBER - Static variable in class org.concord.biologica.engine.EngineProp
PLOIDY_NUMBER simple property name.
PLOIDY_NUMBER_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
PLOIDY_NUMBER_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
PlusExpression - class org.concord.util.script.PlusExpression.
The PlusExpression class implements the semantic node for multiply.
PlusExpression() - Constructor for class org.concord.util.script.PlusExpression
 
pop() - Method in class org.concord.util.script.NameStack
 
pop() - Method in class org.concord.flash.player.StackFrame4
 
pop() - Method in class org.concord.flash.player.StackFrame5
 
pop() - Method in class org.concord.flash.player.builtin.FArray
 
popBoolean() - Method in class org.concord.flash.player.StackFrame4
 
popBoolean() - Method in class org.concord.flash.player.StackFrame5
 
popFloat() - Method in class org.concord.flash.player.StackFrame4
 
popFloat() - Method in class org.concord.flash.player.StackFrame5
 
popFrame() - Method in class org.concord.util.script.ScriptObject
 
popFrame() - Method in class org.concord.util.script.ScriptThread
 
popInt() - Method in class org.concord.flash.player.StackFrame4
 
popInt() - Method in class org.concord.flash.player.StackFrame5
 
popReturnNode() - Method in class org.concord.pedagogica.engine.ActivityNode
 
popup - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
post - Variable in class org.concord.pedagogica.engine.Logging
 
posx - Variable in class org.concord.collisions.ui.PassiveElement
 
posy - Variable in class org.concord.collisions.ui.PassiveElement
 
potentialEnergy - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
pow(double, double) - Method in class org.concord.flash.player.builtin.FMath
 
pr() - Static method in class org.concord.collisions.engine.JPartWorld
 
pr(String) - Static method in class org.concord.collisions.engine.JPartWorld
 
practiceView - Variable in class org.concord.biologica.ui.BioLogicaFrame
 
PracticeView - class org.concord.biologica.ui.PracticeView.
 
PracticeView(JFrame) - Constructor for class org.concord.biologica.ui.PracticeView
 
preferredHeight - Variable in class org.concord.biologica.ui.UIView
Preferred height of this view.
preferredSize - Variable in class org.concord.pedagogica.ui.ActivityView
 
preferredWidth - Variable in class org.concord.biologica.ui.UIView
Preferred width of this view.
prefix - Variable in class org.concord.util.script.HandlerDeclaration
 
PREFIX_BREAK - Static variable in class org.concord.util.PathDialog
 
prefixTable - Variable in class org.concord.util.PathDialog
 
prefixTable - Variable in class org.concord.pedagogica.ui.VariableDialog
 
preloadSpeciesImages(Species) - Method in class org.concord.biologica.ui.OrganismView
Preload the species images for the given species at the current image size.
preloadSpeciesImageSize(int) - Method in class org.concord.biologica.engine.SpeciesImage
 
pressedState - Variable in class org.concord.collisions.engine.JWorldElement
 
pressTime - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
prevFrame() - Method in class org.concord.flash.player.FMovieClip
Sends the playhead to the previous frame and stops it
print() - Method in class org.concord.util.script.NameStack
 
print(Frame, Component[], String) - Method in class org.concord.pedagogica.ui.DefaultPrinter
 
print(Frame, Component, String) - Method in class org.concord.pedagogica.ui.DefaultPrinter
 
print(Frame, Vector, String) - Method in class org.concord.pedagogica.ui.DefaultPrinter
 
print(Object) - Method in interface org.concord.util.script.ScriptRuntime
The print method can be called from inside the script by using "print(someString)".
print(Object) - Method in class org.concord.util.script.ECMA
The print method can be called from inside the script by using "easl.print(someString)".
printAxisInfo() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
printError(String, Throwable) - Method in interface org.concord.util.script.ScriptRuntime
The printError method is called when there is an exception while either parsing or interpreting.
printError(String, Throwable) - Method in class org.concord.util.script.ECMA
The printError method is called when there is an exception while either parsing or interpreting.
printLine(Object) - Method in interface org.concord.util.script.ScriptRuntime
 
printLine(Object) - Method in class org.concord.util.script.ECMA
 
println(String) - Static method in class org.concord.util.Debug
Print out a message to our output stream.
println(String) - Static method in class org.concord.biologica.engine.Debug
Print out a message to our output stream.
printProperties - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
printSessionData(String) - Method in class org.concord.util.LogProcess
 
printStackTrace(Throwable) - Static method in class org.concord.util.Debug
Print a stack trace for the exception passed in to the logging stream.
printStackTrace(Throwable) - Static method in class org.concord.biologica.engine.Debug
Print a stack trace for the exception passed in to the logging stream.
printWriter - Variable in class org.concord.pedagogica.ui.ActivityView
 
PRO - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Proline
process - Variable in class org.concord.pedagogica.ui.ActivityView
 
process(int, String) - Method in class org.concord.util.LogProcess
 
process(String, String) - Method in class org.concord.util.Query
 
processEvent() - Method in class org.concord.util.script.Script
 
processEventHalted - Variable in class org.concord.util.script.Script
 
processingInstruction(String, String) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
processLogFiles(Vector) - Method in class org.concord.pedagogica.ui.LogView
 
processPendingTextEdits() - Method in class org.concord.biologica.ui.PedigreeView
Process pending text edit control modifications before allowing something else to occur in the user interface.
processPendingTextEdits() - Method in class org.concord.biologica.ui.ObjectPropertiesView
Process pending text edit control modifications before allowing something else to occur in the user interface.
processString(String) - Method in class org.concord.util.script.StringLiteral
 
PROLINE - Static variable in class org.concord.biologica.engine.AminoAcid
Proline
properties - Variable in class org.concord.molecular.ui.MolecularView
 
properties - Variable in class org.concord.pedagogica.ui.ActivityView
 
propertiesFile - Variable in class org.concord.pedagogica.ui.ActivityView
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.Species
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.OrganismImage
Handle property change events.
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Handle property change events, mostly DELETED events.
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.OrganismAllelePair
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.engine.SpeciesImageRow
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.ChromosomeView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.PedigreeView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.TreeViewNode
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.OrganismAlleleControl
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.StaticOrganismView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.FertilizationModel
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.MeiosisModel
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.DNAView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.SelectionSet
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.AllInOneView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.TreeView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.MultipleOrganismView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.SexOrganismView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.biologica.ui.SexView
Handle property change events
propertyChange(PropertyChangeEvent) - Method in class org.concord.collisions.engine.JWorldElement
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.collisions.ui.DataCrossPanel
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.molecular.ui.MolecularView
 
propertyChange(PropertyChangeEvent) - Method in class org.concord.pedagogica.ui.TableInputView
 
PropertyChangeEvent - class org.concord.util.beans.PropertyChangeEvent.
A "PropertyChange" event gets delivered whenever a bean changes a "bound" or "constrained" property.
PropertyChangeEvent(Object, String, Object, Object) - Constructor for class org.concord.util.beans.PropertyChangeEvent
Constructs a new PropertyChangeEvent.
PropertyDescriptor - class org.concord.util.beans.PropertyDescriptor.
A PropertyDescriptor describes one property that a Java Bean exports via a pair of accessor methods.
PropertyDescriptor(String, Class) - Constructor for class org.concord.util.beans.PropertyDescriptor
Constructs a PropertyDescriptor for a property that follows the standard Java convention by having getFoo and setFoo accessor methods.
PropertyDescriptor(String, Class, String, String) - Constructor for class org.concord.util.beans.PropertyDescriptor
This constructor takes the name of a simple property, and method names for reading and writing the property.
PropertyDescriptor(String, Method, Method) - Constructor for class org.concord.util.beans.PropertyDescriptor
This constructor takes the name of a simple property, and Method objects for reading and writing the property.
propertyListeners - Variable in class org.concord.collisions.engine.JWorldElement
 
propertyPanel - Variable in class org.concord.pedagogica.PedAgogica
 
propertyPanel - Variable in class org.concord.pedagogica.ui.ActivityView
 
PropertyVetoException - exception org.concord.util.beans.PropertyVetoException.
A PropertyVetoException is thrown when a proposed change to a property represents an unacceptable value.
PropertyVetoException(String, PropertyChangeEvent) - Constructor for class org.concord.util.beans.PropertyVetoException
Constructs a PropertyVetoException with a detailed message.
push(boolean) - Method in class org.concord.flash.player.StackFrame4
 
push(boolean) - Method in class org.concord.flash.player.StackFrame5
 
push(float) - Method in class org.concord.flash.player.StackFrame4
 
push(float) - Method in class org.concord.flash.player.StackFrame5
 
push(int) - Method in class org.concord.flash.player.StackFrame4
 
push(int) - Method in class org.concord.flash.player.StackFrame5
 
push(Object) - Method in class org.concord.util.script.NameStack
 
push(Object) - Method in class org.concord.flash.player.StackFrame4
 
push(Object) - Method in class org.concord.flash.player.StackFrame5
 
push(Object[]) - Method in class org.concord.flash.player.builtin.FArray
 
push(String, Object) - Method in class org.concord.util.script.NameStack
 
pushFrame() - Method in class org.concord.util.script.ScriptObject
 
pushFrame() - Method in class org.concord.util.script.ScriptThread
 
pushReturnNode(ActivityNode) - Method in class org.concord.pedagogica.engine.ActivityNode
 

Q

Q_STRAND_ONE - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
Q_STRAND_TWO - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
Query - class org.concord.util.Query.
 
Query(String) - Constructor for class org.concord.util.Query
 
Question - class org.concord.pedagogica.ui.Question.
 
QUESTION - Static variable in class org.concord.util.LogProcess
 
Question() - Constructor for class org.concord.pedagogica.ui.Question
 
Question(String, boolean) - Constructor for class org.concord.pedagogica.ui.Question
This constructs a fill-in-the-blank type of question.
Question(String, String[], boolean) - Constructor for class org.concord.pedagogica.ui.Question
This constructs a multiple choice question.
questionAnswered(QuestionEvent) - Method in interface org.concord.pedagogica.ui.QuestionListener
 
questionClass - Variable in class org.concord.pedagogica.engine.QuestionState
 
questionCount - Static variable in class org.concord.pedagogica.ui.CustomQuestion
 
QuestionEvent - class org.concord.pedagogica.ui.QuestionEvent.
 
QuestionEvent(QuestionForm, String[]) - Constructor for class org.concord.pedagogica.ui.QuestionEvent
 
questionFont - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
questionFont - Variable in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
QuestionForm - interface org.concord.pedagogica.engine.QuestionForm.
 
QuestionListener - interface org.concord.pedagogica.ui.QuestionListener.
 
questionPrefix - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
questions - Variable in class org.concord.pedagogica.engine.ActivityNode
 
QuestionState - class org.concord.pedagogica.engine.QuestionState.
 
QuestionState(QuestionForm, String, Object[], String[], String[]) - Constructor for class org.concord.pedagogica.engine.QuestionState
 
questionStates - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
questionTable - Static variable in class org.concord.pedagogica.ui.CustomQuestion
 
questionText - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
quit() - Method in class org.concord.util.Editor
 
quitButton - Variable in class org.concord.pedagogica.PedAgogica
 
Quiz - class org.concord.pedagogica.ui.Quiz.
 
Quiz() - Constructor for class org.concord.pedagogica.ui.Quiz
 
Quiz(String) - Constructor for class org.concord.pedagogica.ui.Quiz
 
Quote - class org.concord.util.script.Quote.
 
Quote(boolean) - Constructor for class org.concord.util.script.Quote
 
Quote(byte) - Constructor for class org.concord.util.script.Quote
 
Quote(char) - Constructor for class org.concord.util.script.Quote
 
Quote(double) - Constructor for class org.concord.util.script.Quote
 
Quote(float) - Constructor for class org.concord.util.script.Quote
 
Quote(int) - Constructor for class org.concord.util.script.Quote
 
Quote(long) - Constructor for class org.concord.util.script.Quote
 
Quote(short) - Constructor for class org.concord.util.script.Quote
 

R

r - Variable in class org.concord.collisions.engine.JAtom
 
radian - Variable in class org.concord.util.CCUnit
 
RADIUS - Static variable in class org.concord.pedagogica.ui.ActivityArcItem
 
random() - Method in class org.concord.flash.player.builtin.FMath
 
range - Variable in class org.concord.util.Gauge
 
RAW_NUCLEIC_ACID_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
RAW_NUCLEIC_ACID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
RAW_NUCLEIC_ACID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
RAW_NUCLEIC_ACID_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
RAW_NUCLEIC_ACID_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
RawNucleicAcid - class org.concord.biologica.engine.RawNucleicAcid.
This class represents a nucleic acid stored as a sequence of base values.
RawNucleicAcid(INucleicAcidHolder, int, byte[], int) - Constructor for class org.concord.biologica.engine.RawNucleicAcid
Create a new raw nucleic acid given some base values.
RawNucleicAcid(INucleicAcidHolder, int, RawNucleicAcid, int) - Constructor for class org.concord.biologica.engine.RawNucleicAcid
Create a new raw nucleic acid in the given holder from a given raw nucleic acid.
RawNucleicAcid(INucleicAcidHolder, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.RawNucleicAcid
Create a new raw nucleic acid and start handling XML parsing events to set the properties of this object.
read() - Method in class org.concord.util.TextInputStream
 
read() - Method in class org.concord.util.TextReader
 
read() - Method in class org.concord.util.script.ScriptFileInputStream
 
read(byte[]) - Method in class org.concord.util.TextInputStream
 
read(byte[]) - Method in class org.concord.util.script.ScriptFileInputStream
 
read(byte[], int, int) - Method in class org.concord.util.TextInputStream
 
read(byte[], int, int) - Method in class org.concord.util.script.ScriptFileInputStream
 
read(char[]) - Method in class org.concord.util.TextReader
 
read(char[], int, int) - Method in class org.concord.util.TextReader
 
reader - Variable in class org.concord.util.TextInputStream
 
reader - Variable in class org.concord.util.LogProcess
 
readExternal(DataStream) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
readExternal(DataStream) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
readFile(URL, int, int, Component) - Static method in class org.concord.biologica.datasupport.ImageReader
 
readLine() - Method in interface org.concord.util.script.ScriptRuntime
 
readLine() - Method in class org.concord.util.script.ECMA
 
readLine(String) - Method in interface org.concord.util.script.ScriptRuntime
The readLine method can be called from inside the script by using "readLine()".
readLine(String) - Method in class org.concord.util.script.ECMA
The readLine method can be called from inside the script by using "easl.readLine()".
readObject() - Method in class org.concord.util.beans.XMLDecoder
Reads the next object from the input.
readObject() - Method in class org.concord.util.beans.CCXMLDecoder
 
readString(String, String) - Method in interface org.concord.util.script.ScriptRuntime
 
readString(String, String) - Method in class org.concord.util.script.ECMA
 
readText(InputStream) - Method in class org.concord.pedagogica.engine.ActivityScript
 
readText(InputStream) - Method in class org.concord.pedagogica.ui.HTMLView
 
readToken() - Method in interface org.concord.util.script.ScriptRuntime
 
readToken() - Method in class org.concord.util.script.ECMA
 
readToken(String) - Method in interface org.concord.util.script.ScriptRuntime
 
readToken(String) - Method in class org.concord.util.script.ECMA
 
ready() - Method in class org.concord.util.TextReader
 
receiveBuffer - Variable in class org.concord.util.NetworkTime
 
receivePacket - Variable in class org.concord.util.NetworkTime
 
receiver - Variable in class org.concord.util.NetworkTime
 
reconcileBaseChanges() - Method in class org.concord.biologica.engine.OrganismAllele
Reconcile base changes already made to this organism allele, usually due to a user editing the DNA directly in the DNA View.
rectsForListener - Variable in class org.concord.collisions.engine.JWorldElement
 
redoEdit() - Method in class org.concord.util.Editor
 
redraw() - Method in class org.concord.collisions.ui.GUIPanel
redraw GUIPanel content, actually calls super class repaint method
redrawWorld() - Method in class org.concord.collisions.engine.JPartWorld
 
reference - Variable in class org.concord.util.script.AssignmentStatement
 
ReferenceExpression - class org.concord.util.script.ReferenceExpression.
The ReferenceExpression implements the semantics of the left side of and assignment statement.
ReferenceExpression(Script) - Constructor for class org.concord.util.script.ReferenceExpression
ReferenceExpression constructor.
release() - Method in class org.concord.biologica.engine.EngineObject
 
release(DomainEngine) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
release(DomainModel) - Method in interface org.concord.pedagogica.engine.DomainModel
 
release(DomainView) - Method in interface org.concord.pedagogica.engine.DomainView
 
reload(LabObjectView) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
rememberCurrAllAsInit() - Method in class org.concord.collisions.engine.JWorldElement
 
rememberCurrElementsPropertiesAsInit() - Method in class org.concord.collisions.engine.JPartWorld
 
rememberCurrPosAsInit() - Method in class org.concord.collisions.engine.JWorldElement
 
rememberCurrPosAsInit() - Method in class org.concord.collisions.engine.JRigidBox
 
rememberCurrPosAsInit() - Method in class org.concord.collisions.engine.JWall
 
rememberCurrPosAsInit() - Method in class org.concord.collisions.engine.JDaemon
 
rememberCurrPosAsInit() - Method in class org.concord.collisions.engine.JAtom
 
rememberCurrPropAsInit() - Method in class org.concord.collisions.engine.JWorldElement
 
rememberCurrPropAsInit(String) - Method in class org.concord.collisions.engine.JWorldElement
 
rememberCurrVelAsInit() - Method in class org.concord.collisions.engine.JWorldElement
 
rememberCurrVelAsInit() - Method in class org.concord.collisions.engine.JRigidBox
 
rememberCurrVelAsInit() - Method in class org.concord.collisions.engine.JWall
 
rememberCurrVelAsInit() - Method in class org.concord.collisions.engine.JDaemon
 
rememberCurrVelAsInit() - Method in class org.concord.collisions.engine.JAtom
 
remove(int) - Method in class org.concord.molecular.engine.IndexList
 
remove(Object) - Method in class org.concord.util.beans.Encoder
Removes the entry for this instance, returning the old entry.
remove(String) - Method in class org.concord.util.script.NameStack
 
removeActionListener(ActionListener) - Method in class org.concord.biologica.ui.DNAView
 
removeActionListener(ActionListener) - Method in class org.concord.flash.player.FButton
 
removeActionListener(ActionListener) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
removeActionListener(ActionListener) - Method in class org.concord.pedagogica.ui.TableInputView
 
removeActivationStep(DaemonActivationStep) - Method in class org.concord.collisions.engine.JDaemon
Remove a specific activation step of the daemon
removeActivationStep(float) - Method in class org.concord.collisions.engine.JDaemon
Remove a specific activation step of the daemon, given the activation time
removeActivationStep(int) - Method in class org.concord.collisions.engine.JDaemon
Remove a specific activation step of the daemon, given the index If the index is out of range, it does not throw any exception
removeActivityItemListener(ActivityItemListener) - Method in class org.concord.pedagogica.ui.ActivityView
 
removeAll() - Method in class org.concord.biologica.ui.PedigreeView
Remove all objects in this view, both organisms and families.
removeAll() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Remove all the objects in this view, both organisms and families, without deleting anything.
removeAll() - Method in class org.concord.biologica.ui.PedigreeLevel
Remove everything from this level
removeAll() - Method in class org.concord.molecular.engine.IndexList
 
removeAllActivationSteps() - Method in class org.concord.collisions.engine.JDaemon
Remove all the activation steps of the daemon
removeAllAtomsFromArea(int, int, int, int) - Method in class org.concord.collisions.ui.GUIPanel
 
removeAllElements() - Method in class org.concord.biologica.ui.BioComboBoxModel
Empties the list if the list has some elements.
removeAllFamilies() - Method in class org.concord.biologica.ui.PedigreeView
Remove all pedigreeFamilies, with no notificaition
removeAllOrganisms() - Method in class org.concord.biologica.ui.PedigreeView
Remove all pedigreeOrganisms
removeAllOrganisms() - Method in class org.concord.biologica.ui.MultipleOrganismView
Remove all organisms
removeArcItem(ActivityArcItem) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
removeArcs() - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
removeAreaListener(AreaListener) - Method in class org.concord.collisions.engine.JWorldElement
 
removeAreaToListen(AreaListener, int, int, int, int) - Method in class org.concord.collisions.engine.JWorldElement
 
removeAreaToListen(AreaListener, PassiveElement) - Method in class org.concord.collisions.engine.JWorldElement
 
removeAtom(JAtom) - Method in class org.concord.collisions.ui.GUIPanel
remove the atom with given name from the panel
removeAtom(String) - Method in class org.concord.collisions.ui.GUIPanel
remove the atom with given name from the panel
removeAtomFromWorld(JAtom) - Method in class org.concord.collisions.engine.JPartWorld
remove the atom with given name from the world
removeAtomFromWorld(String) - Method in class org.concord.collisions.engine.JPartWorld
remove the atom with given name from the world
removeAtomicDataListener(AtomicDataListener) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
removeAtomicValue(ConditionValue) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
This method removes the AtomicValue from the graph.
removeAtomsFromWorld() - Method in class org.concord.collisions.engine.JPartWorld
remove atoms from the world
removeAvailableButton() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
removeAvailableField() - Method in class org.concord.pedagogica.ui.BlankFill
 
removeAvailableText() - Method in class org.concord.pedagogica.ui.BlankFill
 
removeBoxesFromWorld() - Method in class org.concord.collisions.engine.JPartWorld
 
removeBoxFromWorld(JRigidBox) - Method in class org.concord.collisions.engine.JPartWorld
 
removeBoxFromWorld(String) - Method in class org.concord.collisions.engine.JPartWorld
 
removeButton - Variable in class org.concord.util.PathDialog
 
removeButton - Variable in class org.concord.pedagogica.ui.VariableDialog
 
removeCaretListener(CaretListener) - Method in class org.concord.util.EditorInternalFrame
 
removeCCGraphReadyListener(CCGraphReadyListener) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
removeChangeListener(ChangeListener) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
removeCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Removes a characteristic from the column.
removeCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageRow
Removes a characteristic from the row.
removeChildPedigreeOrganism(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeFamily
Remove a child pedigree organism, presumably because the child was deleted
removeChildren(PedigreeOrganismView) - Method in class org.concord.biologica.ui.PedigreeFamily
Remove the children of this family.
removeCollisionsListener(CollisionsListener) - Method in class org.concord.collisions.engine.JPartWorld
removeCollisionsListener
removeCollisionsListener(CollisionsListener) - Method in class org.concord.collisions.ui.GUIPanel
 
removeComponent(NodeViewItem) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
removeConditionListener(ConditionListener) - Method in class org.concord.molecular.engine.ConditionValue
 
removeDaemonListener(DaemonListener) - Method in class org.concord.collisions.engine.JDaemon
Remove a daemon listener
removeDaemonsFromWorld() - Method in class org.concord.collisions.engine.JPartWorld
remove daemons from the world
removeDataListener(DataListener) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
removeDataListener(DataListener) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
removeDebugging(String) - Static method in class org.concord.util.Debug
 
removeElement(JWorldElement) - Method in class org.concord.collisions.ui.GUIPanel
remove the element from the panel
removeElseIfExpression(Expression) - Method in class org.concord.util.script.IfThenElseStatement
 
removeElseIfStatement(Statement) - Method in class org.concord.util.script.IfThenElseStatement
 
removeFamily(Family) - Method in class org.concord.biologica.ui.PedigreeView
Removes a family from this view.
removeFamily(Family) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Removes a family from this view.
removeFamily(PedigreeFamily) - Method in class org.concord.biologica.ui.PedigreeLevel
Remove a family from this level.
removeForce(CCForce) - Method in class org.concord.collisions.engine.JWorldElement
Remove force applied to the JWorldElement.
removeForce(int) - Method in class org.concord.collisions.engine.JWorldElement
Remove Nth force applied to the JWorldElement.
removeForceCalculator() - Method in class org.concord.collisions.engine.JPartWorld
 
removeHandler(String) - Method in class org.concord.util.script.event.EventHandler
 
removeHandlerButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
removeHyperlinkListener(HyperlinkListener) - Method in class org.concord.pedagogica.ui.CCXMLText
 
removeLocal(String) - Method in class org.concord.util.script.BlockStatement
 
removeLocals(int) - Method in class org.concord.util.script.NameStack
 
removeMapEntry(int, int, int) - Method in class org.concord.util.BarGraph
Removes an index map for a particular index.
removeMember(String) - Method in class org.concord.flash.player.FScriptObject
Removes a member field
removeMethod(MethodDeclaration) - Method in class org.concord.util.script.Script
 
removeMouseListener(MouseListener) - Method in class org.concord.flash.player.FButton
 
removeMouseListener(MouseListener) - Method in class org.concord.flash.player.FMouseSupport
 
removeMovieClip(String) - Method in class org.concord.flash.player.FMovie
Removes a movie clip from the global name table.
removeMovieClipListener(MovieClipListener) - Method in class org.concord.flash.player.FMovieClip
 
removeNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
removeNodes() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
removeNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.OrganismAllele
Removes a nucleic acid from the holder.
removeNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.NucleicAcid
Removes a nucleic acid from the holder.
removeNucleicAcid(INucleicAcid) - Method in class org.concord.biologica.engine.SpeciesAllele
Removes a nucleic acid from the holder.
removeNucleicAcid(INucleicAcid) - Method in interface org.concord.biologica.engine.INucleicAcidHolder
Removes a nucleic acid from the holder.
removeObject(PedigreeObject) - Method in class org.concord.biologica.ui.PedigreeLevel
Remove an object from this level.
removeOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeView
Removes an organism from this view.
removeOrganism(Organism) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Removes an organism from this view.
removeOrganism(Organism) - Method in class org.concord.biologica.ui.MultipleOrganismView
Removes an organism from this view.
removeOrganism(PedigreeOrganism) - Method in class org.concord.biologica.ui.PedigreeLevel
Remove an organism from this level.
removeParameter(String) - Method in class org.concord.util.script.MethodDeclaration
 
removePassiveElements() - Method in class org.concord.collisions.ui.GUIPanel
remove all passive elements from the panel
removePositionChanger() - Method in class org.concord.collisions.engine.JWorldElement
 
removePrefix(String, String) - Method in class org.concord.util.PathDialog
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.engine.EngineObject
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.engine.BioEngine
Remove a property change listener for all non-vector properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.UIView
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.FertilizationModel
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.MeiosisModel
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.SelectionSet
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.biologica.ui.TreeView
Remove a property change listener for properties.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.collisions.engine.JWorldElement
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.molecular.ui.MolecularView
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.pedagogica.ui.HTMLViewCustomizer
 
removePropertyChangeListener(PropertyChangeListener) - Method in class org.concord.pedagogica.ui.TableInputModel
 
removeQuestion(QuestionForm) - Method in class org.concord.pedagogica.engine.ActivityNode
 
removeQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
removeQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.Question
 
removeQuestionListener(QuestionListener) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
removeScreen(int, int, int, int) - Method in class org.concord.collisions.engine.BedSpringWorld
 
removeSelectionPresenter(SelectionPresenter) - Method in class org.concord.biologica.ui.SelectionSet
Remove a selection presenter
removeSource(int, int) - Method in class org.concord.collisions.engine.BedSpringWorld
 
removeStatement(Statement) - Method in class org.concord.util.script.BlockStatement
 
removeStatement(Statement) - Method in class org.concord.util.script.Script
 
removeStateVariable(String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
removeStepListener(StepListener) - Method in class org.concord.collisions.engine.JPartWorld
 
removeTool(int) - Method in class org.concord.biologica.ui.ToolView
Remove the given tool from the view
removeUpdate(DocumentEvent) - Method in class org.concord.util.TextReader
 
removeUpdate(DocumentEvent) - Method in class org.concord.util.EditorInternalFrame
 
removeValue(int) - Method in class org.concord.molecular.engine.IndexList
 
removeValueFunction(ConditionValue) - Method in class org.concord.molecular.engine.AggregateValue
 
removeVariable(String) - Method in class org.concord.util.script.Script
 
removeView(Container) - Method in class org.concord.biologica.ui.ToolView
Remove a view to the list of views that care about which tool in this tool view is active.
removeWall(JWall) - Method in class org.concord.collisions.ui.GUIPanel
remove the wall with given name from the panel
removeWall(String) - Method in class org.concord.collisions.ui.GUIPanel
remove the wall with given name from the panel
removeWallFromWorld(JWall) - Method in class org.concord.collisions.engine.JPartWorld
remove the wall with given name from the world
removeWallFromWorld(String) - Method in class org.concord.collisions.engine.JPartWorld
remove the wall with given name from the world
removeWallsFromWorld() - Method in class org.concord.collisions.engine.JPartWorld
remove walls from the world
render() - Method in class org.concord.flash.player.FFlash
Immediately paints the frame
render() - Method in class org.concord.flash.player.FMovie
Draw the movie now.
repaint() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
repaint() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
repaint(long, int, int, int, int) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
repaint(Rectangle) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
REPLACE - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
REPLACE_ALL - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
replaceAllButton - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
replaceButton - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
replaceCharacteristic(Characteristic, Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Replace the given old Characteristic with the given new Characteristic.
replaceCharacteristic(Characteristic, Characteristic) - Method in class org.concord.biologica.engine.SpeciesImageRow
Replace the given old Characteristic with the given new Characteristic.
replaceEdit() - Method in class org.concord.util.Editor
 
replaceIfSpeciesAllele(SpeciesAllele, SpeciesAllele) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Replace the given old if species allele with the given new if species allele.
replaceString - Variable in class org.concord.pedagogica.ui.ActivitySearchResult
 
replaceText - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
REPLAY_BUTTON_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
Replay button enabled in sex view.
REPLAY_BUTTON_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
Replay button visible in sex view.
replay() - Method in class org.concord.biologica.ui.SexView
Replay the state of this view back to the very start.
reportOutput - Variable in class org.concord.util.LogProcess
 
RESET_AUTOMATIC - Static variable in class org.concord.biologica.ui.UIProp
Is a reset automatic when an offspring is created in sex view.
RESET_BUTTON_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
Reset button enabled in sex view.
RESET_BUTTON_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
Reset button visible in sex view.
RESET_DELETE_OFFSPRING_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
Reset should delete offspring organism in sex view.
reset() - Method in class org.concord.util.LineGraph
 
reset() - Method in class org.concord.util.script.ScriptFileInputStream
 
reset() - Method in class org.concord.biologica.ui.PracticeView
 
reset() - Method in class org.concord.biologica.ui.ChromosomePracticeView
 
reset() - Method in class org.concord.biologica.ui.PedigreePracticeView
 
reset() - Method in class org.concord.biologica.ui.MutationsPracticeView
 
reset() - Method in class org.concord.biologica.ui.MeiosisPracticeView
 
reset() - Method in class org.concord.biologica.ui.SexView
Reset the state of this view, erasing and recalculating all meiosis state, removing any state for fertilization (e.g.
reset() - Method in class org.concord.collisions.engine.JPartWorld
reset reset simulation all timers will be stopped
reset() - Method in class org.concord.collisions.engine.JDaemon
Reset the daemon (kill it)
reset() - Method in class org.concord.collisions.engine.BedSpringWorld
 
reset() - Method in class org.concord.collisions.ui.GUIPanel
reset simulation
reset() - Method in class org.concord.molecular.ui.MolecularView
Reset the MolecularView object.
reset() - Method in class org.concord.pedagogica.engine.NodeAccess
 
reset() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
resetDaemons() - Method in class org.concord.collisions.engine.JPartWorld
 
resetDefaultColors() - Method in class org.concord.collisions.engine.JImpulseDaemon
Reset default colors for the daemon
resetDefaultColors() - Method in class org.concord.collisions.engine.JBooster
Reset default colors for the daemon
resetItemNumber() - Static method in class org.concord.pedagogica.ui.ActivityNodeItem
 
resetRange() - Method in class org.concord.molecular.engine.ConditionValue
 
resetSqueezeFactor() - Method in class org.concord.biologica.ui.PedigreeObject
Reset squeeze factor.
resetSqueezeFactor() - Method in class org.concord.biologica.ui.PedigreeFamily
Accessor for resetting the squeeze factor.
resetStepListeners() - Method in class org.concord.collisions.engine.JPartWorld
 
resetTimedAverage() - Method in class org.concord.molecular.engine.ConditionValue
 
resourceData - Variable in class org.concord.pedagogica.ui.ActivityView
 
RESPONSE - Static variable in class org.concord.util.LogProcess
 
restore(InputStream) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
restore(Reader) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
restoreQuestion(Object) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
restoreQuestion(Object) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
restoreQuestion(Object) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
restoreQuestion(Object) - Method in class org.concord.pedagogica.ui.BlankFill
 
restoreQuestion(Object) - Method in class org.concord.pedagogica.ui.EssayFill
 
result - Variable in class org.concord.util.script.InvocationExpression
 
result - Variable in class org.concord.util.script.NameStack
 
result - Variable in class org.concord.util.script.IndexExpression
 
returned - Variable in class org.concord.util.script.NameStack
 
returnNode - Variable in class org.concord.pedagogica.engine.ActivityNode
 
ReturnStatement - class org.concord.util.script.ReturnStatement.
The ReturnStatement class implements the node that supports the semantics of the "return" statement.
ReturnStatement() - Constructor for class org.concord.util.script.ReturnStatement
 
revalidate() - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
reverse() - Method in class org.concord.flash.player.builtin.FArray
 
reverseAllVelocityInTheWorld() - Method in class org.concord.collisions.engine.JPartWorld
 
reverseVx() - Method in class org.concord.collisions.engine.JWorldElement
 
reverseVx() - Method in class org.concord.collisions.engine.JRigidBox
 
reverseVy() - Method in class org.concord.collisions.engine.JWorldElement
 
reverseVy() - Method in class org.concord.collisions.engine.JRigidBox
 
REVERT_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Revert button pushed.
revertPendingChanges() - Method in class org.concord.biologica.ui.DNAView
Revert pending changes to DNA
RGB2HSL(int, int, int, int[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
RGB2HSV(int, int, int, int[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
RGBtoHSB(int, int, int, float[]) - Static method in class org.concord.biologica.datasupport.ColorUtil
 
rhs - Variable in class org.concord.util.script.FactAssignStatement
 
RIGHT_BOTTOM_ORIGIN - Static variable in class org.concord.collisions.ui.PassiveIcon
 
RIGHT_DAUGHTER_CELL_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
RIGHT_TOP_ORIGIN - Static variable in class org.concord.collisions.ui.PassiveIcon
 
right(float, float, JComponent) - Method in class org.concord.collisions.engine.JRigidBox
shift wall right
right(float, float, JComponent) - Method in class org.concord.collisions.engine.JWall
shift wall right
rightAct - Variable in class org.concord.util.LogProcess
 
rightFile - Variable in class org.concord.util.LogProcess
 
root - Variable in class org.concord.pedagogica.engine.ActivityScript
 
root - Variable in class org.concord.pedagogica.engine.LogModel
 
ROOT_ENGINE_OBJECT - Static variable in class org.concord.biologica.ui.UIProp
The root engine object in the tree view changed.
rootPane - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
rootScript - Variable in class org.concord.util.script.Script
 
rootSelected(ActivityItemEvent) - Method in class org.concord.pedagogica.PedAgogica
 
rootSelected(ActivityItemEvent) - Method in interface org.concord.pedagogica.ui.event.ActivityItemListener
 
round(double) - Static method in class org.concord.collisions.engine.JPartWorld
 
round(double) - Method in class org.concord.flash.player.builtin.FMath
 
round(float) - Static method in class org.concord.collisions.engine.JPartWorld
 
ROW_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
ROW_INDEX - Static variable in class org.concord.biologica.engine.EngineProp
The row index of an OrganismImage in its SpeciesImage object.
ROW_INDEX_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
ROW_INDEX_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
rows - Variable in class org.concord.pedagogica.ui.TabularView
 
RULE_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
RUN_ACTIVITY - Static variable in class org.concord.pedagogica.ui.ActivityView
 
run() - Method in class org.concord.util.NetworkTime
 
run() - Method in class org.concord.util.script.ECMA
The run method is called by the new thread created to call the interpreter.
run() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
run() - Method in class org.concord.pedagogica.engine.ActivityScript
 
run() - Method in class org.concord.pedagogica.engine.Activity
 
run() - Method in class org.concord.pedagogica.ui.ActivityView
 
run() - Method in class org.concord.pedagogica.ui.DefaultPrinter
 
runActivity - Variable in class org.concord.pedagogica.ui.ActivityView
 
RunActivity - class org.concord.pedagogica.ui.RunActivity.
Runs an activity.
runActivity() - Method in class org.concord.pedagogica.ui.ActivityView
 
RunActivity() - Constructor for class org.concord.pedagogica.ui.RunActivity
RunActivity Constructor.
runButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
runError(ActivityScript) - Method in interface org.concord.pedagogica.engine.ActivityErrorHandler
 
runError(ActivityScript) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
runError(ActivityScript) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
runError(Throwable, int, int, int, int) - Method in interface org.concord.util.script.ScriptError
 
runError(Throwable, int, int, int, int) - Method in class org.concord.pedagogica.engine.ActivityScript
 
runnable(String, boolean) - Method in interface org.concord.util.script.ScriptRuntime
 
runnable(String, boolean) - Method in class org.concord.util.script.ECMA
 
running - Variable in class org.concord.molecular.engine.ConditionValue
 
running - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
runningCount - Variable in class org.concord.molecular.engine.ConditionValue
 
runningMean - Variable in class org.concord.molecular.engine.ConditionValue
 
runScript(Script) - Method in interface org.concord.util.script.ScriptRuntime
 
runScript(Script) - Method in class org.concord.util.script.ECMA
 
runtime - Variable in class org.concord.util.script.Script
 
runtime - Variable in class org.concord.pedagogica.engine.ActivityScript
 
runtime - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
runtimeTable - Static variable in class org.concord.util.script.ScriptObject
 

S

s - Variable in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
SAVE_ACTIVITY - Static variable in class org.concord.pedagogica.ui.ActivityView
 
save() - Method in class org.concord.biologica.engine.World
Save the world state to the current file.
save(Document, Node) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
save(Document, Node) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
save(Document, Node) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
save(File) - Method in class org.concord.pedagogica.ui.ActivityView
 
save(OutputStream) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
save(String) - Method in class org.concord.util.EditorInternalFrame
 
save(String, String) - Method in class org.concord.util.EditorInternalFrame
 
save(Writer) - Method in interface org.concord.pedagogica.engine.DomainEngine
 
save(ZipOutputStream) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
save(ZipOutputStream, String) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
save(ZipOutputStream, String) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
saveActivity() - Method in class org.concord.pedagogica.ui.ActivityView
 
saveAs(File) - Method in class org.concord.biologica.engine.World
Save As the world state to the new given file.
saveAsActivity(File) - Method in class org.concord.pedagogica.ui.ActivityView
 
saveAsDocument() - Method in class org.concord.util.Editor
 
saveAsFile() - Method in class org.concord.util.Editor
 
saveAsItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
saveButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
saveDocument() - Method in class org.concord.util.Editor
 
saveEditView() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
saveExportFile - Variable in class org.concord.pedagogica.ui.LogView
 
saveFile(File) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
saveFile(File) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
saveFile(File) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
saveFileChooser - Variable in class org.concord.pedagogica.ui.ActivityView
 
saveFileData(ScriptFile, OutputStream) - Method in class org.concord.pedagogica.ui.ActivityView
 
saveImmediate - Variable in class org.concord.pedagogica.engine.Logging
 
saveInstance(int, Instance) - Method in class org.concord.flash.player.FMovieBuilder
 
saveQuestion(Object) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
saveQuestion(Object) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
saveQuestion(Object) - Method in class org.concord.pedagogica.ui.CustomTableQuestion
 
saveQuestion(Object) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
saveQuestion(Object) - Method in class org.concord.pedagogica.ui.BlankFill
 
saveQuestion(Object) - Method in class org.concord.pedagogica.ui.EssayFill
 
saveQuestion(Object, QuestionState) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
saveQuitButton - Variable in class org.concord.pedagogica.PedAgogica
 
saveResourceData(ZipOutputStream) - Method in class org.concord.pedagogica.ui.ActivityView
 
saveStringData(ZipOutputStream) - Method in class org.concord.pedagogica.engine.NodeAccess
 
saveSymbol(int, Symbol) - Method in class org.concord.flash.player.FMovieBuilder
 
saveView() - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
SCALE - Static variable in class org.concord.biologica.ui.UIProp
The scale of a view has changed.
scaleL - Variable in class org.concord.collisions.engine.CCScalingFactors
 
scaleM - Variable in class org.concord.collisions.engine.CCScalingFactors
 
scaleT - Variable in class org.concord.collisions.engine.CCScalingFactors
 
SCHEMA_VERSION_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SCHEMA_VERSION_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
scope - Variable in class org.concord.util.script.Script
 
SCOPE_IMAGE_TYPE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
script - Variable in class org.concord.util.script.ScriptObject
This is the currently executing script.
script - Variable in class org.concord.util.script.ScriptClassLoader
 
script - Variable in class org.concord.util.script.ScriptThread
 
script - Variable in class org.concord.pedagogica.engine.ActivityScript
 
Script - class org.concord.util.script.Script.
 
SCRIPT - Static variable in class org.concord.util.script.InvocationExpression
 
Script.ScriptSecuritySupport - class org.concord.util.script.Script.ScriptSecuritySupport.
 
Script.ScriptSecuritySupport(Script) - Constructor for class org.concord.util.script.Script.ScriptSecuritySupport
 
Script() - Constructor for class org.concord.util.script.Script
 
Script(String, NameStack, ScriptRuntime) - Constructor for class org.concord.util.script.Script
 
Script(String, String, ScriptRuntime) - Constructor for class org.concord.util.script.Script
 
ScriptClassLoader - class org.concord.util.script.ScriptClassLoader.
 
ScriptClassLoader(Script) - Constructor for class org.concord.util.script.ScriptClassLoader
 
scriptContexts - Static variable in class org.concord.util.script.Script
 
scriptEASL - Variable in class org.concord.pedagogica.ui.ActivityView
 
scriptECMA - Variable in class org.concord.pedagogica.ui.ActivityView
 
ScriptError - interface org.concord.util.script.ScriptError.
 
scriptFile - Variable in class org.concord.pedagogica.engine.ActivityScript
 
ScriptFile - class org.concord.util.script.ScriptFile.
 
ScriptFile(String) - Constructor for class org.concord.util.script.ScriptFile
 
ScriptFile(String, String) - Constructor for class org.concord.util.script.ScriptFile
 
ScriptFileInputStream - class org.concord.util.script.ScriptFileInputStream.
 
ScriptFileInputStream(ScriptFile) - Constructor for class org.concord.util.script.ScriptFileInputStream
 
ScriptFileOutputStream - class org.concord.util.script.ScriptFileOutputStream.
 
ScriptFileOutputStream(ScriptFile) - Constructor for class org.concord.util.script.ScriptFileOutputStream
 
ScriptObject - class org.concord.util.script.ScriptObject.
The ScriptObject class is the base class of all the nodes in the semantic tree.
ScriptObject() - Constructor for class org.concord.util.script.ScriptObject
 
ScriptObject(Script) - Constructor for class org.concord.util.script.ScriptObject
 
ScriptRuntime - interface org.concord.util.script.ScriptRuntime.
 
scriptText - Variable in class org.concord.pedagogica.engine.ActivityScript
 
scriptThread - Variable in class org.concord.pedagogica.engine.ActivityScript
 
ScriptThread - class org.concord.util.script.ScriptThread.
 
ScriptThread() - Constructor for class org.concord.util.script.ScriptThread
 
ScriptThread(Runnable) - Constructor for class org.concord.util.script.ScriptThread
 
ScriptThread(Runnable, Script) - Constructor for class org.concord.util.script.ScriptThread
 
scriptType - Variable in class org.concord.pedagogica.engine.ActivityScript
 
scriptType - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
scriptType - Variable in class org.concord.pedagogica.ui.ActivityView
 
scriptTypeMenu - Variable in class org.concord.pedagogica.ui.ActivityView
 
scrollPane - Variable in class org.concord.biologica.ui.UIView
Optional scroll pane parent of this view.
scrollPane - Variable in class org.concord.pedagogica.ui.LogView
 
search - Variable in class org.concord.pedagogica.ui.ActivityView
 
SEARCH - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
SEARCH_AND_REPLACE - Static variable in class org.concord.pedagogica.ui.ActivityView
 
SEARCH_TITLE - Static variable in class org.concord.pedagogica.ui.ActivitySearch
 
search(JTextArea, String, Vector) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
search(JTextArea, String, Vector) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
searchAll() - Method in class org.concord.pedagogica.ui.ActivityView
 
searchEdit() - Method in class org.concord.util.Editor
 
searchException - Variable in class org.concord.pedagogica.ui.ActivityView
 
searchGoTo(ActivitySearchResult) - Method in class org.concord.pedagogica.ui.ActivityView
 
searchPanel - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
searchReplace() - Method in class org.concord.pedagogica.ui.ActivityView
 
searchReplaceAll() - Method in class org.concord.pedagogica.ui.ActivityView
 
searchResult - Variable in class org.concord.pedagogica.ui.ActivityView
 
searchResults - Variable in class org.concord.pedagogica.ui.ActivityView
 
searchString - Variable in class org.concord.pedagogica.ui.ActivitySearchResult
 
searchText - Variable in class org.concord.pedagogica.ui.ActivitySearch
 
sec - Variable in class org.concord.util.CCUnit
 
SECOND_ORGANISM_ALLELE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SECOND_ORGANISM_ALLELE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SECOND_ORGANISM_CHROMOSOME_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SECOND_ORGANISM_CHROMOSOME_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SECOND_STRAND - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
SEED - Static variable in class org.concord.biologica.engine.EngineProp
Seed, as used for random number generation, simple property name.
SEED_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SEED_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SELECT_ITEM - Static variable in class org.concord.pedagogica.ui.ActivityView
 
select(boolean) - Method in interface org.concord.util.Editable
 
selectButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
selected - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Selected?
selected - Variable in class org.concord.pedagogica.ui.ActivityView
 
selected - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
SELECTED - Static variable in class org.concord.biologica.engine.EngineProp
Selected state of object changed.
SELECTED - Static variable in class org.concord.biologica.ui.UIProp
The selected state of the event source has changed.
SELECTED_ALLELE - Static variable in class org.concord.biologica.ui.UIProp
The selected allele of the shown organism in a chromosome view has changed.
SELECTED_BASES - Static variable in class org.concord.biologica.ui.UIProp
The selected bases of a string of DNA has changed.
SELECTED_CHROMOSOME - Static variable in class org.concord.biologica.ui.UIProp
The selected chromosome of the shown organism in a chromosome view has changed.
SELECTED_FAMILIES - Static variable in class org.concord.biologica.ui.UIProp
The selected families in a view have changed.
SELECTED_FATHER_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The selected father gamete in a sex view has changed.
SELECTED_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The selected gamete in a meiosis model has changed.
SELECTED_MOTHER_GAMETE - Static variable in class org.concord.biologica.ui.UIProp
The selected mother gamete in a sex view has changed.
SELECTED_OBJECTS - Static variable in class org.concord.biologica.ui.UIProp
The selected objects in a selection set has changed.
selectedActivityColor - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
selectedColor - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
selectedColor - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
selectedItem - Variable in class org.concord.util.PathDialog
 
selectedItem - Variable in class org.concord.pedagogica.ui.ActivityView
 
selectedItem - Variable in class org.concord.pedagogica.ui.VariableDialog
 
selectedItem - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
selectedList - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
selectedValues - Variable in class org.concord.pedagogica.ui.LogView
 
selectGamete(int, int) - Method in class org.concord.biologica.ui.MeiosisModel
Select the gamete closest to the given x, y coordinates.
selectGroup - Variable in class org.concord.pedagogica.ui.ActivityView
 
SELECTION - Static variable in class org.concord.biologica.ui.Tool
 
SELECTION_MODE - Static variable in class org.concord.biologica.ui.UIProp
The selection mode of a view has changed.
SELECTION_MODE_MULTIPLE_OBJECTS - Static variable in class org.concord.biologica.ui.SelectionSet
Normal, multiple object selection mode.
SELECTION_MODE_ONE_OBJECT - Static variable in class org.concord.biologica.ui.SelectionSet
Single objects selection mode.
SELECTION_MODE_TWO_OBJECTS - Static variable in class org.concord.biologica.ui.SelectionSet
Two object selection mode.
SELECTION_MODE_TWO_ORGANISMS_OPPOSITE_SEXES - Static variable in class org.concord.biologica.ui.SelectionSet
Two organism, mixed gender selection mode.
SELECTION_MODE_ZERO_OBJECTS - Static variable in class org.concord.biologica.ui.SelectionSet
Zero objects selection mode.
SELECTION_NAME - Static variable in class org.concord.biologica.ui.Tool
 
SELECTION_TOOL_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the selection tool has enabled.
SELECTION_TOOL_PICK_ON_STATIC_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
Selection tool was used to pick on a static organism.
SELECTION_TOOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the selection tool has changed.
selectionBoxes - Variable in class org.concord.pedagogica.ui.LogView
 
selectionChanged() - Method in interface org.concord.biologica.ui.SelectionPresenter
Selection changed.
selectionChanged() - Method in class org.concord.biologica.ui.PedigreeOrganismView
Selection changed
selectionChanged() - Method in class org.concord.biologica.ui.AllInOneView
Selection changed notification
selectionChanged() - Method in class org.concord.biologica.ui.TreeView
Selection changed.
selectionChanged() - Method in class org.concord.biologica.ui.MultipleOrganismView
Selection changed notification
selectionColor - Variable in class org.concord.biologica.ui.ChromosomeView
Selection color for a particular view
selectionColor - Variable in class org.concord.biologica.ui.OrganismView
Selection color for a particular view
selectionColor - Variable in class org.concord.biologica.ui.TreeView
Selection color for a particular view
selectionLabels - Variable in class org.concord.pedagogica.ui.LogView
 
selectionPanel - Variable in class org.concord.pedagogica.ui.LogView
 
SelectionPresenter - interface org.concord.biologica.ui.SelectionPresenter.
The selection presenter interface, implemented by an object which presents a set of selected engine objects.
SelectionSet - class org.concord.biologica.ui.SelectionSet.
A selection set, an object which manages a set of selected engine objects, notifies listeners that the selection set has changed, etc.
SelectionSet() - Constructor for class org.concord.biologica.ui.SelectionSet
Creates a new, empty selection set.
selectionToolCursor - Static variable in class org.concord.biologica.ui.Tool
Tool cursors
selectionToolImageIcon - Static variable in class org.concord.biologica.ui.Tool
Image icons
selectItems(int, int, boolean) - Method in class org.concord.pedagogica.ui.ActivityView
 
selectObject(EngineObject, boolean, boolean) - Method in class org.concord.biologica.ui.SelectionSet
Select an object.
selectors - Variable in class org.concord.pedagogica.engine.QuestionState
 
selectPathChooser - Variable in class org.concord.util.PathDialog
 
selectText(int, int) - Method in class org.concord.pedagogica.PedAgogica
 
selectText(int, int, int, int) - Method in class org.concord.util.Editor
 
selectText(int, int, int, int) - Method in class org.concord.util.EditorInternalFrame
 
self() - Method in interface org.concord.util.script.ScriptRuntime
 
self() - Method in class org.concord.util.script.ECMA
 
selfTest() - Method in class org.concord.pedagogica.ui.Quiz
Self-test method for Question class
sendBuffer - Variable in class org.concord.util.NetworkTime
 
sendPacket - Variable in class org.concord.util.NetworkTime
 
SequenceLiteral - class org.concord.util.script.SequenceLiteral.
 
SequenceLiteral(Script) - Constructor for class org.concord.util.script.SequenceLiteral
 
SER - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Serine
SERINE - Static variable in class org.concord.biologica.engine.AminoAcid
Serine
SERVER_HOSTS - Static variable in class org.concord.util.NetworkTime
 
SESSION - Static variable in class org.concord.util.LogProcess
 
sessionID - Variable in class org.concord.pedagogica.ui.LogView
 
sessionLabel - Variable in class org.concord.pedagogica.ui.LogView
 
set_alpha(double) - Method in class org.concord.flash.player.FComponent
 
set_alpha(float) - Method in class org.concord.flash.player.FComponent
 
set_currentframe(int) - Method in class org.concord.flash.player.FMovieClip
Sets the current frame pointer.
set_currentframe(String) - Method in class org.concord.flash.player.FMovieClip
Sets the current frame pointer by the label.
set_name(String) - Method in class org.concord.flash.player.FComponent
 
set_rotation(double) - Method in class org.concord.flash.player.FComponent
 
set_rotation(float) - Method in class org.concord.flash.player.FComponent
 
set_rotation(int) - Method in class org.concord.flash.player.FComponent
 
SET_START_NODE - Static variable in class org.concord.pedagogica.ui.ActivityView
 
set_visible(boolean) - Method in class org.concord.flash.player.FComponent
 
set_x(double) - Method in class org.concord.flash.player.FComponent
 
set_x(float) - Method in class org.concord.flash.player.FComponent
 
set_x(int) - Method in class org.concord.flash.player.FComponent
 
set_xscale(double) - Method in class org.concord.flash.player.FComponent
 
set_xscale(float) - Method in class org.concord.flash.player.FComponent
 
set_xscale(int) - Method in class org.concord.flash.player.FComponent
 
set_y(double) - Method in class org.concord.flash.player.FComponent
 
set_y(float) - Method in class org.concord.flash.player.FComponent
 
set_y(int) - Method in class org.concord.flash.player.FComponent
 
set_yscale(double) - Method in class org.concord.flash.player.FComponent
 
set_yscale(float) - Method in class org.concord.flash.player.FComponent
 
set_yscale(int) - Method in class org.concord.flash.player.FComponent
 
set(int, int) - Method in class org.concord.molecular.engine.IndexList
 
setAcceleration(double, double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setActiveColor(Color) - Method in class org.concord.collisions.engine.JDaemon
set color to show when the daemon is active
setActiveTool(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the active tool
setActiveTool(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the active tool
setActiveTool(int) - Method in class org.concord.biologica.ui.ToolView
Set the active tool
setActivity(Activity) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setActivity(Activity) - Method in class org.concord.pedagogica.ui.ActivityView
 
setActivityAlias(String) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
setActivityAlias(String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setActivityAlias(String) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setActivityAlias(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
setActivityAlias(String) - Method in class org.concord.pedagogica.ui.EssayFill
 
setActivityName(String) - Method in class org.concord.pedagogica.engine.Logging
 
setActivityNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityView
 
setActTime(float) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setAddAtom(String) - Method in class org.concord.molecular.ui.MolecularView
Tells the animator panel which type of atom to add.
setAlignmentControlsVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set alignment controls visibility
setAlignmentControlsVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set alignment controls visibility in big meiosis view
setAllEditable(boolean) - Method in class org.concord.pedagogica.ui.TableInputView
A boolean method which can be applied to every cell in a Punnett Square or TableInputView object.
setAllele(int, String, String) - Method in class org.concord.biologica.engine.Organism
Set an allele text symbol of an allele of the given gene on the given chromosome.
setAlleleAndColorVectors(Color) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the vectors for the alleles and colors of this meiosis chromosome model.
setAllelesAlterable(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism's alleles are alterable.
setAllelesVisible(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism's alleles are visible.
setAlleleVectors() - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Set allele vectors to show which alleles are at which array positions on the chromosomes.
setAllSelectable(boolean) - Method in class org.concord.pedagogica.ui.TableInputView
 
setAllSelectable(boolean) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setAllSelected(boolean) - Method in class org.concord.pedagogica.ui.TableInputView
 
setAnimationSliderEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set animation slider enabled.
setAnimationSliderEnabled(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set animation slider enabled.
setAnimationSliderEnabled(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set animation slider enabled.
setAnimationSliderEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set animation slider enabled.
setAnimationSliderVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set animation slider visibility.
setAnimationSliderVisible(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set animation slider visibility.
setAnimationSliderVisible(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set animation slider visibility.
setAnimationSliderVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set animation slider visibility.
setAnswerComponent(JTextComponent) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
setAnswerFont(Font) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setAnswerFont(Font) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.CustomTableQuestion
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.BlankFill
 
setAnswers(String[]) - Method in class org.concord.pedagogica.ui.EssayFill
 
setAnswerTextVisible(boolean) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
setAnswerTextVisible(boolean) - Method in class org.concord.pedagogica.ui.EssayFill
 
setApplet(Applet) - Static method in class org.concord.biologica.engine.PathStrings
 
setApplyVisible(boolean) - Method in class org.concord.biologica.ui.DNAView
 
setArc(ActivityArc) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setArrayValue(Object, int[], Object) - Method in class org.concord.util.script.ScriptObject
 
setArrowsVelDragMode(int) - Method in class org.concord.collisions.ui.GUIPanel
 
setAssignVelocities(boolean) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setAsText(String) - Method in class org.concord.collisions.engine.AtomDragPropertyEditor
 
setAsText(String) - Method in class org.concord.collisions.engine.AtomDragModePropertyEditor
 
setAtom(Atom) - Method in class org.concord.molecular.engine.AtomAccessor
 
setAtomicModel(AtomicModel) - Method in class org.concord.molecular.ui.MolecularView
 
setAtomicModel(DefaultAtomicModel) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
 
setAtomicValue(ConditionValue, int) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
Sets an atomic value for a particular index.
setAtoms(Atom[], int) - Method in class org.concord.molecular.engine.AtomicValue
 
setAtomsDragMode(int) - Method in class org.concord.collisions.ui.GUIPanel
setting drag mode for the atoms
setAttachedForce(boolean) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.EngineObject
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.World
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesChromosome
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesImage
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.Species
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.NucleicAcid
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesAllele
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.Organism
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.Family
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in interface org.concord.biologica.engine.INucleicAcid
Set the automatic locked state of this object.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.OrganismChromosome
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.Gene
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticLocked(boolean) - Method in class org.concord.biologica.engine.Trait
Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
setAutomaticStart(boolean) - Method in class org.concord.collisions.engine.JDaemon
Set automatic daemon or not automatic daemon
setAx(float) - Method in class org.concord.collisions.ui.PassiveElement
 
setAy(float) - Method in class org.concord.collisions.ui.PassiveElement
 
setBackColor(Color) - Method in class org.concord.util.LineGraph
 
setBackColor(Color) - Method in class org.concord.collisions.ui.PassiveElement
 
setBackground(Color) - Method in class org.concord.util.BarGraph
 
setBackground(Color) - Method in class org.concord.biologica.ui.UIView
Set the background color for this view.
setBackground(Color) - Method in class org.concord.biologica.ui.SexView
Set the background color for this view.
setBackground(Color) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overrides JComponent.setForeground to assign the unselected-background color to the specified color.
setBackground(Color) - Method in class org.concord.pedagogica.ui.Question
Set the background color of this and the child component.
setBackground(Color) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.TableInputView
To set the background color of the Punnett Square.
setBackground(Color) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.Quiz
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.BlankFill
 
setBackground(Color) - Method in class org.concord.pedagogica.ui.EssayFill
 
setBackground(Color, int) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
 
setBackgroundCellSubViews(Color) - Method in class org.concord.biologica.ui.SexView
Set the background color for the cell sub views.
setBackgroundIcon(String) - Method in class org.concord.collisions.ui.GUIPanel
 
setBackgroundIcon(String, int, int) - Method in class org.concord.collisions.ui.GUIPanel
 
setBackgroundOrganismSubViews(Color) - Method in class org.concord.biologica.ui.SexView
Set the background color for the organism sub views.
setBarGraphSize(Dimension) - Method in class org.concord.util.BarGraph
 
setBase(int, byte) - Method in class org.concord.biologica.engine.OrganismAllele
Sets the base value at the given index in this allele.
setBase(int, byte) - Method in class org.concord.biologica.engine.SpeciesAllele
Sets the base value at the given index in this allele.
setBase(int, byte) - Method in class org.concord.biologica.engine.RawNucleicAcid
Sets the base value at the given index in this nucleic acid.
setBaseObject(Object) - Method in class org.concord.util.script.Script
 
setBases(byte[]) - Method in class org.concord.biologica.engine.OrganismAllele
Sets the base values array for this allele.
setBases(byte[]) - Method in class org.concord.biologica.engine.SpeciesAllele
Sets the base values array for this allele.
setBases(byte[]) - Method in class org.concord.biologica.engine.RawNucleicAcid
Sets the base values array for this nucleic acid.
setBasesAsString(String) - Method in class org.concord.biologica.engine.SpeciesAllele
Sets the bases for this allele using a String as input.
setBeanInfoSearchPath(String[]) - Static method in class org.concord.util.beans.Introspector
Change the list of package names that will be used for finding BeanInfo classes.
setBedSpringGridLength(float) - Method in class org.concord.collisions.engine.BedSpringWorld
 
setBedSpringMode(boolean) - Method in class org.concord.collisions.engine.JPartWorld
 
setBlank(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
setBound(boolean) - Method in class org.concord.util.beans.PropertyDescriptor
Updates to "bound" properties will cause a "PropertyChange" event to get fired when the property is changed.
setBoundary(String) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setBoundaryType(String) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setBounds(int, int, int, int) - Method in class org.concord.biologica.ui.PedigreeView
Set the bounds of this view.
setBounds(int, int, int, int) - Method in class org.concord.flash.player.FFlash
 
setBounds(Rectangle) - Method in class org.concord.flash.player.FFlash
 
setBoundsValuesVisible(boolean) - Method in class org.concord.util.LineGraph
 
setBranchs(Vector[]) - Method in class org.concord.biologica.ui.MeiosisModel
 
setButton - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
setButtonGroup(ButtonGroup) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setButtonGroup(ButtonGroup) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setButtons(AbstractButton[]) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setButtons(AbstractButton[]) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setCellEditable(boolean, int, int) - Method in class org.concord.pedagogica.ui.TableInputView
A boolean method which can be applied to individual cells in a Punnett Square or TableInputView object.
setCellSelectable(boolean, int, int) - Method in class org.concord.pedagogica.ui.TableInputView
 
setCellSelectable(boolean, int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setCellSelected(boolean, int, int) - Method in class org.concord.pedagogica.ui.TableInputView
A boolean method which can be applied to individual cells in a Punnett Square or TableInputView object.
setCellSelected(boolean, int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setCellSize(int) - Method in class org.concord.util.LineGraph
 
setCellText(String, int, int) - Method in class org.concord.pedagogica.ui.TableInputView
A method which can be applied to individual cells in a Punnett Square or TableInputView object.
setCellText(String, int, int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setCellText(String, int, int, boolean) - Method in class org.concord.pedagogica.ui.TableInputModel
Method that will listen for Textfield changes and constantly update TableInputModel.
setCharacteristicsTextVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the characteristics text visible boolean.
setCharacteristicsTextVisible(boolean) - Method in class org.concord.biologica.ui.OrganismView
Set the characteristics text visible boolean.
setCharacteristicsTextVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set the characteristics text visible boolean.
setCharge(int) - Method in class org.concord.molecular.engine.AtomAccessor
 
setChoices(String[]) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setChoices(String[]) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setChromosome(OrganismChromosome) - Method in class org.concord.biologica.engine.Branch
 
setChromosomeBranchs(OrganismAllele[], Color[], OrganismAllele[], Color[]) - Method in class org.concord.biologica.engine.OrganismChromosome
This method is used to remember the paint information for this chromosome, Special for drawing the new chromosome for the crossing over offspring.
setChromosomePaintInfo(Branch[]) - Method in class org.concord.biologica.engine.Organism
 
setChromosomesSelectable(boolean) - Method in class org.concord.biologica.ui.ChromosomeView
 
setChromosomesToShow(int) - Method in class org.concord.biologica.ui.ChromosomeView
Set the chromosomes to show.
setChromosomeToolEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the chromosome tool enabled state.
setChromosomeToolVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the chromosome tool visibility.
setChromosomeViewHeight(int) - Method in class org.concord.biologica.engine.OrganismChromosome
 
setClassName(String) - Method in class org.concord.util.script.HandlerDeclaration
 
setClipDepth(int) - Method in class org.concord.flash.player.FComponent
 
setCodeBase(URL) - Method in class org.concord.pedagogica.ui.ViewerStub
 
setCollidedParticle(JWorldElement) - Method in class org.concord.collisions.engine.JWorldElement
 
setCollisionSensitive(boolean) - Method in class org.concord.collisions.engine.JWorldElement
 
setColor(Color) - Method in class org.concord.util.Gauge
Sets the color.
setColor(Color) - Method in class org.concord.biologica.engine.Terrain
Set the color of this terrain
setColor(Color) - Method in class org.concord.collisions.engine.JWorldElement
 
setColor(Color, Color) - Method in class org.concord.collisions.ui.PassiveGrid
 
setColor(Color, int) - Method in class org.concord.util.BarGraph
Sets the color associated with a particular index.
setColor(Color, int) - Method in class org.concord.util.Gauge
Sets the color associated with a particular index.
setColor(Color, int) - Method in interface org.concord.util.ValueGraph
 
setColor(Color, int) - Method in class org.concord.util.LineGraph
Sets the color associated with a particular index.
setColor(int, int, int) - Method in class org.concord.collisions.engine.JWorldElement
 
setColorFilter(boolean) - Method in class org.concord.collisions.engine.JDaemon
 
setColorForLine(int, int, int, int) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
setColorRange(Color, Color) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setColors(int, int, Color) - Method in class org.concord.biologica.engine.Branch
 
setColorTempDependencies(Color, float, Color, float) - Method in class org.concord.collisions.engine.JPartWorld
set color dependency parameters between element's temperature and element's color
setColorTempDependencies(Color, float, Color, float) - Method in class org.concord.collisions.engine.BedSpringWorld
 
setColorTransform(AlphaTransform) - Method in class org.concord.flash.player.FComponent
 
setColumn(int) - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
setColumnAlignment(int, int) - Method in class org.concord.pedagogica.ui.TabularView
 
setColumnAndRowIndices(int, int) - Method in class org.concord.biologica.engine.OrganismImage
Sets the column and row indices of this organism image.
setColumnIdentifiers(Object[]) - Method in class org.concord.pedagogica.ui.CCJTable
 
setColumnIdentifiers(Vector) - Method in class org.concord.pedagogica.ui.CCJTable
 
setColumnIndex(int) - Method in class org.concord.biologica.engine.OrganismImage
Sets the column index of this organism image.
setComponent(NodeViewItem) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
setConnectedDotMode(int, boolean) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
setConstrained(boolean) - Method in class org.concord.util.beans.PropertyDescriptor
Attempted updates to "Constrained" properties will cause a "VetoableChange" event to get fired when the property is changed.
setConstraints(float, float, float, float) - Method in class org.concord.collisions.engine.JWorldElement
 
setConstraints(float, float, float, float) - Method in class org.concord.collisions.engine.JRigidBox
 
setConstraints(float, float, float, float) - Method in class org.concord.collisions.engine.JWall
setting wall's constraints
setConstructor(boolean) - Method in class org.concord.util.script.InvocationExpression
 
setConstructor(boolean) - Method in class org.concord.util.script.IndexExpression
 
setControllable(boolean) - Method in class org.concord.collisions.engine.JWorldElement
 
setControllable(boolean) - Method in class org.concord.collisions.engine.JRigidBox
 
setCoord(float, float) - Method in class org.concord.collisions.engine.JAtom
set atom's coordinates
setCourseName(String, String) - Method in class org.concord.pedagogica.engine.Logging
 
setCrossOverCheckBox(JCheckBox) - Method in class org.concord.biologica.ui.PedigreeOrganismView
 
setCrossoverControlsVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set crossover controls visibility
setCrossoverControlsVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set crossover controls visibility
setCrossOverEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
set the Cross over check box enabled state
setCrossOverHappened(boolean) - Method in class org.concord.biologica.ui.MeiosisModel
 
setCrossOverPossibility(double) - Method in class org.concord.biologica.ui.PedigreeOrganismView
 
setCrossOverPossibility(int) - Method in class org.concord.biologica.ui.PedigreeView
set Cross over possibility
setCrossOverTurnOn(boolean) - Method in class org.concord.biologica.ui.PedigreeView
 
setCrossOverTurnOn(boolean) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set cross over turn on?
setCrossOverVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
set the Cross over check box visible state
setCrossToolEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the cross tool enabled state.
setCrossToolVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the cross tool visibility.
setCurrentChromosome(OrganismChromosome) - Method in class org.concord.biologica.ui.ChromosomeView
 
setCurrentFrame(NameStack) - Method in class org.concord.util.script.ScriptObject
 
setCurrentFrame(NameStack) - Method in class org.concord.util.script.ScriptThread
 
setCurrentNode(ActivityNode) - Method in class org.concord.pedagogica.engine.Activity
 
setCurrentSpecies(Species) - Method in class org.concord.biologica.engine.World
Set the current species.
setCurrentWorld(World) - Method in class org.concord.biologica.ui.AllInOneView
Set the current world.
setCursorColor(Color) - Method in class org.concord.biologica.ui.DNAView
Set the cursor color.
setDaemonsDragMode(int) - Method in class org.concord.collisions.ui.GUIPanel
setting drag mode for the daemons
setDataViewable(boolean) - Method in class org.concord.molecular.ui.MolecularView
Set atom data viewable in animator panel.
setDebug(boolean) - Static method in class org.concord.util.Debug
 
setDebug(boolean) - Method in class org.concord.util.script.ScriptThread
 
setDebugAll(boolean) - Static method in class org.concord.util.script.ScriptThread
 
setDebugInstance(Debug) - Static method in class org.concord.util.Debug
Set the instance of Debug that we use when calling writeString() - this allows writeString() to be overridden for situations where there are no streams (e.g.
setDebugInstance(Debug) - Static method in class org.concord.biologica.engine.Debug
Set the instance of Debug that we use when calling writeString() - this allows writeString() to be overridden for situations where there are no streams (e.g.
setDefaultCursorColor(Color) - Static method in class org.concord.biologica.ui.DNAView
Set the default cursor color.
setDefaultDifferentBaseColor(Color) - Static method in class org.concord.biologica.ui.DNAView
Set the default different base color.
setDefaultEqualBaseColor(Color) - Static method in class org.concord.biologica.ui.DNAView
Set the default equal base color.
setDefaultHighlightColor(Color) - Static method in class org.concord.biologica.ui.OrganismView
Set the default Highlight color.
setDefaultSelectionColor(Color) - Static method in class org.concord.biologica.ui.ChromosomeView
Set the default selection color.
setDefaultSelectionColor(Color) - Static method in class org.concord.biologica.ui.OrganismView
Set the default selection color.
setDefaultSelectionColor(Color) - Static method in class org.concord.biologica.ui.TreeView
Set the default selection color.
setDefaultSelectionSet(SelectionSet) - Static method in class org.concord.biologica.ui.SelectionSet
Set default selection set
setDeferApply(boolean) - Method in class org.concord.biologica.ui.DNAView
Set the defer apply setting.
setDeferRevert(boolean) - Method in class org.concord.biologica.ui.DNAView
Set the defer revert setting.
setDelay(int) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setDelta(double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setDeltaVelColor(Color) - Method in class org.concord.collisions.engine.JBooster
set color for velocity's arrows
setDeltaVx(float) - Method in class org.concord.collisions.engine.JBooster
set delta vel
setDeltaVy(float) - Method in class org.concord.collisions.engine.JBooster
set delta vel
setDepth(int) - Method in class org.concord.flash.player.FComponent
 
setDescription(String) - Method in class org.concord.biologica.engine.Species
Set the description of this species.
setDescription(String) - Method in class org.concord.biologica.engine.SpeciesAllele
Set the description of this allele.
setDescription(String) - Method in class org.concord.biologica.engine.Gene
Set the description of this gene.
setDifferentBaseColor(Color) - Method in class org.concord.biologica.ui.DNAView
Set the different base color.
setDiploidType(int) - Method in class org.concord.biologica.engine.Species
Set the diploid type of this species, which may either be DIPLOID_TYPE_XX_FEMALE_XY_MALE, DIPLOID_TYPE_XY_FEMALE_XX_MALE or DIPLOID_TYPE_NO_SEX_CHROMOSOMES.
setDiploidTypeAsString(String) - Method in class org.concord.biologica.engine.Species
Set the diploid type of this species, which may either be DIPLOID_TYPE_XX_FEMALE_XY_MALE, DIPLOID_TYPE_XY_FEMALE_XX_MALE or DIPLOID_TYPE_NO_SEX_CHROMOSOMES.
setDirectoryName(String) - Method in class org.concord.pedagogica.engine.Logging
 
setDirty() - Method in class org.concord.biologica.engine.World
Set the dirty state of this engine to true.
setDisplayName(String) - Method in class org.concord.util.beans.FeatureDescriptor
Sets the localized display name of this feature.
setDNAAlterable(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism's DNA is visible.
setDNAVisible(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism's DNA is visible.
setDoAACollisions(boolean) - Method in class org.concord.collisions.engine.JPartWorld
 
setDoAACollisions(boolean) - Method in class org.concord.collisions.engine.BedSpringWorld
 
setDoAACollisions(boolean) - Method in class org.concord.collisions.ui.GUIPanel
 
setDoAWCollisions(boolean) - Method in class org.concord.collisions.engine.JPartWorld
 
setDoAWCollisions(boolean) - Method in class org.concord.collisions.engine.BedSpringWorld
 
setDoAWCollisions(boolean) - Method in class org.concord.collisions.ui.GUIPanel
 
setDoCollisions(boolean) - Method in class org.concord.collisions.engine.JPartWorld
 
setDocumentBase(URL) - Method in class org.concord.pedagogica.ui.ViewerStub
 
setDocumentLocator(Locator) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
setDot(int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setDot(int) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setDot(int) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setDoTrace(boolean) - Method in class org.concord.collisions.engine.JAtom
 
setDotSelection(int) - Method in class org.concord.pedagogica.PedAgogica
 
setDraggable(boolean) - Method in class org.concord.collisions.engine.JWorldElement
 
setDraggable(boolean) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
setDraggable(boolean) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
setDraggable(boolean) - Method in class org.concord.collisions.ui.PassiveElement
 
setDraggable(boolean) - Method in interface org.concord.collisions.ui.CCDraggable
 
setDraggedClip(FMovieClip, boolean, boolean, float, float, float, float) - Method in class org.concord.flash.player.FMouseSupport
 
setDragMode(int) - Method in class org.concord.collisions.engine.JDaemon
 
setDragMode(int) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
setDrawForce(boolean) - Method in class org.concord.collisions.engine.CCBedSpringForce
 
setDrawMode(int) - Method in class org.concord.collisions.engine.CCConstantForce
 
setEditable(boolean) - Method in class org.concord.util.BarGraph
Make gauges editable.
setEditable(boolean) - Method in class org.concord.util.Gauge
Make gauges editable.
setEditable(boolean) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setEditable(boolean) - Method in class org.concord.collisions.ui.GUIPanel
 
setEditable(boolean) - Method in class org.concord.molecular.ui.MolecularView
Sets contained AnimatorPanel editable.
setEditor(Editor) - Method in interface org.concord.util.Editable
 
setElement(int, Object) - Method in class org.concord.flash.player.FArray
 
setElement(int, Object) - Method in class org.concord.flash.player.builtin.FArray
 
setElseCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Sets the else characteristic of this genotype to phenotype rule.
setElseStatement(Statement) - Method in class org.concord.util.script.IfThenElseStatement
 
setEnabled(boolean) - Method in class org.concord.collisions.engine.JWorldElement
Set the enabled state of the JWorldElement.
setEnabled(boolean) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setEnabled(boolean) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setEnclosingViewRectangle(Rectangle) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the enclosing rectangle for the view containing a display of this chromosome model.
setEnclosingViewRectangle(Rectangle) - Method in class org.concord.biologica.ui.FertilizationModel
Set the rectangle within which the fertilization model must confine itself and its chromosomes.
setEnclosingViewRectangle(Rectangle) - Method in class org.concord.biologica.ui.MeiosisModel
Set the rectangle within which the meiosis model must confine itself and its chromosomes.
setEnclosingViewRectangle(Rectangle) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Set the enclosing rectangle for the view containing a display of this chromosome model.
setEnterCount(int) - Method in class org.concord.pedagogica.engine.ActivityNode
 
setEpsilon(double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setEqualBaseColor(Color) - Method in class org.concord.biologica.ui.DNAView
Set the equal base color.
setError(Throwable) - Method in class org.concord.pedagogica.engine.NodeAccess
 
setError(Throwable) - Method in class org.concord.pedagogica.ui.RunActivity
 
setErrorHandler(ActivityErrorHandler) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setErrorHandler(ActivityItemErrorHandler) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setErrorHandler(ActivityItemErrorHandler) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setErrorHandler(ActivityItemErrorHandler) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setErrorHandler(ScriptError) - Method in interface org.concord.util.script.ScriptRuntime
 
setErrorHandler(ScriptError) - Method in class org.concord.util.script.ECMA
 
setExceptionListener(ExceptionListener) - Method in class org.concord.util.beans.XMLDecoder
Sets the exception handler for this stream to exceptionListener.
setExceptionListener(ExceptionListener) - Method in class org.concord.util.beans.Encoder
Sets the exception handler for this stream to exceptionListener.
setExpert(boolean) - Method in class org.concord.util.beans.FeatureDescriptor
The "expert" flag is used to distinguish between features that are intended for expert users from those that are intended for normal users.
setExpression(Expression) - Method in class org.concord.util.script.ExpressionStatement
 
setExpression(Expression) - Method in class org.concord.util.script.AssignmentStatement
 
setExpression(Expression) - Method in class org.concord.util.script.ReturnStatement
 
setExtendsExpression(InvocationExpression) - Method in class org.concord.util.script.ExtendsDeclaration
 
setFatal(boolean) - Method in class org.concord.biologica.engine.Characteristic
Set the fatality of this characteristic.
setFatherOrganism(Organism) - Method in class org.concord.biologica.ui.SexView
Set the father organism for this view
setFertilizationManuallyDisabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set whether fertilization is manually disabled or not.
setFertilizationManuallyDisabled(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set whether fertilization is manually disabled or not.
setFertilizationManuallyDisabled(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether fertilization is manually disabled or not.
setField(String) - Method in class org.concord.molecular.engine.AtomicProperty
 
setFieldValue(Object, String, Object) - Method in class org.concord.util.script.ScriptObject
 
setFile(File) - Method in class org.concord.biologica.engine.World
Set file.
setFileControlsVisible(boolean) - Method in class org.concord.biologica.ui.AllInOneView
Set file controls visible
setFilled(boolean) - Method in class org.concord.collisions.ui.PassiveRect
 
setFillStyle0(int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
setFillStyle1(int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
setFilter(JWorldElementFilter) - Method in class org.concord.collisions.engine.JDaemon
 
setFixedNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the fixed number of children from a breeding.
setFixedNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the fixed number of children from a breeding.
setFlashing(boolean) - Method in class org.concord.collisions.engine.JWorldElement
 
setFont(Font) - Method in class org.concord.biologica.ui.UIView
Set the font for this view.
setFont(Font) - Method in class org.concord.biologica.ui.AllInOneView
Set the font for this view.
setFont(Font) - Method in class org.concord.biologica.ui.SexView
Set the font for this view.
setFont(Font) - Method in class org.concord.collisions.ui.PassiveText
 
setForce(double, double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setForceCalculator(CCForceCalculator) - Method in class org.concord.collisions.engine.JWorldElement
 
setForceCalculator(CCForceCalculator) - Method in class org.concord.collisions.engine.JPartWorld
 
setForeColor(Color) - Method in class org.concord.collisions.ui.PassiveElement
 
setForeground(Color) - Method in class org.concord.biologica.ui.UIView
Set the foreground color for this view.
setForeground(Color) - Method in class org.concord.biologica.ui.SexView
Set the foreground color for this view.
setForeground(Color) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overrides JComponent.setForeground to assign the unselected-foreground color to the specified color.
setForegroundCellSubViews(Color) - Method in class org.concord.biologica.ui.SexView
Set the foreground color for the cell sub views.
setForegroundOrganismSubViews(Color) - Method in class org.concord.biologica.ui.SexView
Set the foreground color for the organism sub views.
setFrame(JFrame) - Method in class org.concord.pedagogica.ui.ActivityView
 
setFrameRateDrawn(boolean) - Method in class org.concord.flash.player.FFlash
if frameRateDrawn is true then the current frame rate is displayed at the top left corner of the movie.
setGameteMoveButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether the replay button is enabled.
setGauge - Variable in class org.concord.util.Gauge
 
setGaugeSize(Dimension) - Method in class org.concord.util.Gauge
 
setGaugeWidth(int) - Method in class org.concord.util.BarGraph
Sets value that determines pixel spaceing between gauges.
setGender(int) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Set the gender of the images in this column.
setGender(int) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Set the gender of this genotype to phenotype rule.
setGender(int) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the gender of the images in this row.
setGenderAsString(String) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Set the gender of the images in this column as a string.
setGenderAsString(String) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Set the gender of this genotype to phenotype rule.
setGenderAsString(String) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the gender of the images in this row as a string.
setGeometry(float, float) - Method in class org.concord.collisions.engine.JDaemon
set geometry's parameters
setGeometry(float, float, float) - Method in class org.concord.collisions.engine.JAtom
set geometry's parameters
setGeometry(float, float, float, float) - Method in class org.concord.collisions.engine.JWall
set geometry's parameters for the wall with default thickness
setGeometry(float, float, float, float) - Method in class org.concord.collisions.engine.JDaemon
set geometry's parameters
setGeometry(float, float, float, float, float) - Method in class org.concord.collisions.engine.JRigidBox
 
setGeometry(float, float, float, float, float) - Method in class org.concord.collisions.engine.JWall
set geometry's parameters for the wall
setGeometry(GUIPanel, float, float, float) - Method in class org.concord.collisions.engine.JAtom
set geometry's parameters
setGeometry(GUIPanel, float, float, float, float) - Method in class org.concord.collisions.engine.JWall
set geometry's parameters for the wall with default thickness
setGeometry(GUIPanel, float, float, float, float, float) - Method in class org.concord.collisions.engine.JWall
set geometry's parameters for the wall
setGeometry(Object) - Method in class org.concord.collisions.engine.JWorldElement
 
setGeometry(Object) - Method in class org.concord.collisions.engine.JRigidBox
 
setGeometry(Object) - Method in class org.concord.collisions.engine.JWall
 
setGeometry(Object) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
setGeometry(Object) - Method in class org.concord.collisions.engine.JAtom
 
setGeometry(Object) - Method in class org.concord.collisions.engine.JBooster
 
setGlobals(NameStack) - Method in class org.concord.util.script.NameStack
 
setGlobals(NameStack) - Method in class org.concord.util.script.Script
 
setGlobalUnits(int, int) - Method in class org.concord.util.CCUnit
 
setGoToEndButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set go to end button enabled.
setGoToEndButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set go to end button enabled.
setGoToEndButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set go to end button visibility.
setGoToEndButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set go to end button visibility.
setGoToStartButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set go to start button enabled.
setGoToStartButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set go to start button enabled.
setGoToStartButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set go to start button visibility.
setGoToStartButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set go to start button visibility.
setGravity(float, float) - Method in class org.concord.collisions.engine.JPartWorld
 
setGravityX(float) - Method in class org.concord.collisions.engine.JPartWorld
 
setGravityY(float) - Method in class org.concord.collisions.engine.JPartWorld
 
setGrid() - Method in class org.concord.collisions.ui.GUIPanel
 
setGrid(int, int, int, int) - Method in class org.concord.collisions.ui.GUIPanel
 
setGridColor(Color) - Method in class org.concord.util.LineGraph
 
setGuiPanel(GUIPanel) - Method in class org.concord.collisions.engine.JPartWorld
 
setHandlerName(String) - Method in class org.concord.util.script.ListenStatement
 
setHandlerName(String) - Method in class org.concord.util.script.HandlerDeclaration
 
setHandlerType(String) - Method in class org.concord.util.script.ListenStatement
 
setHasFocus(boolean) - Method in class org.concord.biologica.ui.TreeViewNode
Set whether this node has focus.
setHeatConductKoeff(float) - Method in class org.concord.collisions.engine.JWall
set heat conducting koeff.
setHeight(float) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setHeight(int) - Method in class org.concord.biologica.engine.Environment
Set the height of the environment.
setHeight(int) - Method in class org.concord.biologica.ui.PedigreeObject
Set the height
setHeight(int) - Method in class org.concord.collisions.event.AreaEvent
 
setHeight(int) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setHidden(boolean) - Method in class org.concord.util.beans.FeatureDescriptor
The "hidden" flag is used to identify features that are intended only for tool use, and which should not be exposed to humans.
setHighlightColor(Color) - Method in class org.concord.biologica.ui.OrganismView
Set the highlight color.
setHotspotColor(Color) - Method in class org.concord.biologica.engine.SpeciesImage
Set the hotspot color of this species image
setHotspotRadius(int) - Method in class org.concord.biologica.engine.SpeciesImage
Set the hotspot radius of this species image.
setHtmlPage(String) - Method in class org.concord.pedagogica.ui.HTMLView
 
setHtmlPage(String, String) - Method in class org.concord.pedagogica.ui.HTMLView
 
setHTMLText(String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setHtmlText2(String, int) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setHTMLView(String, String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setIcon(Component, String) - Method in class org.concord.collisions.ui.PassiveIcon
 
setIcon(String) - Method in class org.concord.collisions.engine.JAtom
sets icon to show by default the icon is as big as the atom and scales with it
setIcon(String) - Method in class org.concord.collisions.ui.PassiveIcon
 
setIcon(String, int, int, boolean) - Method in class org.concord.collisions.engine.JAtom
sets icon to show, specifying width and height in pixels
setIconSize(int, int, boolean) - Method in class org.concord.collisions.engine.JAtom
sets the size of the icon to show, specifying width and height in pixels
setId(int) - Method in class org.concord.molecular.engine.AtomAccessor
 
setID(int) - Method in class org.concord.biologica.engine.EngineObject
Set the id of the object.
setIfExpression(Expression) - Method in class org.concord.util.script.IfThenElseStatement
 
setIfStatement(Statement) - Method in class org.concord.util.script.IfThenElseStatement
 
setImageColumnWidth(int, int) - Method in class org.concord.biologica.engine.Species
Set the image column width of a particular image size for this species.
setImageID(int) - Method in class org.concord.biologica.engine.Characteristic
Set the image ID of this characteristic.
setImageNumber(int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Sets the image number of this chromosome.
setImageNumber(int) - Method in class org.concord.biologica.engine.OrganismChromosome
Sets the image number of this chromosome.
setImageRowHeight(int, int) - Method in class org.concord.biologica.engine.Species
Set the image row height of a particular image size for this species.
setImageType(int) - Method in class org.concord.biologica.engine.SpeciesImage
Set the image type of this species image.
setImageVisible(boolean) - Static method in class org.concord.biologica.engine.SpeciesImage
 
setImportName(String) - Method in class org.concord.util.script.ImportDeclaration
 
setImports(NameStack) - Method in class org.concord.util.script.NameStack
 
setImportThrowUp(boolean) - Method in class org.concord.util.script.Script
 
setInactiveColor(Color) - Method in class org.concord.collisions.engine.JDaemon
set color to show when the daemon is inactive
setInDefaultEventSet(boolean) - Method in class org.concord.util.beans.EventSetDescriptor
Marks an event set as being in the "default" set (or not).
setIndex(int) - Method in class org.concord.collisions.engine.JWorldElement
 
setIndex(int) - Method in class org.concord.molecular.engine.ConditionValue
 
setIndex(int) - Method in class org.concord.molecular.engine.AtomAccessor
 
setIndexedReadMethod(Method) - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Sets the method that should be used to read an indexed property value.
setIndexedWriteMethod(Method) - Method in class org.concord.util.beans.IndexedPropertyDescriptor
Sets the method that should be used to write an indexed property value.
setIndexExpression(Expression) - Method in class org.concord.util.script.ReferenceExpression
Set the index expression.
setIndices(int[]) - Method in class org.concord.molecular.engine.ConditionValue
 
setIndices(Vector) - Method in class org.concord.molecular.engine.ConditionValue
 
setInfo(String) - Method in interface org.concord.collisions.ui.CCInfoDrawer
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JRigidBox
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JWall
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JDaemon
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JAtom
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
setInfoDrawer(CCInfoDrawer) - Method in class org.concord.collisions.ui.PassiveElement
 
setInfoDrawer(CCInfoDrawer) - Method in interface org.concord.collisions.ui.CCDraggable
 
setInitDelay(float) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setInitializer(Expression) - Method in class org.concord.util.script.VariableDeclaration
 
setInputStream(InputStream) - Method in class org.concord.flash.player.FFlash
Sets the input stream of the flash movie file.
setInstructorName(String) - Method in class org.concord.pedagogica.engine.Logging
 
setInterval(int) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setInterval(int) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
This sets the graph interval.
setIntervalCm(int, int) - Method in class org.concord.collisions.ui.PassiveGrid
 
setIntervalPixels(int, int) - Method in class org.concord.collisions.ui.PassiveGrid
 
setItemName(String) - Method in class org.concord.pedagogica.ui.ActivityView
 
setItemNumber(int) - Static method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setJavaHome(String) - Method in class org.concord.util.PathDialog
 
setJavaHome(String) - Method in class org.concord.pedagogica.ui.ActivityView
 
setJavaHome(String) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
setK(float) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
setK(float) - Method in class org.concord.collisions.engine.CCFrictionForce
 
setK(float) - Method in class org.concord.collisions.engine.CCBedSpringForce
 
setK(float) - Method in class org.concord.collisions.engine.CCFrictionForceCalculator
 
setKEConstant(double) - Method in class org.concord.molecular.ui.MolecularView
 
setKEConstant(float) - Method in class org.concord.molecular.ui.MolecularView
 
setKEFactor(double) - Method in class org.concord.molecular.ui.MolecularView
 
setKEFactor(float) - Method in class org.concord.molecular.ui.MolecularView
 
setKind(int) - Method in class org.concord.collisions.engine.CCFrictionForce
 
setKind(int) - Method in class org.concord.collisions.engine.CCFrictionForceCalculator
 
setKm(float[]) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
setLargeHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the large hotspot location.
setLastError(Throwable) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setLength0(float) - Method in class org.concord.collisions.engine.CCBedSpringForceCalculator
 
setLengthInBases(int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Sets the length of the chromosome in bases.
setLengthInBases(int) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Set the length in bases of this nucleic acid.
setLengthInBases(int) - Method in class org.concord.biologica.engine.Gene
Set the length in bases of this gene.
setLHS(String) - Method in class org.concord.util.script.FactAssignStatement
 
setLineGraphSize(Dimension) - Method in class org.concord.util.LineGraph
 
setLineStyle(int) - Method in class org.concord.flash.player.FMovieBuilder.ShapeBuilder
 
setLocalVariable(String, Object) - Method in class org.concord.flash.player.StackFrame4
 
setLocation(double, double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setLocation(int, int) - Method in class org.concord.biologica.ui.CursorText
 
setLocation(int, int) - Method in class org.concord.collisions.ui.PassiveLine
 
setLocation(int, int, int) - Method in class org.concord.collisions.ui.PassiveIcon
 
setLockedState(int) - Method in class org.concord.biologica.engine.EngineObject
Set the locked state of the object.
setLockedState(int) - Method in class org.concord.biologica.engine.World
Set the locked state of the object, recursively setting the locked state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.SpeciesImage
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.Species
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.NucleicAcid
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.SpeciesAllele
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.Organism
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.Family
Set the locked state of the object, recursively setting the locked state of children objects.
setLockedState(int) - Method in interface org.concord.biologica.engine.INucleicAcid
Set the lock state of the object.
setLockedState(int) - Method in class org.concord.biologica.engine.OrganismChromosome
Set the lock state of the object, recursively setting the lock state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.Gene
Set the locked state of the object, recursively setting the locked state of children objects.
setLockedState(int) - Method in class org.concord.biologica.engine.Trait
Set the locked state of the object, recursively setting the lock state of children objects.
setLockedStateAsString(String) - Method in class org.concord.biologica.engine.EngineObject
Set locked state of this object using a string.
setLockSymbolVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the lock symbol visible boolean.
setLockSymbolVisible(boolean) - Method in class org.concord.biologica.ui.OrganismView
Set the lock symbol visible boolean.
setLogDirectory(String) - Method in class org.concord.pedagogica.engine.LogModel
 
setLogDirectory(String) - Method in class org.concord.pedagogica.ui.LogView
 
setLogging(Logging) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setLoginButtonText(String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setLoginHTML(String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setLoginLabelText(String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setLogLevel(int) - Static method in class org.concord.util.Debug
Set the log level.
setLogLevel(int) - Static method in class org.concord.biologica.engine.Debug
Set the log level.
setLooping(boolean) - Method in class org.concord.collisions.engine.JDaemon
Set looping daemon or not looping daemon
setMagnifyButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set magnify button enabled.
setMagnifyButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set magnify button enabled.
setMagnifyButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set magnify button enabled.
setMagnifyButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set magnify button enabled.
setMagnifyButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set magnify button visibility.
setMagnifyButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set magnify button visibility.
setMagnifyButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set magnify button visibility.
setMagnifyButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set magnify button visibility.
setMajorTickMarks(int) - Method in class org.concord.util.Gauge
 
setMakeSound(boolean) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setMakeSound(boolean) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
setManualLocked(boolean) - Method in class org.concord.biologica.engine.EngineObject
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.World
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesChromosome
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesImage
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.Species
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.NucleicAcid
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.SpeciesAllele
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.Organism
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.Family
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in interface org.concord.biologica.engine.INucleicAcid
Set the manual locked state of this object.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.OrganismChromosome
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.Gene
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setManualLocked(boolean) - Method in class org.concord.biologica.engine.Trait
Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
setMass(double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setMass(float) - Method in class org.concord.collisions.engine.JWorldElement
 
setMass(float) - Method in class org.concord.collisions.engine.JRigidBox
 
setMax(double) - Method in class org.concord.util.BarGraph
 
setMax(double) - Method in class org.concord.util.Gauge
Set the maximum value of the gauge.
setMax(double) - Method in class org.concord.util.LineGraph
 
setMax(double) - Method in class org.concord.molecular.engine.ConditionValue
 
setMax(float) - Method in class org.concord.util.LineGraph
 
setMaximumNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the maximum number of children from a breeding.
setMaximumNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the maximum number of children from a breeding.
setMaxVel(float) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setMediumHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the medium hotspot location.
setMeiosisChromosomeModelType(int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set chromosome model type.
setMeiosisModels(MeiosisModel, MeiosisModel) - Method in class org.concord.biologica.ui.FertilizationModel
Set the meiosis models of this fertilization model, deleting any existing state for other meiosis models.
setMember(String, Object) - Method in class org.concord.flash.player.FScriptObject
Sets a member field.
setMembers(NameStack) - Method in class org.concord.util.script.NameStack
 
setMemberValue(String, Object) - Method in class org.concord.util.script.Script
 
setMemoryMenuVisible(boolean) - Method in class org.concord.biologica.ui.AllInOneView
Set memory menu visible
setMenuEnabled(String, boolean) - Method in class org.concord.util.Editor
 
setMethodThrowUp(boolean) - Method in class org.concord.util.script.Script
 
setMin(double) - Method in class org.concord.util.Gauge
Set the minimum value of the gauge.
setMin(double) - Method in class org.concord.molecular.engine.ConditionValue
 
setMinimumNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the minimum number of children from a breeding.
setMinimumNumberChildren(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the minimum number of children from a breeding.
setMinMaxNumberChildren(int, int) - Method in class org.concord.biologica.ui.PedigreeView
Set the minimum and maximum number of children from a breeding.
setMinMaxNumberChildren(int, int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the minimum and maximum number of children from a breeding.
setMinorTickMarks(int) - Method in class org.concord.util.Gauge
 
setModelType(String) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setModified(boolean) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setModified(boolean) - Method in class org.concord.pedagogica.ui.ActivityView
 
setModify(boolean) - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
setMolecularModel(MolecularModel) - Method in class org.concord.molecular.ui.MolecularView
 
setMotherOrganism(Organism) - Method in class org.concord.biologica.ui.SexView
Set the mother organism for this view
setMoveable(boolean) - Method in class org.concord.collisions.engine.JRigidBox
 
setMoveable(boolean) - Method in class org.concord.collisions.engine.JWall
set moveable property
setMoveable(boolean) - Method in class org.concord.collisions.ui.PassiveElement
 
setMutationAllele(boolean) - Method in class org.concord.biologica.engine.SpeciesAllele
Set whether or not this allele is the mutation allele for its gene.
setName(String) - Method in class org.concord.util.beans.FeatureDescriptor
Sets the programmatic name of this feature.
setName(String) - Method in class org.concord.util.script.ScriptObject
Set the node name.
setName(String) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Set the name of this species image column.
setName(String) - Method in class org.concord.biologica.engine.Environment
Set the name of this environment.
setName(String) - Method in class org.concord.biologica.engine.SpeciesImage
Set the name of this species image.
setName(String) - Method in class org.concord.biologica.engine.Species
Set the name of this species.
setName(String) - Method in class org.concord.biologica.engine.Organism
Set the name of this organism.
setName(String) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Sets the name.
setName(String) - Method in class org.concord.biologica.engine.Characteristic
Set the name of this characteristic.
setName(String) - Method in class org.concord.biologica.engine.BioEngine
Sets the name of the bioengine.
setName(String) - Method in class org.concord.biologica.engine.Gene
Set the name of this gene.
setName(String) - Method in class org.concord.biologica.engine.Trait
Set the name of this trait.
setName(String) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the name of this species image row.
setName(String) - Method in class org.concord.biologica.engine.Terrain
Set the name of this terrain.
setName(String) - Method in class org.concord.collisions.engine.JWorldElement
set name's property
setName(String) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setName(String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setName(String) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setName(String) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setName(String) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setName(String) - Method in class org.concord.pedagogica.ui.NamedTreeNode
 
setName(String) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
setNameSuperVisible(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism's name is super visible, meaning that the name should be shown even when a view isn't showing names in general.
setNameTextVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the name text visible boolean.
setNameTextVisible(boolean) - Method in class org.concord.biologica.ui.OrganismView
Set the name text visible boolean.
setNameTextVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set the name text visible boolean.
setNegate(boolean) - Method in class org.concord.molecular.engine.ConditionValue
 
setNewAllele(String) - Method in class org.concord.biologica.ui.ChromosomeView
 
setNode(ActivityNode) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setNode(ActivityNode) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
setNodeAccess(NodeAccess) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setNodeAccess(NodeAccess) - Method in class org.concord.pedagogica.engine.Activity
 
setNodeList(Vector) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
setNumberFemaleChildren(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberFemaleChildren(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberMaleChildren(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberMaleChildren(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberMaleFemaleChildren(int, int) - Method in class org.concord.biologica.ui.PedigreeView
Set the number of female and male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberMaleFemaleChildren(int, int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the number of female and male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
setNumberOfAtoms(int) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setNumberOfBars(int) - Method in class org.concord.util.Gauge
 
setNumberOfBends(int) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
setNumberOfBonds(int) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
setNumberOfGauges(int) - Method in class org.concord.util.BarGraph
Sets the number of gauges in this graph.
setNumberOfMolecules(int) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
setNumberType(int) - Method in class org.concord.biologica.engine.SpeciesChromosome
Sets the number or type of this chromosome.
setNumberType(int) - Method in class org.concord.biologica.engine.OrganismChromosome
Sets the number or type of this chromosome.
setNumberTypeAsString(String) - Method in class org.concord.biologica.engine.SpeciesChromosome
Sets the number or type of this chromosome, using a string as input.
setNumberTypeAsString(String) - Method in class org.concord.biologica.engine.OrganismChromosome
Sets the number or type of this chromosome, using a string as input.
setObject(EngineObject) - Method in class org.concord.biologica.ui.ObjectPropertiesView
Set the engine object whose properties should be shown in this view.
setObject(Object) - Method in class org.concord.pedagogica.ui.HTMLViewCustomizer
 
setObjectExpression(Expression) - Method in class org.concord.util.script.ReferenceExpression
Set the object expression.
setObstacles(ObstacleCollection) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setObstacles(ObstacleCollection) - Method in class org.concord.molecular.engine.DefaultMolecularModel
 
setOffsets(int, int) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setOffspringMode(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the offspring mode
setOffspringMode(int) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the offspring mode
setOffspringModePulldown(BioComboBox) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the offspring mode pulldown.
setOffspringModePulldownEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the offspring mode pulldown enabled state.
setOffspringModePulldownVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the offspring mode pulldown visibility.
setOldAllele(String) - Method in class org.concord.biologica.ui.ChromosomeView
 
setOnlyLiveChildren(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the Only Live Children flag
setOnlyLiveChildren(boolean) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the Only Live Children flag
setOperand(Expression) - Method in class org.concord.util.script.UnaryExpression
 
setOrganism(Organism) - Method in class org.concord.biologica.ui.ChromosomeView
Set the shown organism for this view.
setOrganism(Organism) - Method in class org.concord.biologica.ui.StaticOrganismView
Set the current organism to be shown in this view.
setOrganismAllele(OrganismAllele) - Method in class org.concord.biologica.ui.DNAView
Set the shown organism allele for this view.
setOrganismAllelePair(OrganismAllelePair) - Method in class org.concord.biologica.ui.DNAView
Set the shown organism allele pair for this view.
setOrganismImageSize(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the organism image size for this view.
setOrganismImageSize(int) - Method in class org.concord.biologica.ui.OrganismView
Set the organism image size for this view.
setOrganismImageSize(int) - Method in class org.concord.biologica.ui.SexView
Set the organism image size for this view.
setOrganismImagesVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the organism images visible
setOrganismImagesVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the organism images visible
setOrganismLayoutStyle(int) - Method in class org.concord.biologica.ui.MultipleOrganismView
Set the current organism layout style.
setOrganismViewHeightPercentage(int) - Method in class org.concord.biologica.ui.SexView
Set the organism view height percentage.
setOrientation(int) - Method in class org.concord.biologica.ui.ToolView
Set the orientation of the view - horizontal or vertical.
setOriginElement(CCMassive) - Method in class org.concord.collisions.ui.GUIPanel
 
setOwner(JWorldElement) - Method in class org.concord.collisions.engine.JWorldElement
 
setOwner(Object) - Method in class org.concord.util.beans.XMLDecoder
Sets the owner of this decoder to owner.
setOwner(Object) - Method in class org.concord.util.beans.XMLEncoder
Sets the owner of this encoder to owner.
setOwner(Principal) - Method in class org.concord.util.script.ScriptThread
 
setPadding(int, int) - Method in class org.concord.pedagogica.ui.TabularView
 
setPage(String, String) - Method in class org.concord.pedagogica.ui.HelpView
 
setParameters(Properties) - Method in class org.concord.pedagogica.ui.ViewerStub
 
setParameters(Stack) - Method in class org.concord.util.script.MethodDeclaration
 
setParentCrossOver(boolean) - Method in class org.concord.biologica.engine.Organism
 
setParentFamily(Family) - Method in class org.concord.biologica.engine.Organism
Set the parent family for this organism.
setParentNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setParentNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setParentNode(ActivityNodeItem) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setPartialMatch(boolean) - Static method in class org.concord.util.Debug
 
setPath(Stack) - Method in class org.concord.util.script.ImportDeclaration
 
setPath(String) - Method in class org.concord.util.PathDialog
 
setPathList(Vector) - Method in class org.concord.pedagogica.engine.LogModel
 
setPause(boolean) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setPedigreeSymbolFirstColor(Color) - Method in class org.concord.biologica.engine.Characteristic
Set the first pedigree symbol color of this characteristic
setPedigreeSymbolSecondColor(Color) - Method in class org.concord.biologica.engine.Characteristic
Set the second pedigree symbol color of this characteristic
setPedigreeSymbolType(int) - Method in class org.concord.biologica.engine.Characteristic
Set the first pedigree symbol type of this characteristic
setPedigreeSymbolTypeAsString(String) - Method in class org.concord.biologica.engine.Characteristic
Set the first pedigree symbol type of this characteristic, using a string as input.
setPersistenceDelegate(Class, PersistenceDelegate) - Method in class org.concord.util.beans.Encoder
Sets the persistence delegate associated with this type to persistenceDelegate.
setPlayBackwardFastToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play backward fast toggle button enabled.
setPlayBackwardFastToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play backward fast toggle button enabled.
setPlayBackwardFastToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play backward fast toggle button visibility.
setPlayBackwardFastToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play backward fast toggle button visibility.
setPlayBackwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play backward toggle button enabled.
setPlayBackwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play backward toggle button enabled.
setPlayBackwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play backward toggle button visibility.
setPlayBackwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play backward toggle button visibility.
setplayForwardFastToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play forward fast toggle button enabled.
setplayForwardFastToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play forward fast toggle button enabled.
setplayForwardFastToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play forward fast toggle button visibility.
setplayForwardFastToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play forward fast toggle button visibility.
setPlayForwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play forward toggle button enabled.
setPlayForwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set play forward toggle button enabled.
setPlayForwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set play forward toggle button enabled.
setPlayForwardToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play forward toggle button enabled.
setPlayForwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set play forward toggle button visibility.
setPlayForwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set play forward toggle button visibility.
setPlayForwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set play forward toggle button visibility.
setPlayForwardToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set play forward toggle button visibility.
setPloidyNumber(int) - Method in class org.concord.biologica.engine.Species
Set the ploidy number, which must be 1 or 2.
setPLStrand(OrganismAllele[]) - Method in class org.concord.biologica.engine.Branch
 
setPLStrandColor(Color[]) - Method in class org.concord.biologica.engine.Branch
 
setPoints() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setPositionChanger(CCElementPositionChanger) - Method in class org.concord.collisions.engine.JWorldElement
 
setPositions(JWorldElement) - Method in interface org.concord.collisions.engine.CCElementPositionChanger
 
setPositions(JWorldElement) - Method in class org.concord.collisions.engine.CCHarmonicPositionChanger
 
setPossibility(double) - Method in class org.concord.biologica.engine.CrossOver
change the possibility of crossover
setPossibility(double) - Method in class org.concord.biologica.engine.Branch
 
setPreferred(boolean) - Method in class org.concord.util.beans.FeatureDescriptor
The "preferred" flag is used to identify features that are particularly important for presenting to humans.
setPressedState(boolean) - Method in class org.concord.collisions.engine.JWorldElement
 
setPreviousMeiosisChromosomeModel(MeiosisChromosomeModel) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the previous chromosome model of this chromosome model.
setPrinter(PrintWriter) - Method in interface org.concord.util.script.ScriptRuntime
 
setPrinter(PrintWriter) - Method in class org.concord.util.script.ECMA
 
setPrintWriter(PrintWriter, boolean) - Static method in class org.concord.util.Debug
Set the printStream to print logging output to.
setPrintWriter(PrintWriter, boolean) - Static method in class org.concord.biologica.engine.Debug
Set the printStream to print logging output to.
setPrintWriter2(PrintWriter, boolean) - Static method in class org.concord.util.Debug
Set the printStream2 to print logging output to.
setPrintWriter2(PrintWriter, boolean) - Static method in class org.concord.biologica.engine.Debug
Set the printStream2 to print logging output to.
setProjectionX(float) - Method in class org.concord.collisions.engine.CCConstantForce
 
setProjectionY(float) - Method in class org.concord.collisions.engine.CCConstantForce
 
setPropagationId(Object) - Method in class org.concord.util.beans.PropertyChangeEvent
Sets the propagationId object for the event.
setProperties(ClientProperties) - Method in class org.concord.pedagogica.ui.ActivityView
 
setProperty(String, Object) - Method in class org.concord.collisions.engine.JWorldElement
 
setProperty(String, Object) - Method in class org.concord.collisions.engine.JAtom
set propertie's value
setProperty(String, String) - Method in interface org.concord.util.script.ScriptRuntime
 
setProperty(String, String) - Method in class org.concord.util.script.ECMA
 
setPropertyEditorClass(Class) - Method in class org.concord.util.beans.PropertyDescriptor
Normally PropertyEditors will be found using the PropertyEditorManager.
setPropertyForAlElementsInRect(String, int, float, float, float, float, Object) - Method in class org.concord.collisions.ui.GUIPanel
 
setPropertyForAtomsInRect(String, float, float, float, float, Object) - Method in class org.concord.collisions.engine.JPartWorld
set propertie's value for all atoms in given rectangle
setPropertyForWallsInRect(String, float, float, float, float, Object) - Method in class org.concord.collisions.engine.JPartWorld
 
setPRStrand(OrganismAllele[]) - Method in class org.concord.biologica.engine.Branch
 
setPRStrandColor(Color[]) - Method in class org.concord.biologica.engine.Branch
 
setPStrandOneAlleles(OrganismAllele[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setPStrandOneColors(Color[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setPStrandTwoAlleles(OrganismAllele[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setPStrandTwoColors(Color[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setQLStrand(OrganismAllele[]) - Method in class org.concord.biologica.engine.Branch
 
setQLStrandColor(Color[]) - Method in class org.concord.biologica.engine.Branch
 
setQRStrand(OrganismAllele[]) - Method in class org.concord.biologica.engine.Branch
 
setQRStrandColor(Color[]) - Method in class org.concord.biologica.engine.Branch
 
setQStrandOneAlleles(OrganismAllele[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setQStrandOneColors(Color[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setQStrandTwoAlleles(OrganismAllele[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setQStrandTwoColors(Color[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
 
setQuestion(JTextComponent) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionFont(Font) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionFont(Font) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setQuestionID(String) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
setQuestionID(String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionID(String) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setQuestionID(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
setQuestionID(String) - Method in class org.concord.pedagogica.ui.EssayFill
 
setQuestionID(String, String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionPrefix(String) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
setQuestionPrefix(String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionPrefix(String) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setQuestionPrefix(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
setQuestionPrefix(String) - Method in class org.concord.pedagogica.ui.EssayFill
 
setQuestionState(QuestionState) - Method in interface org.concord.pedagogica.engine.QuestionForm
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.CustomEssayFill
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.CustomChoiceQuestion
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.BlankFill
 
setQuestionState(QuestionState) - Method in class org.concord.pedagogica.ui.EssayFill
 
setQuestionTextVisible(boolean) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setQuestionTextVisible(boolean) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setQuestionTextVisible(boolean) - Method in class org.concord.pedagogica.ui.BlankFill
 
setQuestionTextVisible(boolean) - Method in class org.concord.pedagogica.ui.EssayFill
 
setR(float) - Method in class org.concord.collisions.engine.JAtom
 
setRange(double, double) - Method in class org.concord.molecular.engine.ConditionValue
 
setReader(Reader) - Method in interface org.concord.util.script.ScriptRuntime
 
setReader(Reader) - Method in class org.concord.util.script.ECMA
 
setReadMethod(Method) - Method in class org.concord.util.beans.PropertyDescriptor
Sets the method that should be used to read the property value.
setReference(ReferenceExpression) - Method in class org.concord.util.script.AssignmentStatement
 
setReplaceString(String) - Method in class org.concord.pedagogica.ui.ActivitySearchResult
 
setReplayButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether the replay button is enabled.
setReplayButtonVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether the replay button is visible.
setResetAutomatic(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether a reset is automatic when an offspring is created.
setResetButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether the reset button is enabled.
setResetButtonVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether the reset button is visible.
setResetDeleteOffspringOrganism(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether reset should automaticallly delete an offspring organism.
setRestraint(float, float) - Method in class org.concord.molecular.engine.AtomAccessor
 
setRestraint(int) - Method in class org.concord.molecular.engine.AtomAccessor
 
setRevertVisible(boolean) - Method in class org.concord.biologica.ui.DNAView
 
setRHS(ScriptObject) - Method in class org.concord.util.script.FactAssignStatement
 
setRootEngineObject(EngineObject) - Method in class org.concord.biologica.ui.TreeView
Set the root engine object of this view.
setRootScript(Script) - Method in class org.concord.util.script.Script
 
setRow(int) - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
setRowCount(int) - Method in class org.concord.pedagogica.ui.CCJTable
 
setRowIndex(int) - Method in class org.concord.biologica.engine.OrganismImage
Sets the row index of this organism image.
setRunDirectory(String) - Method in interface org.concord.util.script.ScriptRuntime
 
setRunDirectory(String) - Method in class org.concord.util.script.ECMA
 
setRunning(boolean) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setRuntime(ScriptRuntime) - Method in class org.concord.util.script.Script
 
setRuntime(ScriptRuntime) - Method in class org.concord.pedagogica.engine.Activity
 
setSaveImmediate(boolean) - Method in class org.concord.pedagogica.engine.Logging
 
setScale(double) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setScaleL(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
setScaleM(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
setScaleMax(int) - Method in class org.concord.util.BarGraph
 
setScaleMax(int) - Method in class org.concord.util.Gauge
 
setScaleMax(int) - Method in class org.concord.util.LineGraph
 
setScaleSnapX(int) - Method in class org.concord.collisions.ui.PassiveGrid
 
setScaleSnapY(int) - Method in class org.concord.collisions.ui.PassiveGrid
 
setScaleT(double) - Method in class org.concord.collisions.engine.CCScalingFactors
 
setScalingFactor(CCScalingFactors) - Method in class org.concord.collisions.engine.CCGravityForce
 
setScript(Script) - Method in class org.concord.util.script.ScriptObject
 
setScript(Script) - Method in class org.concord.util.script.ECMA
 
setScript(Script) - Static method in class org.concord.util.script.ScriptThread
 
setScriptParent(Script) - Method in class org.concord.util.script.Script
 
setScriptType(String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setScriptType(String) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setScriptType(String) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setScriptType(String) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setScroll(double) - Method in class org.concord.flash.player.FEditField
 
setScroll(float) - Method in class org.concord.flash.player.FEditField
 
setScroll(int) - Method in class org.concord.flash.player.FEditField
Sets the current scroll location
setScrollPane(JScrollPane) - Method in class org.concord.biologica.ui.UIView
Tell this view its scroll pane.
setScrollPane(JScrollPane) - Method in class org.concord.biologica.ui.ChromosomeView
Tell this view its scroll pane.
setScrollPane(JScrollPane) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Tell this view its scroll pane.
setScrollPane(JScrollPane) - Method in class org.concord.biologica.ui.MultipleOrganismView
Tell this view its scroll pane.
setSearchResult(Vector) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
setSeed(long) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Set the seed of this nucleic acid.
setSelectable(boolean) - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
setSelected(boolean) - Method in class org.concord.biologica.ui.TreeViewNode
Set the selected state of this node.
setSelected(boolean) - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
setSelectedAllele(OrganismAllele) - Method in class org.concord.biologica.ui.ChromosomeView
Set the selected allele.
setSelectedChromosome(OrganismChromosome) - Method in class org.concord.biologica.ui.ChromosomeView
Set the selected chromosome.
setSelectedIndex(int) - Method in class org.concord.biologica.ui.BioComboBox
Selects the item at index anIndex.
setSelectionColor(Color) - Method in class org.concord.biologica.ui.ChromosomeView
Set the selection color.
setSelectionColor(Color) - Method in class org.concord.biologica.ui.OrganismView
Set the selection color.
setSelectionColor(Color) - Method in class org.concord.biologica.ui.TreeView
Set the selection color.
setSelectionMode(int) - Method in class org.concord.biologica.ui.SelectionSet
Set the current selection mode.
setSelectionMode(int) - Method in class org.concord.pedagogica.ui.ClassTree
 
setSelectionSet(SelectionSet) - Method in interface org.concord.biologica.ui.SelectionPresenter
Set the current selection set.
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.ChromosomeView
 
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.PedigreeView
Set the current selection set.
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the current selection set.
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.AllInOneView
Set the current selection set.
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.TreeView
Set the current selection set.
setSelectionSet(SelectionSet) - Method in class org.concord.biologica.ui.MultipleOrganismView
Set the current selection set.
setSelectionToolEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the selection tool enabled state.
setSelectionToolVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the selection tool visibility.
setSexTextVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the sex text visible boolean.
setSexTextVisible(boolean) - Method in class org.concord.biologica.ui.OrganismView
Set the sex text visible boolean.
setSexTextVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set the sex text visible boolean.
setSexViewMode(int) - Method in class org.concord.biologica.ui.SexView
Set sex view mode, updating view and subviews appropriately.
setShortDescription(String) - Method in class org.concord.util.beans.FeatureDescriptor
You can associate a short descriptive string with a feature.
setShowAsTextInOrganismView(boolean) - Method in class org.concord.biologica.engine.Trait
Set whether this trait should be shown as text in the organism view.
setShowingNegative(boolean) - Method in class org.concord.util.LineGraph
 
setShowMaxValues(boolean) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setSigma(double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setSink(ActivityNode) - Method in class org.concord.pedagogica.engine.ActivityArc
 
setSinkLocation(int, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setSinkNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setSiteName(String) - Method in class org.concord.pedagogica.engine.Logging
 
setSize(Dimension) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setSize(Dimension) - Method in class org.concord.flash.player.FFlash
 
setSize(Dimension) - Method in class org.concord.pedagogica.ui.CCXMLText
 
setSize(Dimension) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
setSize(int, int) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setSize(int, int) - Method in class org.concord.collisions.ui.GUIPanel
Resizes this component so that it has width width and height.
setSize(int, int) - Method in class org.concord.flash.player.FFlash
 
setSize(int, int) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setSize(int, int) - Method in class org.concord.molecular.ui.MolecularView
 
setSize(int, int) - Method in class org.concord.pedagogica.ui.CCXMLText
 
setSize(int, int) - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
setSkippingFrames(boolean) - Method in class org.concord.flash.player.FFlash
 
setSkippingFrames(boolean) - Method in class org.concord.flash.player.FMovie
 
setSlider(JSlider) - Method in class org.concord.util.BarGraph
 
setSlider(JSlider) - Method in class org.concord.util.LineGraph
 
setSliderValue() - Method in class org.concord.util.BarGraph
 
setSliderValue() - Method in class org.concord.util.LineGraph
 
setSmallHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the small hotspot location.
setSnapToGrid(boolean, boolean) - Method in class org.concord.collisions.ui.GUIPanel
 
setSnapToGrid(boolean, boolean, int, int) - Method in class org.concord.collisions.ui.GUIPanel
 
setSnipToolEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the snip tool enabled state.
setSnipToolVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the snip tool visibility.
setSoundFileName(String) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setSoundFileName(String) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
setSoundOn() - Method in class org.concord.collisions.engine.JPartWorld
set soundOn property to true so you can use sound threads
setSoundToggle() - Method in class org.concord.collisions.engine.JPartWorld
 
setSource(ActivityNode) - Method in class org.concord.pedagogica.engine.ActivityArc
 
setSourceBounds(TextBounds) - Method in class org.concord.util.script.ScriptObject
 
setSourceBounds(TextBounds) - Method in class org.concord.util.script.AssignmentStatement
 
setSourceLocation(int, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setSourceNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setSpecies(Species) - Method in class org.concord.biologica.engine.Organism
Set the species of this organism.
setSpecies(Species) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the current species.
setSpeciesAllele(SpeciesAllele) - Method in class org.concord.biologica.engine.OrganismAllele
Set the organism's species allele.
setSpeciesPulldownVisible(boolean) - Method in class org.concord.biologica.ui.AllInOneView
Set species pulldown visible
setSpeciesTextVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the species text visible boolean.
setSpeciesTextVisible(boolean) - Method in class org.concord.biologica.ui.OrganismView
Set the species text visible boolean.
setSpeciesTextVisible(boolean) - Method in class org.concord.biologica.ui.SexView
Set the species text visible boolean.
setSpringParam(double, double) - Method in class org.concord.collisions.engine.CCSpring
 
setStandalone(boolean) - Method in class org.concord.util.script.ECMA
 
setStartIndexInHolder(int) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Set the start index of this nucleic acid in its holder.
setStartIndexInHolder(int) - Method in class org.concord.biologica.engine.NucleicAcid
Set the start index of this nucleic acid in its holder.
setStartIndexInHolder(int) - Method in class org.concord.biologica.engine.Gene
Set the start index of this gene in its chromosome.
setStartIndexInHolder(int) - Method in class org.concord.biologica.engine.RawNucleicAcid
Set the start index of this nucleic acid in its holder.
setStartNode() - Method in class org.concord.pedagogica.engine.ActivityNode
 
setStartNode(ActivityNode) - Method in class org.concord.pedagogica.engine.Activity
 
setStartNode(ActivityNodeItem) - Method in class org.concord.pedagogica.ui.ActivityView
 
setState(OrganismAllele, int, int, int, int, boolean) - Method in class org.concord.biologica.ui.OrganismAlleleControl
Set the state needed to draw and use this control.
setStatement(Statement) - Method in class org.concord.util.script.LoopStatement
 
setStatement(Statement) - Method in class org.concord.util.script.MethodDeclaration
 
setStep(int) - Method in class org.concord.biologica.ui.FertilizationModel
Set the current step of the fertilization
setStep(int) - Method in class org.concord.biologica.ui.MeiosisModel
Set the current step of the meiosis.
setStepBackwardButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set step backward button enabled.
setStepBackwardButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set step backward button enabled.
setStepBackwardButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set step backward button visibility.
setStepBackwardButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set step backward button visibility.
setStepForwardButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set step forward button enabled.
setStepForwardButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set step forward button enabled.
setStepForwardButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set step forward button visibility.
setStepForwardButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set step forward button visibility.
setStepTime(float) - Method in class org.concord.collisions.event.StepEvent
 
setStopToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set stop toggle enabled.
setStopToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set stop toggle enabled.
setStopToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set stop toggle enabled.
setStopToggleButtonEnabled(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set stop toggle enabled.
setStopToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigFertilizationView
Set stop toggle visibility.
setStopToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallMeiosisView
Set stop toggle visibility.
setStopToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Set stop toggle visibility.
setStopToggleButtonVisible(boolean) - Method in class org.concord.biologica.ui.BigMeiosisView
Set stop toggle visibility.
setStopWhenFertilizationStarts(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether fertilization should immediately stop when it starts.
setStopWhenMeiosisStarts(boolean) - Method in class org.concord.biologica.ui.SexView
Set whether meiosis should immediately stop when it starts.
setStrand(int) - Method in class org.concord.biologica.engine.Gene
Set the strand of this gene.
setStrandAlleles(int, OrganismAllele[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the array of Alleles for the given strand.
setStrandColors(int, Color[]) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the array of Colors for the given strand.
setSuspendingCallers(boolean) - Static method in class org.concord.util.script.Script
 
setTable(TableInputView) - Method in class org.concord.pedagogica.ui.CustomTableQuestion
 
setTableInputModel(TableInputModel) - Method in class org.concord.pedagogica.ui.TableInputView
Method which associates a particular TableInputModel with a TableInputView object.
setTableSize(int) - Method in class org.concord.pedagogica.ui.TableInputView
 
setTableSize(int) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setTableSize(int, String) - Method in class org.concord.pedagogica.ui.TableInputView
Method to set the Punnett Square table size.
setTableSize(int, String) - Method in class org.concord.pedagogica.ui.TableInputModel
 
setTemperature(int) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setTemporaryOffsets(int, int) - Method in class org.concord.biologica.ui.MeiosisChromosomeModel
Set the temporary offsets of this chromosome.
setTemporaryOffsets(int, int) - Method in class org.concord.biologica.ui.FertilizationChromosomeModel
Set the temporary offsets of this chromosome.
setTerrain(int, int, Terrain) - Method in class org.concord.biologica.engine.Environment
Set the terrain at the given indexes into the terrain array.
setText(String) - Method in class org.concord.collisions.ui.PassiveText
 
setText(String) - Method in class org.concord.flash.player.FEditField
 
setText(String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setText(String) - Method in class org.concord.pedagogica.ui.CCXMLText
 
setText(String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setText(String) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
setText(String) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setText(String) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
setText(String) - Method in class org.concord.pedagogica.ui.HTMLView
 
setText(String) - Method in class org.concord.pedagogica.ui.TableInputModel.CellData
 
setText(String) - Method in interface org.concord.pedagogica.ui.ActivityItem
 
setText(String) - Method in class org.concord.pedagogica.ui.BlankFill
 
setText(String) - Method in class org.concord.pedagogica.ui.EssayFill
 
setText(String, boolean) - Method in class org.concord.pedagogica.ui.CCXMLText
 
setText(String, String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setText(String, String) - Method in class org.concord.pedagogica.ui.CustomQuestion
 
setTextColor(Color) - Method in class org.concord.util.LineGraph
 
setTextIndent(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the text indent for this view.
setTextIndent(int) - Method in class org.concord.biologica.ui.OrganismView
Set the text indent for this view.
setTextIndent(int) - Method in class org.concord.biologica.ui.SexView
Set the text indent for this view.
setTextLineSpacing(int) - Method in class org.concord.biologica.ui.PedigreeView
Set the text line spacing for this view, the number of pixels between lines of text below an organism.
setTextLineSpacing(int) - Method in class org.concord.biologica.ui.OrganismView
Set the text line spacing for this view, the number of pixels between lines of text below an organism.
setTextLineSpacing(int) - Method in class org.concord.biologica.ui.SexView
Set the text line spacing for this view, the number of pixels between lines of text below an organism.
setTextSelection(int, int, int, int) - Method in class org.concord.util.TextSelection
 
setTextSymbol(String) - Method in class org.concord.biologica.engine.OrganismAllele
Set the text symbol of the allele.
setTextSymbol(String) - Method in class org.concord.biologica.engine.SpeciesAllele
Set the text symbol of the allele.
setThenCharacteristic(Characteristic) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Sets the then characteristic of this genotype to phenotype rule.
setTimedAverage(boolean) - Method in class org.concord.molecular.engine.ConditionValue
 
setTimedAverageInterval(int) - Method in class org.concord.molecular.engine.ConditionValue
 
setTimeStep(double) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
SETTING_DEBUG_LOG_LEVEL_TO - Static variable in class org.concord.biologica.engine.EngineStrings
 
setToolEnabled(int, boolean) - Method in class org.concord.biologica.ui.ToolView
Set the tool enabled state.
setToolTipText(String) - Method in class org.concord.flash.player.FComponent
Sets the tool tip text on this component.
setToolVisible(int, boolean) - Method in class org.concord.biologica.ui.ToolView
Set the tool visibility.
setTraceColor(Color) - Method in class org.concord.collisions.engine.JAtom
set trace's color
setTracePossible(boolean) - Method in class org.concord.collisions.ui.GUIPanel
set GUIPanel trace property
setTraceProperties(int) - Method in class org.concord.collisions.engine.JAtom
 
setTraceProperties(int, int, int) - Method in class org.concord.collisions.engine.JAtom
 
setTrait(String) - Method in class org.concord.biologica.ui.PedigreeView
Set the trait for this view.
setTrait(String) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the trait for this view.
setTraitPulldown(BioComboBox) - Method in class org.concord.biologica.ui.PedigreeOrganismView
Set the trait pulldown.
setTraitPulldownEnabled(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the trait pulldown enabled state.
setTraitPulldownVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
Set the trait pulldown visibility.
setTransform(AffineTransform) - Method in class org.concord.flash.player.FComponent
 
setTransform(AffineTransform) - Method in class org.concord.flash.player.fill.FFillMethod
 
setTransform(AffineTransform) - Method in class org.concord.flash.player.fill.FGradientFillMethod
 
setTransform(AffineTransform) - Method in class org.concord.flash.player.fill.FColorFillMethod
 
setTransform(AffineTransform) - Method in class org.concord.flash.player.fill.FImageFillMethod
 
setTransformParam(float, float) - Method in class org.concord.collisions.ui.GUIPanel
 
setTranslation(double, double) - Method in class org.concord.flash.player.FComponent
 
setTranslation(float, float) - Method in class org.concord.flash.player.FComponent
 
setTreePaneVisible(boolean) - Method in class org.concord.biologica.ui.AllInOneView
Set the tree pane visibility.
setType(int) - Method in class org.concord.molecular.engine.ConditionValue
 
setType(String) - Method in class org.concord.util.script.VariableDeclaration
 
setUnicast(boolean) - Method in class org.concord.util.beans.EventSetDescriptor
Mark an event set as unicast (or not).
setUnit(CCUnit) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
setUnit(CCUnit) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
setUploadHost(String) - Method in class org.concord.pedagogica.engine.Logging
 
setUploadPort(int) - Method in class org.concord.pedagogica.engine.Logging
 
setUseConsole(boolean) - Method in class org.concord.pedagogica.engine.Logging
 
setValue(Object) - Method in class org.concord.util.beans.Expression
Sets the value of this expression to value.
setValue(Object) - Method in class org.concord.util.script.IndexExpression
 
setValue(Object) - Method in class org.concord.util.script.VariableDeclaration
 
setValue(Object) - Method in class org.concord.util.script.ReferenceExpression
This is invoked when the semantic engine interprets an assignment node and has to set the left side of the assignment.
setValue(Object) - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Sets the string for the cell being rendered to value.
setValue(String) - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
setValue(String, Object) - Method in class org.concord.util.beans.FeatureDescriptor
Associate a named attribute with this feature.
setValue(String, String) - Method in class org.concord.util.Query
 
setValueFromMouseEvent(MouseEvent) - Method in class org.concord.util.Gauge
 
setValueFunction(ConditionValue, int) - Method in class org.concord.molecular.engine.AggregateValue
 
setValueGraph(ValueGraph) - Method in class org.concord.molecular.ui.AtomicValueDispatcher
Set the ValueGraph object.
setValues(int, int, int, int) - Method in class org.concord.biologica.ui.CellLine
Set values
setVariable(String) - Method in class org.concord.util.script.ReferenceExpression
Set the variable name.
setVariable(String) - Method in class org.concord.pedagogica.ui.ModifyValueDialog
 
setVariable(String, Object) - Method in class org.concord.flash.player.StackFrame4
Sets a variable~ If the variable has been defined as a local variable, then set it as a local variable.
setVelColor(Color) - Method in class org.concord.collisions.engine.JAtom
set color for velocity's arrows
setVelocity(double, double) - Method in class org.concord.molecular.engine.AtomAccessor
 
setVerticalLayout() - Method in class org.concord.pedagogica.ui.Question
 
setVerticalLayout() - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setViewBefore(boolean) - Method in interface org.concord.util.script.ScriptRuntime
 
setViewBefore(boolean) - Method in class org.concord.util.script.ECMA
 
setViewHtml(String, String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
setViewText(String) - Method in class org.concord.pedagogica.engine.ActivityScript
 
setVisible(boolean) - Method in class org.concord.biologica.engine.SpeciesChromosome
Set whether this chromosome is visible.
setVisible(boolean) - Method in class org.concord.biologica.engine.SpeciesAllele
Set whether or not this allele is visible.
setVisible(boolean) - Method in class org.concord.biologica.engine.Organism
Set whether this organism is visible.
setVisible(boolean) - Method in class org.concord.biologica.engine.Gene
Set whether this gene is visible.
setVisible(boolean) - Method in class org.concord.biologica.ui.CursorText
 
setVisible(boolean) - Method in class org.concord.biologica.ui.PedigreeView
 
setVisible(boolean) - Method in class org.concord.collisions.engine.JWorldElement
Set the visible state of the JWorldElement.
setVisible(boolean) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
setVisitor(Object) - Method in class org.concord.collisions.event.AreaEvent
 
setVx(float) - Method in class org.concord.collisions.engine.JWorldElement
set element's velocity
setVx(float) - Method in class org.concord.collisions.engine.JRigidBox
 
setVx(float) - Method in class org.concord.collisions.engine.JAtom
 
setVx(float) - Method in class org.concord.collisions.ui.PassiveElement
 
setVx(float) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setVy(float) - Method in class org.concord.collisions.engine.JWorldElement
 
setVy(float) - Method in class org.concord.collisions.engine.JRigidBox
 
setVy(float) - Method in class org.concord.collisions.engine.JAtom
 
setVy(float) - Method in class org.concord.collisions.ui.PassiveElement
 
setVy(float) - Method in class org.concord.collisions.ui.DataCrossPanel
 
setWaitingThread(Thread) - Method in class org.concord.util.script.Script
 
setWallTemperature(float) - Method in class org.concord.collisions.engine.JWall
set wall's "temperature"
setWallTemperatureMode(int) - Method in class org.concord.collisions.engine.JWall
 
setWatchableElement(JWorldElement) - Method in class org.concord.collisions.ui.GUIPanel
 
setWatchMode(int) - Method in class org.concord.collisions.ui.GUIPanel
 
setWeight(int) - Method in class org.concord.biologica.engine.SpeciesAllele
Set the weight of this allele.
setWhichVelocity(char) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
setWidth(float) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setWidth(int) - Method in class org.concord.biologica.engine.Environment
Set the width of the environment.
setWidth(int) - Method in class org.concord.biologica.ui.PedigreeObject
Set the width
setWidth(int) - Method in class org.concord.collisions.event.AreaEvent
 
setWidth(int) - Method in class org.concord.pedagogica.ui.ChoiceQuestion
 
setWindowMode(int) - Method in class org.concord.biologica.ui.AllInOneView
Set window mode, updating window appropriately.
setWorld(JPartWorld) - Method in class org.concord.collisions.ui.GUIPanel
 
setWorldAperture(float, float) - Method in class org.concord.collisions.ui.GUIPanel
 
setWorldModel(JPartWorld) - Method in class org.concord.collisions.engine.JWorldElement
 
setWorldModel(JPartWorld) - Method in class org.concord.collisions.engine.JRigidBox
 
setWorldModel(JPartWorld) - Method in class org.concord.collisions.engine.CCForce
 
setWorldModel(JPartWorld) - Method in class org.concord.collisions.engine.CCImpulseForce
 
setWorldModel(JPartWorld) - Method in class org.concord.collisions.engine.JImpulseDaemon
 
setWorldOrigin(float, float) - Method in class org.concord.collisions.ui.GUIPanel
 
setWorldTime(float) - Method in class org.concord.collisions.event.StepEvent
 
setWriteMethod(Method) - Method in class org.concord.util.beans.PropertyDescriptor
Sets the method that should be used to write the property value.
setX(float) - Method in class org.concord.collisions.engine.CCPoint
 
setX(float) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setX(int) - Method in class org.concord.collisions.event.AreaEvent
 
setX(int) - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
setXConstraints(float, float) - Method in class org.concord.collisions.engine.JWorldElement
 
setXConstraints(float, float) - Method in class org.concord.collisions.engine.JRigidBox
setting horizontal wall's constraints
setXConstraints(float, float) - Method in class org.concord.collisions.engine.JWall
setting horizontal wall's constraints
setXLargeHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the xLarge hotspot location.
setXLocation(int) - Method in class org.concord.biologica.ui.PedigreeObject
Set the X location
setXSmallHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the xSmall hotspot location.
setXXSmallHotspot(Point) - Method in class org.concord.biologica.engine.SpeciesImageRow
Set the xxSmall hotspot location.
setY(float) - Method in class org.concord.collisions.engine.CCPoint
 
setY(float) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
setY(int) - Method in class org.concord.collisions.event.AreaEvent
 
setY(int) - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
setYConstraints(float, float) - Method in class org.concord.collisions.engine.JWorldElement
 
setYConstraints(float, float) - Method in class org.concord.collisions.engine.JRigidBox
setting vertical wall's constraints
setYConstraints(float, float) - Method in class org.concord.collisions.engine.JWall
setting vertical wall's constraints
setYLocation(int) - Method in class org.concord.biologica.ui.PedigreeObject
Set the Y location
setYOrigin(double) - Method in class org.concord.util.LineGraph
 
setYOrigin(float) - Method in class org.concord.util.LineGraph
 
SEX - Static variable in class org.concord.biologica.engine.EngineProp
Sex of an organism.
SEX_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
Chromosome type - sex chromosome
SEX_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SEX_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SEX_TEXT_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The flag indicating whether a view should draw the text for an organism's sex under the organism has changed.
SEX_VIEW_BOTTOM_BUTTON_HEIGHT - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE - Static variable in class org.concord.biologica.ui.UIProp
The sex view mode changed (e.g.
SEX_VIEW_MODE_ALL_VIEWS - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE_FERTILIZATION_VIEW - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE_MEIOSIS_VIEW_FATHER - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE_MEIOSIS_VIEW_MOTHER - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE_NO_VIEWS - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_MODE_SIX_VIEWS - Static variable in class org.concord.biologica.ui.SexView
 
SEX_VIEW_TOP_TEXT_HEIGHT - Static variable in class org.concord.biologica.ui.SexView
 
SexOrganismView - class org.concord.biologica.ui.SexOrganismView.
This class represents a view which shows a parent or offspring organism in the sex view.
SexOrganismView() - Constructor for class org.concord.biologica.ui.SexOrganismView
Creates a parent organism view.
sexTextVisible - Variable in class org.concord.biologica.ui.OrganismView
Sex text visible boolean flag.
SexView - class org.concord.biologica.ui.SexView.
An object of this class will generate the following property change events:
SexView() - Constructor for class org.concord.biologica.ui.SexView
Creates a sex view.
shape1 - Variable in class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
sharedScope - Static variable in class org.concord.util.script.Script
 
shift() - Method in class org.concord.flash.player.builtin.FArray
 
shift(float) - Method in class org.concord.collisions.engine.JRigidBox
 
shift(float) - Method in class org.concord.collisions.engine.JDaemon
 
shift(float) - Method in class org.concord.collisions.engine.JAtom
shift atom
shiftV(float) - Method in class org.concord.collisions.engine.JDaemon
 
shiftV(float) - Method in class org.concord.collisions.engine.JAtom
 
shootRocket(float) - Method in class org.concord.collisions.ui.IngridProblem
 
SHORT_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
SHORTER_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
SHORTEST_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
ShortImageDescription - class org.concord.biologica.datasupport.ShortImageDescription.
 
ShortImageDescription(int, int, int, int, boolean, Image[], int[], int[]) - Constructor for class org.concord.biologica.datasupport.ShortImageDescription
 
SHOW_AS_TEXT_IN_ORGANISM_VIEW_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SHOW_AS_TEXT_IN_ORGANISM_VIEW_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SHOW_TRAIT_AS_TEXT_IN_ORGANISM_VIEW - Static variable in class org.concord.biologica.engine.EngineProp
Show trait as text in the organism view.
show() - Method in class org.concord.pedagogica.ui.VariableDialog
 
show(ActivityScript) - Method in class org.concord.pedagogica.engine.NodeAccess
 
show(ActivityScript) - Method in class org.concord.pedagogica.ui.RunActivity
 
showAcceleration - Variable in class org.concord.collisions.engine.JWorldElement
 
showCM() - Method in class org.concord.collisions.ui.GUIPanel
show Center of Mass point Center of Mass will be represented as point
showCM(boolean) - Method in class org.concord.collisions.ui.GUIPanel
show Center of Mass point
showDocument(URL) - Method in class org.concord.pedagogica.ui.ViewerContext
 
showDocument(URL, String) - Method in class org.concord.pedagogica.ui.ViewerContext
 
showError(Throwable) - Static method in class org.concord.util.script.ScriptThread
 
showError(Throwable) - Method in class org.concord.pedagogica.engine.ActivityScript
 
showError(Throwable, PrintWriter) - Static method in class org.concord.util.script.ScriptThread
 
showGlossary(String) - Method in class org.concord.biologica.ui.GlossaryFrame
 
showingNegative - Variable in class org.concord.util.LineGraph
 
showMaxVelMenu() - Method in class org.concord.collisions.ui.DataCrossPanel
 
showNodeInTitle(ActivityScript) - Method in class org.concord.pedagogica.ui.RunActivity
 
showProperties - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
showStatus(String) - Method in class org.concord.pedagogica.ui.ViewerContext
 
showSwitchAlignmentButtons() - Method in class org.concord.biologica.ui.BigMeiosisView
Show switch alignment buttons
showVelocity - Variable in class org.concord.collisions.engine.JWorldElement
 
showVelocityNumber - Variable in class org.concord.collisions.engine.JWorldElement
 
SIGMA - Static variable in class org.concord.molecular.engine.ConditionValue
 
sigma(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
sigma1 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
sigma1 - Variable in class org.concord.molecular.ui.MolecularView
 
sigma2 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
sigma2 - Variable in class org.concord.molecular.ui.MolecularView
 
sigma3 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
sigma3 - Variable in class org.concord.molecular.ui.MolecularView
 
sigma4 - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
sigma4 - Variable in class org.concord.molecular.ui.MolecularView
 
SimpleBeanInfo - class org.concord.util.beans.SimpleBeanInfo.
This is a support class to make it easier for people to provide BeanInfo classes.
SimpleBeanInfo() - Constructor for class org.concord.util.beans.SimpleBeanInfo
 
simulationState - Variable in class org.concord.collisions.engine.JPartWorld
 
sin(double) - Method in class org.concord.flash.player.builtin.FMath
 
sin(float) - Static method in class org.concord.collisions.engine.JPartWorld
 
SINGLE - Static variable in class org.concord.molecular.engine.ConditionValue
 
SINGLE_SELECTION - Static variable in class org.concord.pedagogica.ui.ClassTree
 
single(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
singleAct - Variable in class org.concord.util.LogProcess
 
singleIndex - Variable in class org.concord.molecular.engine.ConditionValue
 
singleStudent - Variable in class org.concord.util.LogProcess
 
sink - Variable in class org.concord.pedagogica.engine.ActivityArc
 
siteName - Variable in class org.concord.pedagogica.engine.Logging
 
size - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
size() - Method in class org.concord.molecular.engine.IndexList
 
sizeChanged - Variable in class org.concord.util.BarGraph
 
sizeChanged - Variable in class org.concord.util.Gauge
 
sizeChanged - Variable in class org.concord.util.LineGraph
 
sizeNames - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
sizeSuffixes - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 
skip(long) - Method in class org.concord.util.script.ScriptFileInputStream
 
skipped - Variable in class org.concord.util.script.NameStack
 
SkipStatement - class org.concord.util.script.SkipStatement.
The SkipStatement class implements the node that supports the semantics of the "skip" statement.
SkipStatement() - Constructor for class org.concord.util.script.SkipStatement
 
sleep() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
sleep(int) - Method in class org.concord.util.LineGraph
 
sleep(int) - Method in interface org.concord.util.script.ScriptRuntime
 
sleep(int) - Method in class org.concord.util.script.ECMA
 
slice(int, int) - Method in class org.concord.flash.player.builtin.FArray
 
slider - Variable in class org.concord.util.BarGraph
 
slider - Variable in class org.concord.util.LineGraph
 
sliderChanged - Variable in class org.concord.util.BarGraph
 
sliderChanged - Variable in class org.concord.util.LineGraph
 
SMALL_FATHER_MEIOSIS_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the small father meiosis view was pushed.
SMALL_FERTILIZATION_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the small fertilization view was pushed.
SMALL_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
Small hotspot location.
SMALL_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
Small image column width of a Species object.
SMALL_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
Small image row height of a Species object.
SMALL_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SMALL_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
SMALL_MOTHER_MEIOSIS_MAGNIFY_BUTTON_PUSHED - Static variable in class org.concord.biologica.ui.UIProp
Indicates that the magnify button in the small mother meiosis view was pushed.
SmallFertilizationView - class org.concord.biologica.ui.SmallFertilizationView.
This class represents a view which shows the 2 sex cells of 2 parents in the sex view and has controls for the user to conduct fertilization within this view of those 2 cells.
SmallFertilizationView() - Constructor for class org.concord.biologica.ui.SmallFertilizationView
Creates a small fertilization view.
smallFont - Variable in class org.concord.util.LineGraph
 
SmallMeiosisView - class org.concord.biologica.ui.SmallMeiosisView.
This class represents a view which shows the sex cell of a parent in the sex view and has controls for the user to conduct meiosis within this view on that sex cell.
SmallMeiosisView(int) - Constructor for class org.concord.biologica.ui.SmallMeiosisView
Creates a small meiosis view.
snapToGrid(Rectangle) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
SNIP - Static variable in class org.concord.biologica.ui.Tool
 
SNIP_NAME - Static variable in class org.concord.biologica.ui.Tool
 
SNIP_TOOL_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The enabled state of the snip tool has changed.
SNIP_TOOL_PICK_ON_FAMILY - Static variable in class org.concord.biologica.ui.UIProp
Snip tool was used to pick on a family.
SNIP_TOOL_PICK_ON_ORGANISM - Static variable in class org.concord.biologica.ui.UIProp
Snip tool was used to pick on an organism.
SNIP_TOOL_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the snip tool has changed.
snipToolCursor - Static variable in class org.concord.biologica.ui.Tool
 
snipToolImageIcon - Static variable in class org.concord.biologica.ui.Tool
 
socket - Variable in class org.concord.util.NetworkTime
 
sort() - Method in class org.concord.flash.player.builtin.FArray
 
sort(FFunction) - Method in class org.concord.flash.player.builtin.FArray
 
sortFormat - Variable in class org.concord.pedagogica.engine.Logging
 
source - Variable in class org.concord.pedagogica.engine.ActivityArc
 
sourceGlobalUnit - Static variable in class org.concord.util.CCUnit
 
SPACE - Static variable in class org.concord.biologica.engine.EngineStrings
 
SpecieFileDesc - class org.concord.biologica.datasupport.SpecieFileDesc.
 
SpecieFileDesc(int, int) - Constructor for class org.concord.biologica.datasupport.SpecieFileDesc
 
Species - class org.concord.biologica.engine.Species.
This class represents a species.
SPECIES - Static variable in class org.concord.biologica.engine.EngineProp
Species of an organism.
SPECIES_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Species object was added.
SPECIES_ALLELE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A SpeciesAllele object was added to a SpeciesChromosome.
SPECIES_ALLELE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ALLELE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ALLELE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ALLELE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ALLELE_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_ALLELE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A SpeciesAllele object was removed from a SpeciesChromosome.
SPECIES_CHROMOSOME_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Species chromosome added.
SPECIES_CHROMOSOME_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_CHROMOSOME_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_CHROMOSOME_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_CHROMOSOME_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_CHROMOSOME_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_CHROMOSOME_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Species chromosome removed.
SPECIES_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
SPECIES_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Species image added to a Species object.
SPECIES_IMAGE_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
SPECIES_IMAGE_COLUMN_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Species image column added to a species image.
SPECIES_IMAGE_COLUMN_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_COLUMN_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_COLUMN_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_COLUMN_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_COLUMN_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_IMAGE_COLUMN_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Species image column removed from a species image.
SPECIES_IMAGE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_IMAGE_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Species image removed from a Species object.
SPECIES_IMAGE_ROW_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
Species image row added to a species image.
SPECIES_IMAGE_ROW_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ROW_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ROW_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ROW_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
SPECIES_IMAGE_ROW_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_IMAGE_ROW_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
Species image row removed from a species image New value is the removed SpeciesImageRow object.
SPECIES_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
SPECIES_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Species object was removed.
SPECIES_TEXT_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The flag indicating whether a view should draw the text for an organism's species under the organism has changed.
Species(World, File) - Constructor for class org.concord.biologica.engine.Species
Creates a new species given a world and a species file.
Species(World, int, String) - Constructor for class org.concord.biologica.engine.Species
Creates a new species given a world, ploidy number and name.
Species(World, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Species
Create a new species and start handling XML parsing events to set the properties of this object.
SpeciesAllele - class org.concord.biologica.engine.SpeciesAllele.
This class represents a species allele - a known, fixed variation of a species gene.
SpeciesAllele(Gene, String, byte[]) - Constructor for class org.concord.biologica.engine.SpeciesAllele
Create a new allele given a gene and the base values to use.
SpeciesAllele(Gene, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.SpeciesAllele
Create a new species allele and start handling XML parsing events to set the properties of this object.
SpeciesChromosome - class org.concord.biologica.engine.SpeciesChromosome.
This class represents a species chromosome - a chromosome which has a length, some genes and their alleles, etc.
SpeciesChromosome(Species, int, int) - Constructor for class org.concord.biologica.engine.SpeciesChromosome
Create a new species chromosome.
SpeciesChromosome(Species, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.SpeciesChromosome
Create a new species chromosome and start handling XML parsing events to set the properties of this object.
SpeciesFileFilter - class org.concord.biologica.ui.SpeciesFileFilter.
 
SpeciesFileFilter() - Constructor for class org.concord.biologica.ui.SpeciesFileFilter
 
SpeciesImage - class org.concord.biologica.engine.SpeciesImage.
This class represents an image containing some of the graphics for drawing the organisms of a particular species.
SpeciesImage(Species, String) - Constructor for class org.concord.biologica.engine.SpeciesImage
Creates a new species image given a species and a name.
SpeciesImage(Species, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.SpeciesImage
Create a new species image and start handling XML parsing events to set the properties of this object.
SpeciesImageColumn - class org.concord.biologica.engine.SpeciesImageColumn.
This class represents a column of a SpeciesImage.
SpeciesImageColumn(SpeciesImage, String) - Constructor for class org.concord.biologica.engine.SpeciesImageColumn
Creates a new species image column.
SpeciesImageColumn(SpeciesImage, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.SpeciesImageColumn
Create a new SpeciesImageColumn and start handling XML parsing events to set the properties of this object.
SpeciesImageRow - class org.concord.biologica.engine.SpeciesImageRow.
This class represents a row of a SpeciesImage.
SpeciesImageRow(SpeciesImage, String) - Constructor for class org.concord.biologica.engine.SpeciesImageRow
Creates a new species image row.
SpeciesImageRow(SpeciesImage, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.SpeciesImageRow
Create a new SpeciesImageRow and start handling XML parsing events to set the properties of this object.
speciesTextVisible - Variable in class org.concord.biologica.ui.OrganismView
Species text visible boolean flag.
SpindleLine - class org.concord.biologica.ui.SpindleLine.
SpindleLine has the information necessary to draw a line to represent a portion of a spindle.
SpindleLine(int, int, int, int) - Constructor for class org.concord.biologica.ui.SpindleLine
Create a new SpindleLine
splice(Object[]) - Method in class org.concord.flash.player.builtin.FArray
 
sqrt(double) - Method in class org.concord.flash.player.builtin.FMath
 
SQRT1_2 - Static variable in class org.concord.flash.player.builtin.FMath
 
SQRT2 - Static variable in class org.concord.flash.player.builtin.FMath
 
squeeze() - Method in class org.concord.biologica.ui.PedigreeObject
Squeeze object.
squeeze() - Method in class org.concord.biologica.ui.PedigreeFamily
Public interface for squeezing family and redoing the placement.
StackFrame4 - class org.concord.flash.player.StackFrame4.
Holds stack frame.
StackFrame4(FScriptObject, String[], Object[]) - Constructor for class org.concord.flash.player.StackFrame4
 
StackFrame5 - class org.concord.flash.player.StackFrame5.
Holds stack frame.
StackFrame5(FScriptObject, String[], Object[]) - Constructor for class org.concord.flash.player.StackFrame5
 
start - Variable in class org.concord.pedagogica.ui.ActivitySearchResult
 
START - Static variable in class org.concord.biologica.engine.Codon
Start codon.
START_INDEX_IN_HOLDER - Static variable in class org.concord.biologica.engine.EngineProp
Start index in holder simple property name.
START_INDEX_IN_HOLDER_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
START_INDEX_IN_HOLDER_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
start() - Method in class org.concord.util.script.ECMA
 
start() - Method in class org.concord.collisions.engine.JPartWorld
start start simulation all timers will be started
start() - Method in class org.concord.collisions.engine.JDaemon
Start running the daemon
start() - Method in class org.concord.collisions.engine.BedSpringWorld
 
start() - Method in class org.concord.collisions.ui.GUIPanel
start simulation
start(int) - Method in class org.concord.flash.player.FMovieBuilder.ActionsBuilder
 
start(int) - Method in class org.concord.flash.player.FMovieBuilder.ButtonActionBuilder
 
start(ViewerAppletEvent) - Method in interface org.concord.pedagogica.ui.event.ViewerAppletListener
 
startAll() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
startBlinking() - Method in class org.concord.biologica.ui.BigMeiosisView
Start blinking if there is a first cut and the blinking timer isn't already running.
startBounds - Variable in class org.concord.flash.player.FMovieBuilder.MorphShapeBuilder
 
startBuildBedSpringWorld(float, float) - Method in class org.concord.collisions.engine.BedSpringWorld
 
startButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
startDataDelivery(LabBookSession) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
startDataDelivery(LabBookSession) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
startDocument() - Method in class org.concord.util.LogProcess
 
startDocument() - Method in class org.concord.biologica.engine.World
Handle notification that a new document parse has started.
startDocument() - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JRigidBox
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JWall
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JDaemon
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JAtom
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JAtom.VelocityDraggable
 
startDrag(int, int) - Method in class org.concord.collisions.engine.JAtom.AtomDraggable
 
startDrag(int, int) - Method in class org.concord.collisions.ui.PassiveElement
 
startDrag(int, int) - Method in interface org.concord.collisions.ui.CCDraggable
 
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.World
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.SpeciesChromosome
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.OrganismAllele
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Environment
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.SpeciesImage
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Species
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.SpeciesAllele
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Organism
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Family
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.OrganismImage
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Characteristic
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.OrganismChromosome
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Gene
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Trait
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.OrganismAllelePair
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.SpeciesImageRow
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.Terrain
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.BioLogicaSpecies
 
startElement(String, AttributeList) - Method in class org.concord.biologica.engine.RawNucleicAcid
Handle notification that the parser has hit the start of a new element with the given name and attributes.
startElement(String, String, String, Attributes) - Method in class org.concord.util.LogProcess
 
startElement(String, String, String, Attributes) - Method in class org.concord.pedagogica.engine.NodeAccess
 
startEventProcessing() - Method in class org.concord.pedagogica.engine.ActivityScript
 
startLog() - Method in class org.concord.pedagogica.engine.Logging
 
startMouseMotionListener(int, int) - Method in class org.concord.biologica.ui.DNAView
Start mouse motion listener given the start and end index of any current selection.
startName - Variable in class org.concord.pedagogica.ui.ActivityView
 
startNameLabel - Variable in class org.concord.pedagogica.ui.ActivityView
 
startProcessEvent() - Method in class org.concord.util.script.Script
 
state - Variable in class org.concord.pedagogica.engine.ActivityScript
 
stateChanged(ChangeEvent) - Method in class org.concord.biologica.ui.BigFertilizationView
Change listener events
stateChanged(ChangeEvent) - Method in class org.concord.biologica.ui.SmallMeiosisView
Change listener events
stateChanged(ChangeEvent) - Method in class org.concord.biologica.ui.DNAView
Handle change event
stateChanged(ChangeEvent) - Method in class org.concord.biologica.ui.SmallFertilizationView
Change listener events
stateChanged(ChangeEvent) - Method in class org.concord.biologica.ui.BigMeiosisView
Change listener events
stateChanged(ChangeEvent) - Method in class org.concord.pedagogica.ui.ActivityView
 
statement - Variable in class org.concord.util.script.LoopStatement
 
statement - Variable in class org.concord.util.script.MethodDeclaration
 
Statement - class org.concord.util.beans.Statement.
A Statement object represents a primitive statement in which a single method is applied to a target and a set of arguments - as in "a.setFoo(b)".
Statement - class org.concord.util.script.Statement.
The Statement class is the base class of all statement nodes in the semantic tree.
Statement() - Constructor for class org.concord.util.script.Statement
 
Statement(Object, String, Object[]) - Constructor for class org.concord.util.beans.Statement
Creates a new Statement object with a target, methodName and arguments as per the parameters.
Statement(Script) - Constructor for class org.concord.util.script.Statement
 
statements - Variable in class org.concord.util.script.BlockStatement
 
statements - Variable in class org.concord.util.script.Script
 
StaticOrganismView - class org.concord.biologica.ui.StaticOrganismView.
A simple, static view that shows an organism and does nothing else.
StaticOrganismView() - Constructor for class org.concord.biologica.ui.StaticOrganismView
Creates a parent organism view.
statusMessage(String) - Method in interface org.concord.util.script.ScriptRuntime
 
statusMessage(String) - Method in class org.concord.util.script.ECMA
 
statusPanel - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
stdFile - Variable in class org.concord.util.script.ScriptFile
 
step - Variable in class org.concord.molecular.ui.MolecularView
 
step(float) - Method in class org.concord.collisions.engine.JDaemon
This method is called by JPartWorld every step
stepAnimationBackward() - Method in class org.concord.biologica.ui.BigFertilizationView
Step animation backward one step
stepAnimationBackward() - Method in class org.concord.biologica.ui.BigMeiosisView
Step animation backward one step
stepAnimationForward() - Method in class org.concord.biologica.ui.BigFertilizationView
Step animation forward one step
stepAnimationForward() - Method in class org.concord.biologica.ui.BigMeiosisView
Step animation forward one step
StepEvent - class org.concord.collisions.event.StepEvent.
 
StepEvent(Object, float, float) - Constructor for class org.concord.collisions.event.StepEvent
 
stepFinished(StepEvent) - Method in interface org.concord.collisions.event.StepListener
 
stepFinished(StepEvent) - Method in class org.concord.collisions.ui.GUIElementsFrame
 
stepFinished(StepEvent) - Method in class org.concord.collisions.ui.GUITestIngrid
 
stepFinished(StepEvent) - Method in class org.concord.collisions.ui.IngridProblem
 
stepFinished(StepEvent) - Method in class org.concord.collisions.ui.GUIPanel
 
StepListener - interface org.concord.collisions.event.StepListener.
 
stepTime - Variable in class org.concord.collisions.event.StepEvent
 
steradian - Variable in class org.concord.util.CCUnit
 
STOP - Static variable in class org.concord.biologica.engine.Codon
Stop codon.
STOP_ACTIVITY - Static variable in class org.concord.pedagogica.ui.ActivityView
 
STOP_WHEN_FERTILIZATION_STARTS - Static variable in class org.concord.biologica.ui.UIProp
Stop immediately when fertilization starts.
STOP_WHEN_MEIOSIS_STARTS - Static variable in class org.concord.biologica.ui.UIProp
Stop immediately when meiosis starts.
stop() - Method in interface org.concord.util.script.ScriptRuntime
 
stop() - Method in class org.concord.util.script.ECMA
 
stop() - Method in class org.concord.collisions.engine.JPartWorld
stop stop simulation all timers will be stopped
stop() - Method in class org.concord.collisions.engine.BedSpringWorld
 
stop() - Method in class org.concord.collisions.ui.GUIPanel
stop simulation
stop() - Method in class org.concord.flash.player.FFlash
Stops playing the movie.
stop() - Method in class org.concord.flash.player.FMovieClip
Stop playing
stop() - Method in class org.concord.flash.player.FMovie
Stops the movie and stops the periodic timer.
stop(ViewerAppletEvent) - Method in interface org.concord.pedagogica.ui.event.ViewerAppletListener
 
stopAll() - Method in class org.concord.flash.player.FMovieClip
Stops playing and removes all button entries
stopAll() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
stopAnimation() - Method in class org.concord.biologica.ui.BigFertilizationView
Stop playing animation
stopAnimation() - Method in class org.concord.biologica.ui.SmallMeiosisView
Stop playing animation
stopAnimation() - Method in class org.concord.biologica.ui.SmallFertilizationView
Stop playing animation
stopAnimation() - Method in class org.concord.biologica.ui.BigMeiosisView
Stop playing animation
stopBlinking() - Method in class org.concord.biologica.ui.BigMeiosisView
Stop blinking
stopBuildBedSpringWorld() - Method in class org.concord.collisions.engine.BedSpringWorld
 
stopButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
stopDataDelivery() - Method in class org.concord.pedagogica.graph.GenericDataSource
 
stopDataDelivery() - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
stopEventProcessing() - Method in class org.concord.pedagogica.engine.ActivityScript
 
stopProcessEvent() - Method in class org.concord.util.script.Script
 
STRAND - Static variable in class org.concord.biologica.engine.EngineProp
Strand of a gene on its chromosome.
STRAND_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
STRAND_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
streamHandlerFactory - Static variable in class org.concord.pedagogica.engine.Activity
 
StringDialog - class org.concord.pedagogica.ui.StringDialog.
 
StringDialog(JFrame, Vector, Vector) - Constructor for class org.concord.pedagogica.ui.StringDialog
 
StringLiteral - class org.concord.util.script.StringLiteral.
 
StringLiteral(String) - Constructor for class org.concord.util.script.StringLiteral
 
strings - Variable in class org.concord.util.LogProcess
 
STRINGS - Static variable in class org.concord.pedagogica.engine.NodeAccess
 
stringSort(Vector) - Method in class org.concord.pedagogica.ui.ClassTree
 
stringSort(Vector) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
stringValues - Variable in class org.concord.pedagogica.engine.NodeAccess
 
stringVariables - Variable in class org.concord.pedagogica.engine.NodeAccess
 
stripTags(String) - Static method in class org.concord.pedagogica.engine.QuestionState
 
STUDENT - Static variable in class org.concord.util.LogProcess
 
studentGenders - Variable in class org.concord.pedagogica.engine.Logging
 
studentGenders - Variable in class org.concord.pedagogica.ui.LoginPanel
 
studentName - Variable in class org.concord.util.LogProcess
 
studentNames - Variable in class org.concord.pedagogica.engine.Logging
 
students - Variable in class org.concord.pedagogica.ui.LoginPanel
 
subArcItems - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
subNodeItems - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
SUBSTITUTE - Static variable in class org.concord.util.Query
 
substitute(String) - Method in class org.concord.util.Query
 
substitutePrefix(String) - Method in class org.concord.util.PathDialog
 
suggestedCollisionTime - Variable in class org.concord.collisions.engine.JWorldElement
 
support - Variable in class org.concord.molecular.ui.MolecularView
 
SurveyChoice - class org.concord.pedagogica.ui.SurveyChoice.
 
SurveyChoice() - Constructor for class org.concord.pedagogica.ui.SurveyChoice
 
SurveyChoice(String, String[]) - Constructor for class org.concord.pedagogica.ui.SurveyChoice
This constructs a multiple choice question.
suspendingCallers - Static variable in class org.concord.util.script.Script
 
switchAlleles(Branch, Branch) - Method in class org.concord.biologica.engine.CrossOver
 
switchHorizontalAlignment(int) - Method in class org.concord.biologica.ui.MeiosisModel
Switch horizontal alignment of 2 chromosomes at step 33 and beyond in meiosis.
switchVerticalAlignment(int) - Method in class org.concord.biologica.ui.MeiosisModel
Switch vertical alignment of 2 chromosomes at step 73 and beyond in meiosis.
symbol - Variable in class org.concord.flash.player.FComponent
 
symbol - Variable in class org.concord.flash.player.FMovieBuilder.ClipActionBuilder
 
symbols - Variable in class org.concord.flash.player.FMovieBuilder
 
synchronizeGraph() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraphPanel
 
synchronizeGraph() - Method in class org.concord.pedagogica.graph.CCPedagogicaGraph
 
synchronizer - Variable in class org.concord.pedagogica.engine.ActivityScript
 

T

t - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
TABLE_SIZE - Static variable in class org.concord.pedagogica.ui.TableInputModel
 
TableInputModel - class org.concord.pedagogica.ui.TableInputModel.
 
TableInputModel.CellData - class org.concord.pedagogica.ui.TableInputModel.CellData.
 
TableInputModel.CellData(TableInputModel, String, int, int) - Constructor for class org.concord.pedagogica.ui.TableInputModel.CellData
 
TableInputModel() - Constructor for class org.concord.pedagogica.ui.TableInputModel
 
TableInputModel(int) - Constructor for class org.concord.pedagogica.ui.TableInputModel
 
TableInputModel(int, String) - Constructor for class org.concord.pedagogica.ui.TableInputModel
 
TableInputView - class org.concord.pedagogica.ui.TableInputView.
Class that generates an n x n table for use as a Punnett Square.
TableInputView() - Constructor for class org.concord.pedagogica.ui.TableInputView
Constructor with no arguments.
TableInputView(int) - Constructor for class org.concord.pedagogica.ui.TableInputView
Constructor that allows user to provide an argument to set the size of the Punnett Square table.
TabularView - class org.concord.pedagogica.ui.TabularView.
 
TabularView() - Constructor for class org.concord.pedagogica.ui.TabularView
 
tag - Static variable in class org.concord.pedagogica.ui.RunActivity
 
tag(int, boolean, byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTags interface
tagButtonCXForm(int, ColorTransform) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineBits(int, byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagDefineBitsJPEG2(int, byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineBitsJPEG2(int, InputStream) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineBitsJPEG3(int, byte[], byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagDefineBitsLossless(int, int, int, int, Color[], byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineBitsLossless2(int, int, int, int, Color[], byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineButton(int, Vector) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineButton2(int, boolean, Vector) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineButtonSound(int, int, SoundInfo, int, SoundInfo, int, SoundInfo, int, SoundInfo) - Method in class org.concord.flash.player.FMovieBuilder
 
tagDefineFont(int, int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineFont2(int, int, String, int, int, int, int, int[], int[], Rect[], int[], int[], int[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineFontInfo(int, String, int, int[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineMorphShape(int, Rect, Rect) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineQuickTimeMovie(int, String) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineShape(int, Rect) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineShape2(int, Rect) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineShape3(int, Rect) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineSound(int, int, int, boolean, boolean, int, byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagDefineSprite(int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineText(int, Rect, Matrix) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineText2(int, Rect, Matrix) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDefineTextField(int, String, String, Rect, int, AlphaColor, int, int, int, int, int, int, int, int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagDoAction() - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagEnableDebug(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagEnd() - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagExport(String[], int[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagFrameLabel(String) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagFreeCharacter(int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagGenerator(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagGeneratorCommand(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagGeneratorFont(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagGeneratorText(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagImport(String, String[], int[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagJPEGTables(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagList - Variable in class org.concord.pedagogica.ui.LogView
 
tagNameCharacter(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagPlaceObject(int, int, Matrix, AlphaTransform) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagPlaceObject2(boolean, int, int, int, Matrix, AlphaTransform, int, String, int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagProtect(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagRemoveObject(int, int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagRemoveObject2(int) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tags - Variable in class org.concord.pedagogica.ui.LogView
 
tagsButton - Variable in class org.concord.pedagogica.ui.LogView
 
tagScroll - Variable in class org.concord.pedagogica.ui.LogView
 
tagSerialNumber(String) - Method in class org.concord.flash.player.FMovieBuilder
 
tagSetBackgroundColor(Color) - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagShowFrame() - Method in class org.concord.flash.player.FMovieBuilder
SWFTagTypes interface
tagSoundStreamBlock(byte[]) - Method in class org.concord.flash.player.FMovieBuilder
 
tagSoundStreamHead(int, boolean, boolean, int, int, boolean, boolean, int) - Method in class org.concord.flash.player.FMovieBuilder
 
tagSoundStreamHead2(int, boolean, boolean, int, int, boolean, boolean, int) - Method in class org.concord.flash.player.FMovieBuilder
 
tagStartSound(int, SoundInfo) - Method in class org.concord.flash.player.FMovieBuilder
 
tan(double) - Method in class org.concord.flash.player.builtin.FMath
 
teacherField - Variable in class org.concord.pedagogica.ui.LoginPanel
 
teachers - Variable in class org.concord.pedagogica.ui.LoginPanel
 
temperature - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
Terrain - class org.concord.biologica.engine.Terrain.
This class represents a type of terrain in a world.
TERRAIN_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Terrain object was added to a world.
TERRAIN_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
TERRAIN_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_IDS_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_IDS_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
TERRAIN_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
TERRAIN_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Terrain object was removed from a world.
Terrain(World, String, Color) - Constructor for class org.concord.biologica.engine.Terrain
Creates a new terrain in the given world with the given name and color.
Terrain(World, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Terrain
Create a new terrain and start handling XML parsing events to set the properties of this object.
TERRAINS - Static variable in class org.concord.biologica.engine.EngineProp
A terrain or multiple terrains was changed in an environment.
test() - Static method in class org.concord.collisions.ui.GUIElementsFrame
 
test() - Static method in class org.concord.collisions.ui.GUITestIngrid
 
test() - Method in class org.concord.pedagogica.engine.ActivityNode
 
test() - Method in class org.concord.pedagogica.engine.ActivityArc
 
test(int, Vector, Vector, Vector) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Test this rule given a sex, a set of species alleles and generating zero or one characteristic, which is placed on the given characteristics vector and its trait put on the traits UNLESS there is already another characteristic of that trait on the traits vector.
testFileWrite(String) - Static method in class org.concord.pedagogica.engine.Logging
 
TestWindow - class org.concord.biologica.test.TestWindow.
This class is a test window for running BioLogica without a script.
TestWindow.WindowCloser - class org.concord.biologica.test.TestWindow.WindowCloser.
 
TestWindow.WindowCloser() - Constructor for class org.concord.biologica.test.TestWindow.WindowCloser
 
TestWindow() - Constructor for class org.concord.biologica.test.TestWindow
 
text - Variable in class org.concord.util.TextReader
 
text - Variable in class org.concord.pedagogica.engine.QuestionState
 
text - Variable in class org.concord.pedagogica.ui.CustomQuestion
 
text - Variable in class org.concord.pedagogica.ui.ActivityView
 
TEXT_INDENT - Static variable in class org.concord.biologica.ui.UIProp
The text indent of the text underneath organisms in the multiple organism view.
TEXT_LINE_SPACING - Static variable in class org.concord.biologica.ui.UIProp
The text line spacing of the text underneath organisms in the multiple organism view.
TEXT_SYMBOL - Static variable in class org.concord.biologica.engine.EngineProp
Text symbol simple property name.
TEXT_SYMBOL_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TEXT_SYMBOL_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
text(int[], int[]) - Method in class org.concord.flash.player.FMovieBuilder.TextBuilder
SWFText interface
textArea - Variable in class org.concord.pedagogica.PedAgogica
 
textArea - Variable in class org.concord.pedagogica.ui.ActivityView
 
textArea - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
textArea - Variable in class org.concord.pedagogica.ui.LogView
 
TextBounds - interface org.concord.util.TextBounds.
 
textColor - Variable in class org.concord.util.LineGraph
 
textColor - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
textIndent - Variable in class org.concord.biologica.ui.OrganismView
Indentation in pixels from left edge of image for text underneath the organism.
TextInputBox - class org.concord.pedagogica.ui.TextInputBox.
 
TextInputBox() - Constructor for class org.concord.pedagogica.ui.TextInputBox
 
TextInputStream - class org.concord.util.TextInputStream.
 
TextInputStream(JTextArea) - Constructor for class org.concord.util.TextInputStream
 
textLineSpacing - Variable in class org.concord.biologica.ui.OrganismView
Text line spacing, the distance between lines of text under an organism.
TextOutputStream - class org.concord.util.TextOutputStream.
 
TextOutputStream(JTextArea) - Constructor for class org.concord.util.TextOutputStream
 
TextPropertyEditor - class org.concord.collisions.ui.TextPropertyEditor.
 
TextPropertyEditor() - Constructor for class org.concord.collisions.ui.TextPropertyEditor
 
TextReader - class org.concord.util.TextReader.
 
TextReader(JTextArea) - Constructor for class org.concord.util.TextReader
 
textScroll - Variable in class org.concord.pedagogica.PedAgogica
 
textScroll - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
textSelection - Variable in class org.concord.pedagogica.engine.ActivityScript
 
textSelection - Variable in class org.concord.pedagogica.ui.ActivityArcItem
 
TextSelection - class org.concord.util.TextSelection.
 
TextSelection() - Constructor for class org.concord.util.TextSelection
 
TextSelection(int, int, int, int) - Constructor for class org.concord.util.TextSelection
 
TextWriter - class org.concord.util.TextWriter.
The TextWriter class allows a TextArea to be used a an output object which will accept write commands.
TextWriter(JTextArea) - Constructor for class org.concord.util.TextWriter
 
textX - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
textY - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
theClassName - Variable in class org.concord.util.LogProcess
 
THEN_CHARACTERISTIC - Static variable in class org.concord.biologica.engine.EngineProp
The "then characteristic" of a genotype to phenotype rule changed.
THEN_CHARACTERISTIC_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
THEN_CHARACTERISTIC_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
thickness - Variable in class org.concord.collisions.engine.JRigidBox
 
thickness - Variable in class org.concord.collisions.engine.JWall
wall's thickness.
THR - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Threonine
thread - Variable in class org.concord.molecular.engine.DefaultAtomicModel
 
THREONINE - Static variable in class org.concord.biologica.engine.AminoAcid
Threonine
throwUp - Variable in class org.concord.util.script.NameStack
 
THYMINE - Static variable in class org.concord.biologica.engine.Base
A pyrimidine which links with adenine only in DNA, not RNA.
tickSpace - Variable in class org.concord.util.Gauge
 
TIME - Static variable in class org.concord.util.LogProcess
 
timedAverageInterval - Variable in class org.concord.molecular.engine.ConditionValue
 
timeFormat - Variable in class org.concord.util.LogProcess
 
timeline - Variable in class org.concord.flash.player.FMovieBuilder
 
timer(int, String, boolean) - Method in interface org.concord.util.script.ScriptRuntime
 
timer(int, String, boolean) - Method in class org.concord.util.script.ECMA
 
TINY_CHROMOSOME_IMAGE - Static variable in class org.concord.biologica.engine.SpeciesChromosome
 
TIP_CHROMOSOME - Static variable in class org.concord.biologica.ui.Tool
 
TIP_CROSS - Static variable in class org.concord.biologica.ui.Tool
 
TIP_PEDIGREE - Static variable in class org.concord.biologica.ui.Tool
 
TIP_SELECTION - Static variable in class org.concord.biologica.ui.Tool
 
TIP_SNIP - Static variable in class org.concord.biologica.ui.Tool
 
title - Variable in class org.concord.pedagogica.ui.DefaultPrinter
 
titleField - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
titleLabel - Variable in class org.concord.pedagogica.ui.NodeViewEditor
 
tokenize(String) - Method in class org.concord.pedagogica.ui.LogView
 
Tool - class org.concord.biologica.ui.Tool.
The BioLogica Tool class.
TOOL_VIEW_HORIZONTAL - Static variable in class org.concord.biologica.ui.ToolView
Horizontal orientation
TOOL_VIEW_VERTICAL - Static variable in class org.concord.biologica.ui.ToolView
Vertical orientation
Tool() - Constructor for class org.concord.biologica.ui.Tool
 
toolChanged(int) - Method in class org.concord.biologica.ui.UIView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.PedigreeView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.StaticOrganismView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.MultipleOrganismView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.SexOrganismView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.BigMeiosisView
Method called by ToolView when the current tool changes.
toolChanged(int) - Method in class org.concord.biologica.ui.SexView
Method called by ToolView when the current tool changes.
ToolView - class org.concord.biologica.ui.ToolView.
The tool view of BioLogica.
ToolView() - Constructor for class org.concord.biologica.ui.ToolView
Creates a tool view.
ToolView(int) - Constructor for class org.concord.biologica.ui.ToolView
 
top - Variable in class org.concord.pedagogica.ui.ClassTree
 
TOP_ALLELE - Static variable in class org.concord.biologica.ui.DNAView
Top or bottom allele?
TOP_LEFT_GAMETE - Static variable in class org.concord.biologica.ui.MeiosisModel
 
TOP_LEFT_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
TOP_RIGHT_GAMETE - Static variable in class org.concord.biologica.ui.MeiosisModel
 
TOP_RIGHT_GAMETE_CHROMOSOME - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
 
TOP_STRAND - Static variable in class org.concord.biologica.engine.Gene
Bottom strand
topPanel - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
toString() - Method in class org.concord.util.beans.Statement
Prints the value of this statement using a Java-style syntax.
toString() - Method in class org.concord.util.beans.Expression
Prints the value of this expression using a Java-style syntax.
toString() - Method in class org.concord.util.script.Expression
 
toString() - Method in class org.concord.util.script.BooleanLiteral
 
toString() - Method in class org.concord.util.script.FloatLiteral
 
toString() - Method in class org.concord.util.script.Nil
 
toString() - Method in class org.concord.util.script.NullLiteral
 
toString() - Method in class org.concord.util.script.CharacterLiteral
 
toString() - Method in class org.concord.util.script.IntegerLiteral
 
toString() - Method in class org.concord.util.script.StringLiteral
 
toString() - Method in class org.concord.util.script.event.EventHandler
 
toString() - Method in class org.concord.biologica.engine.EngineObject
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.World
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.SpeciesChromosome
Return a string representation of this object, based on the chromosome's number type.
toString() - Method in class org.concord.biologica.engine.OrganismAllele
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.SpeciesImageColumn
Return a string representation of this object.
toString() - Method in class org.concord.biologica.engine.Environment
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.SpeciesImage
Return a string representation of this object.
toString() - Method in class org.concord.biologica.engine.Species
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.NucleicAcid
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.SpeciesAllele
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.Organism
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.Family
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.OrganismImage
Return a string representation of this object.
toString() - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.Characteristic
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.OrganismChromosomePair
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.BioEngine
Returns a string describing this object.
toString() - Method in class org.concord.biologica.engine.OrganismChromosome
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.Gene
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.Trait
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.OrganismAllelePair
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.SpeciesImageRow
Return a string representation of this object.
toString() - Method in class org.concord.biologica.engine.Terrain
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.engine.RawNucleicAcid
Return a string representation of this object, usually the object's name.
toString() - Method in class org.concord.biologica.ui.TreeViewNode
Get the string corresponding to this node.
toString() - Method in class org.concord.collisions.engine.JPartWorld.Distance2Line
 
toString() - Method in class org.concord.flash.player.FScriptObject
 
toString() - Method in class org.concord.flash.player.FEditField
 
toString() - Method in class org.concord.flash.player.StackFrame5
 
toString() - Method in class org.concord.flash.player.builtin.FArray
 
toString() - Method in class org.concord.flash.player.fill.FGradientFillMethod
 
toString() - Method in class org.concord.flash.player.fill.FColorFillMethod
 
toString() - Method in class org.concord.flash.util.MovieViewer.ElementObj
 
toString() - Method in class org.concord.molecular.engine.IndexList
 
toString() - Method in class org.concord.pedagogica.engine.QuestionState
 
toString() - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
toString() - Method in class org.concord.pedagogica.ui.NamedTreeNode
 
toString() - Method in class org.concord.pedagogica.ui.ActivitySearchResult
 
toString(double, int) - Static method in class org.concord.flash.player.FUtil
 
TOTAL - Static variable in class org.concord.molecular.engine.ConditionValue
 
total(double[]) - Method in class org.concord.molecular.engine.ConditionValue
 
totalAtomsEnergy - Variable in class org.concord.collisions.engine.JPartWorld
 
totalBoxesEnergy - Variable in class org.concord.collisions.engine.JPartWorld
 
totalSize - Variable in class org.concord.pedagogica.ui.TabularView
 
totalWallsEnergy - Variable in class org.concord.collisions.engine.JPartWorld
 
traceColor - Variable in class org.concord.collisions.engine.JAtom
 
tracePossible - Variable in class org.concord.collisions.ui.GUIPanel
 
Trait - class org.concord.biologica.engine.Trait.
This class represents a trait of a species.
TRAIT - Static variable in class org.concord.biologica.ui.UIProp
Indicates the trait of the source view changed.
TRAIT_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
A Trait object was added.
TRAIT_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
TRAIT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TRAIT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
TRAIT_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
TRAIT_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
TRAIT_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
 
TRAIT_PULLDOWN_ENABLED - Static variable in class org.concord.biologica.ui.UIProp
The enabled state of the trait pulldown has changed.
TRAIT_PULLDOWN_VISIBLE - Static variable in class org.concord.biologica.ui.UIProp
The visibility of the trait pulldown has changed.
TRAIT_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
A Trait object was removed.
Trait(Species, String) - Constructor for class org.concord.biologica.engine.Trait
Creates a new trait with the given name.
Trait(Species, String, int, Parser, ImportContext) - Constructor for class org.concord.biologica.engine.Trait
Create a new trait and start handling XML parsing events to set the properties of this object.
Transfer - class org.concord.util.Transfer.
 
Transfer() - Constructor for class org.concord.util.Transfer
 
transfer(Reader, Writer) - Method in class org.concord.util.Transfer
 
transferAborted(TransferEvent) - Method in interface org.concord.util.event.TransferListener
 
TransferEvent - class org.concord.util.event.TransferEvent.
 
TransferEvent(Transfer, Object) - Constructor for class org.concord.util.event.TransferEvent
 
TransferEvent(Transfer, Object, Exception) - Constructor for class org.concord.util.event.TransferEvent
 
transferFinished(TransferEvent) - Method in interface org.concord.util.event.TransferListener
 
TransferListener - interface org.concord.util.event.TransferListener.
 
transferStarted(TransferEvent) - Method in interface org.concord.util.event.TransferListener
 
transformPolygon(Point, Point, float) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
translate(double, double) - Method in class org.concord.flash.player.FComponent
 
translate(float, float) - Method in class org.concord.flash.player.FComponent
 
translate(int, int) - Method in class org.concord.biologica.ui.PedigreeObject
Translate the organism by the given amount
translate(int, int) - Method in class org.concord.biologica.ui.PedigreeLevel
Translate the level by the given amount.
translate(int, int) - Method in class org.concord.biologica.ui.PedigreeFamily
Translate the family by the given amount.
translate(int, int) - Method in class org.concord.pedagogica.ui.ActivityArcItem
 
translate(int, int) - Method in class org.concord.pedagogica.ui.ActivityNodeItem
 
traverse() - Method in class org.concord.pedagogica.engine.ActivityArc
 
TreeView - class org.concord.biologica.ui.TreeView.
The tree view of BioLogica.
TreeView() - Constructor for class org.concord.biologica.ui.TreeView
Creates a species tree view.
TreeViewCellRenderer - class org.concord.biologica.ui.TreeViewCellRenderer.
This class knows how to render (draw) the cells in the species' tree view.
TreeViewCellRenderer(TreeView) - Constructor for class org.concord.biologica.ui.TreeViewCellRenderer
 
TreeViewModel - class org.concord.biologica.ui.TreeViewModel.
TreeViewModel extends JTreeModel to extends valueForPathChanged.
TreeViewModel(TreeNode) - Constructor for class org.concord.biologica.ui.TreeViewModel
Creates a new instance of TreeViewModel with newRoot set to the root of this model.
TreeViewNode - class org.concord.biologica.ui.TreeViewNode.
A node of the tree in the left hand panel of the Species main window.
TreeViewNode(TreeView, EngineObject) - Constructor for class org.concord.biologica.ui.TreeViewNode
Constructs a new TreeViewNode object.
TRP - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Tryptophan
TRUE - Static variable in class org.concord.biologica.engine.EngineObject
TRUE Boolean object.
tryName - Variable in class org.concord.pedagogica.engine.ActivityScript
 
TRYPTOPHAN - Static variable in class org.concord.biologica.engine.AminoAcid
Tryptophan
tuneX(float) - Method in interface org.concord.collisions.ui.CCCoordinateTuner
 
tuneX(float) - Method in class org.concord.collisions.ui.PassiveGrid
 
tuneY(float) - Method in interface org.concord.collisions.ui.CCCoordinateTuner
 
tuneY(float) - Method in class org.concord.collisions.ui.PassiveGrid
 
TURBULENT_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForce
 
TURBULENT_FRICTION - Static variable in class org.concord.collisions.engine.CCFrictionForceCalculator
 
type - Variable in class org.concord.molecular.engine.ConditionValue
 
TYPE_ATOM - Static variable in class org.concord.collisions.engine.JPartWorld
 
TYPE_BOX - Static variable in class org.concord.collisions.engine.JPartWorld
 
TYPE_WALL - Static variable in class org.concord.collisions.engine.JPartWorld
 
TYR - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Tyrosine
TYROSINE - Static variable in class org.concord.biologica.engine.AminoAcid
Tyrosine

U

UIGraphics - class org.concord.biologica.ui.UIGraphics.
BioLogica graphics colors, fonts and other static stuff and methods.
UIGraphics() - Constructor for class org.concord.biologica.ui.UIGraphics
 
UIProp - class org.concord.biologica.ui.UIProp.
This class contains definitions for BioLogica UI properties.
UIProp() - Constructor for class org.concord.biologica.ui.UIProp
 
UIView - class org.concord.biologica.ui.UIView.
The basic user interface view of BioLogica.
UIView() - Constructor for class org.concord.biologica.ui.UIView
Creates a user interface view.
UNABLE_TO_FIND_CHARACTERISTIC - Static variable in class org.concord.biologica.engine.EngineStrings
 
UNABLE_TO_OPEN_SPECIES_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
UNABLE_TO_OPEN_WORLD_FILE - Static variable in class org.concord.biologica.engine.EngineStrings
 
UnaryExpression - class org.concord.util.script.UnaryExpression.
The UnaryExpression class is the base class for unary operations.
UnaryExpression() - Constructor for class org.concord.util.script.UnaryExpression
 
undoEdit() - Method in class org.concord.util.Editor
 
undoManager - Variable in class org.concord.pedagogica.PedAgogica
 
UNIT_CAT_AREA - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_ELECTRICITY - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_ENERGY - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_FORCE - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_LENGTH - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_LIGHT - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_MASS - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_MISC - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_POWER - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_PRESSURE - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_TEMPERATURE - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_TIME - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_UNKNOWN - Static variable in class org.concord.util.CCUnit
 
UNIT_CAT_VOL_CAP - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_ACRE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_AMPERE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_AMU - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_ANG_VEL - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_ARE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_ATM - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_BAR - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_BBL_D - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_BBL_L - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_BU - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_CALORIE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_CC - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_CELSIUS - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_CMH2O - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_COULOMB - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_DAY - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_DYNE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_ERG - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_EV - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_FAHRENHEIT - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_FEET - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_G - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_GAL_D - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_GAL_L - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_HECTARE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_HOUR - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_HP_EL - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_HP_MECH - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_HP_METR - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_INCH - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_JOULE - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_KELVIN - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_KG - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_KGF - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LB - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LBF - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LINEAR_VEL - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LITER - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LUMEN - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_LUX - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_M2 - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_M3 - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_METER - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MICRON - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MILE_ST - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MILLIVOLT - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MIN - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MMHG - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_MT - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_NEWTON - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_OZ - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_PASCAL - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_PT_D - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_PT_L - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_QT_D - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_QT_L - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_S - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_TORR - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_UNKNOWN - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_VOLT - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_WATT - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_WHR - Static variable in class org.concord.util.CCUnit
 
UNIT_CODE_YARD - Static variable in class org.concord.util.CCUnit
 
UNIT_TABLE_LENGTH - Static variable in class org.concord.util.CCUnit
 
unitCategory - Variable in class org.concord.util.CCUnit
 
unitConvert(CCUnit, float, CCUnit) - Static method in class org.concord.util.CCUnit
 
unitConvert(float) - Static method in class org.concord.util.CCUnit
 
unitConvert(int, float, int) - Static method in class org.concord.util.CCUnit
 
UNKNOWN - Static variable in class org.concord.pedagogica.engine.Logging
 
UNKNOWN_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
Image sizes, generally used as follows:
UNLOCKED - Static variable in class org.concord.biologica.engine.EngineObject
Unlocked locked value.
UNLOCKED_STRING - Static variable in class org.concord.biologica.engine.EngineObject
 
unlockedCharacteristicIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked characteristic
unlockedEnvironmentIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked environment
unlockedGeneIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked gene
unlockedOrganismIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked organism
unlockedRuleIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked rule
unlockedSpeciesAlleleIcon1 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked allele
unlockedSpeciesAlleleIcon2 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
unlockedSpeciesAlleleIcon3 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
unlockedSpeciesAlleleIcon4 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
unlockedSpeciesAlleleIcon5 - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
 
unlockedSpeciesChromosomeIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked species chromosome
unlockedSpeciesIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked species.
unlockedSpeciesImageColumnIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked species image column
unlockedSpeciesImageIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked species image
unlockedSpeciesImageRowIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked species image row
unlockedTerrainIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked terrain
unlockedTraitIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked trait
unlockedWorldIcon - Static variable in class org.concord.biologica.ui.TreeViewCellRenderer
Icon to use when the item is an unlocked world.
unmoveGamete() - Method in class org.concord.biologica.ui.MeiosisModel
Unmove gamete.
unOp(Object) - Method in class org.concord.util.script.UnaryExpression
 
unOp(Object) - Method in class org.concord.util.script.NotExpression
 
unOp(Object) - Method in class org.concord.util.script.NewExpression
 
unOp(Object) - Method in class org.concord.util.script.NegateExpression
 
unOp(Object) - Method in class org.concord.util.script.BitNotExpression
 
UNRECOGNIZED_FIELD_TYPE - Static variable in class org.concord.biologica.engine.EngineStrings
 
UNRECOGNIZED_XML_ELEMENT_ID - Static variable in class org.concord.biologica.engine.EngineStrings
 
UNRECOGNIZED_XML_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.EngineStrings
 
unshift(Object[]) - Method in class org.concord.flash.player.builtin.FArray
 
UNSPECIFIED_STRAND - Static variable in class org.concord.biologica.ui.MeiosisChromosomeModel
Number of chromosome model strands, used in creating gamete chromosome models only.
UP_STATE - Static variable in class org.concord.flash.player.FButton
 
up(float, float, JComponent) - Method in class org.concord.collisions.engine.JRigidBox
 
up(float, float, JComponent) - Method in class org.concord.collisions.engine.JWall
shift wall up
upButton - Variable in class org.concord.util.PathDialog
 
upButton - Variable in class org.concord.pedagogica.ui.ActivityView
 
update(BufferedImage, AffineTransform, ColorTransform) - Method in class org.concord.flash.player.FMorphShape
 
update(BufferedImage, AffineTransform, ColorTransform) - Method in class org.concord.flash.player.FFrame
Draws the frame.
update(Graphics) - Method in class org.concord.util.LineGraph
 
updateActivityItem(ActivityItem) - Method in class org.concord.pedagogica.PedAgogica
 
updateControls() - Method in class org.concord.biologica.ui.PedigreeView
Update the state (visibility, enabled, values) of the controls.
updateFilename() - Method in class org.concord.biologica.engine.SpeciesImage
Called by parent species when it's name changes, as this image cares.
updateFont(Graphics) - Method in class org.concord.biologica.ui.UIView
Update the font settings
updateGenotypeAndPhenotype(boolean) - Method in class org.concord.biologica.engine.Organism
Update the genotype and phenotype of this organism.
updateHotspotOnMousePress(Organism, int, int) - Method in class org.concord.biologica.ui.OrganismView
Update the hotspot state given that the user has pressed the mouse on the given organism at the given location in this view.
updateHotspotOnMouseReleased() - Method in class org.concord.biologica.ui.OrganismView
Update the hotspot state given that the user has released the mouse.
updateOffsets(Vector, int) - Method in class org.concord.pedagogica.ui.ActivitySearchResult
 
updateOrganismImage(OrganismImage) - Method in class org.concord.biologica.engine.SpeciesImage
Update an organism image given the current state of this species image, its rows and columns.
updatePresenters() - Method in class org.concord.biologica.ui.SelectionSet
Update the selection presenters because the selection changed.
updateScrollBars() - Method in class org.concord.biologica.ui.ChromosomeView
Update the scroll bar extents based on the number of organisms
updateScrollBars() - Method in class org.concord.biologica.ui.MultipleOrganismView
Update the scroll bar extents based on the number of organisms
updateSelections() - Method in class org.concord.pedagogica.ui.LogView
 
updateSize() - Method in class org.concord.biologica.ui.PedigreeView
Update the size of this view.
updateSize() - Method in class org.concord.biologica.ui.BigFertilizationView
Update the size of this view.
updateSize() - Method in class org.concord.biologica.ui.SmallMeiosisView
Update the size of this view.
updateSize() - Method in class org.concord.biologica.ui.SmallFertilizationView
 
updateSize() - Method in class org.concord.biologica.ui.ToolView
Update the size of this view.
updateSize() - Method in class org.concord.biologica.ui.BigMeiosisView
Update the size of this view.
updateSize() - Method in class org.concord.biologica.ui.SexView
Update the size of this view.
updateSize(boolean) - Method in class org.concord.biologica.ui.SmallFertilizationView
Update the size of this view.
updateState() - Method in class org.concord.biologica.ui.ChromosomeView
Update our view state.
updateState() - Method in class org.concord.biologica.ui.BigFertilizationView
Update the state of this view, usually called because the state of the underlying fertilization model has changed somehow and this view should reflect that changed state.
updateState() - Method in class org.concord.biologica.ui.SmallMeiosisView
Update the state of this view, usually called because the state of the underlying meiosis model has changed somehow and this view should reflect that changed state.
updateState() - Method in class org.concord.biologica.ui.SmallFertilizationView
Update the state of this view, usually called because the state of the underlying fertilization model has changed somehow and this view should reflect that changed state.
updateState() - Method in class org.concord.biologica.ui.ObjectPropertiesView
Update our state
updateState() - Method in class org.concord.biologica.ui.BigMeiosisView
Update the state of this view, usually called because the state of the underlying meiosis model has changed somehow and this view should reflect that changed state.
updateUI() - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Notification from the UIManager that the look and feel [L&F] has changed.
updateValue(double) - Method in class org.concord.util.BarGraph
 
updateValue(double) - Method in class org.concord.util.Gauge
 
updateValue(double) - Method in interface org.concord.util.ValueGraph
 
updateValue(double) - Method in class org.concord.util.LineGraph
 
updateValue(double, int) - Method in class org.concord.util.BarGraph
Updates graph element at index with new value.
updateValue(double, int) - Method in class org.concord.util.Gauge
Updates gauge sub-bar at index with new value.
updateValue(double, int) - Method in interface org.concord.util.ValueGraph
 
updateValue(double, int) - Method in class org.concord.util.LineGraph
Updates graph element at index with new value.
updateValue(float) - Method in class org.concord.util.BarGraph
 
updateValue(float) - Method in class org.concord.util.Gauge
 
updateValue(float) - Method in interface org.concord.util.ValueGraph
 
updateValue(float) - Method in class org.concord.util.LineGraph
 
updateValue(float, int) - Method in class org.concord.util.BarGraph
 
updateValue(float, int) - Method in class org.concord.util.Gauge
 
updateValue(float, int) - Method in interface org.concord.util.ValueGraph
 
updateValue(float, int) - Method in class org.concord.util.LineGraph
 
uploadFile(File, String) - Method in class org.concord.pedagogica.engine.Logging
 
uploadHost - Variable in class org.concord.pedagogica.engine.Logging
 
uploadLog() - Method in class org.concord.pedagogica.engine.Logging
 
uploadPort - Variable in class org.concord.pedagogica.engine.Logging
 
URACIL - Static variable in class org.concord.biologica.engine.Base
A pyrimidine which links with adenine only in RNA, not DNA.
USE_ALL_BEANINFO - Static variable in class org.concord.util.beans.Introspector
 
useConsole - Variable in class org.concord.pedagogica.engine.Logging
 
USER_DIR - Static variable in class org.concord.util.PathDialog
 
userDir - Variable in class org.concord.pedagogica.engine.LogModel
 
userDir - Variable in class org.concord.pedagogica.ui.LogView
 
userDirectory - Variable in class org.concord.pedagogica.ui.ActivityView
 
Util - class org.concord.util.Util.
 
UTIL - Static variable in class org.concord.util.Debug
 
Util() - Constructor for class org.concord.util.Util
 

V

VAL - Static variable in class org.concord.biologica.engine.AminoAcid
An abbreviation for Valine
val1 - Variable in class org.concord.collisions.engine.FloatPair
 
val2 - Variable in class org.concord.collisions.engine.FloatPair
 
validate() - Method in class org.concord.pedagogica.ui.CCTableCellRenderer
Overridden for performance reasons.
validateNameField(String) - Method in class org.concord.pedagogica.ui.LoginPanel
 
validTool(int) - Static method in class org.concord.biologica.ui.Tool
Get whether or not this is a valid tool.
VALINE - Static variable in class org.concord.biologica.engine.AminoAcid
Valine
value - Variable in class org.concord.util.script.Quote
 
value - Static variable in class org.concord.flash.player.FUndefined
 
valueChanged(ListSelectionEvent) - Method in class org.concord.util.PathDialog
 
valueChanged(ListSelectionEvent) - Method in class org.concord.pedagogica.ui.ActivitySearch
 
valueChanged(ListSelectionEvent) - Method in class org.concord.pedagogica.ui.VariableDialog
 
valueChanged(ListSelectionEvent) - Method in class org.concord.pedagogica.ui.LogView
 
valueChanged(ListSelectionEvent) - Method in class org.concord.pedagogica.ui.NodeViewEditor
 
valueChanged(TreeSelectionEvent) - Method in class org.concord.biologica.ui.TreeView
Handle tree selection change events
valueChanged(TreeSelectionEvent) - Method in class org.concord.flash.util.MovieViewer
 
valueForPathChanged(TreePath, Object) - Method in class org.concord.biologica.ui.TreeViewModel
Subclassed to message setString() to the changed path item.
valueGraph - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
ValueGraph - interface org.concord.util.ValueGraph.
 
valueList - Variable in class org.concord.molecular.engine.ConditionValue
 
values - Variable in class org.concord.util.Gauge
 
values - Variable in class org.concord.util.script.SequenceLiteral
 
values - Variable in class org.concord.util.script.NameStack
 
values - Variable in class org.concord.util.script.IndexExpression
 
values - Variable in class org.concord.molecular.engine.ConditionValue
 
values - Variable in class org.concord.molecular.ui.AtomicValueDispatcher
 
values - Variable in class org.concord.pedagogica.ui.VariableDialog
 
valueStrings - Variable in class org.concord.util.Gauge
 
VariableDeclaration - class org.concord.util.script.VariableDeclaration.
 
VariableDeclaration() - Constructor for class org.concord.util.script.VariableDeclaration
 
VariableDialog - class org.concord.pedagogica.ui.VariableDialog.
 
VariableDialog(JFrame, String, Vector, Vector) - Constructor for class org.concord.pedagogica.ui.VariableDialog
 
variableField - Variable in class org.concord.pedagogica.ui.ModifyValueDialog
 
variableList - Variable in class org.concord.pedagogica.ui.VariableDialog
 
variables - Variable in class org.concord.util.script.Script
 
variables - Variable in class org.concord.pedagogica.ui.VariableDialog
 
vel - Variable in class org.concord.collisions.engine.VelDistFraction
 
vel_scale - Static variable in class org.concord.collisions.engine.JWorldElement
 
velColor - Variable in class org.concord.collisions.engine.JAtom
 
VelDistFraction - class org.concord.collisions.engine.VelDistFraction.
 
VelDistFraction(int, int) - Constructor for class org.concord.collisions.engine.VelDistFraction
 
velDistribution(int) - Static method in class org.concord.collisions.ui.GUIElementsFrame
 
velDistribution(int) - Static method in class org.concord.collisions.ui.GUITestIngrid
 
VelocityMagnitude - class org.concord.molecular.engine.VelocityMagnitude.
 
VelocityMagnitude() - Constructor for class org.concord.molecular.engine.VelocityMagnitude
 
VelocitySquare - class org.concord.molecular.engine.VelocitySquare.
 
VelocitySquare() - Constructor for class org.concord.molecular.engine.VelocitySquare
 
version - Variable in class org.concord.flash.player.FMovieBuilder.ActionsBuilder
 
vertical - Variable in class org.concord.collisions.engine.JWall
 
VERTICAL_WALL - Static variable in class org.concord.collisions.engine.JRigidBox
 
VERTICAL_WALL - Static variable in class org.concord.collisions.engine.JWall
 
viewEditor - Variable in class org.concord.pedagogica.ui.ActivityNodeItem
 
viewEditor - Variable in class org.concord.pedagogica.ui.ActivityView
 
ViewerApplet - class org.concord.pedagogica.ui.ViewerApplet.
 
ViewerApplet() - Constructor for class org.concord.pedagogica.ui.ViewerApplet
 
ViewerAppletEvent - class org.concord.pedagogica.ui.event.ViewerAppletEvent.
 
ViewerAppletEvent(Object) - Constructor for class org.concord.pedagogica.ui.event.ViewerAppletEvent
 
ViewerAppletListener - interface org.concord.pedagogica.ui.event.ViewerAppletListener.
 
ViewerContext - class org.concord.pedagogica.ui.ViewerContext.
 
ViewerContext() - Constructor for class org.concord.pedagogica.ui.ViewerContext
 
ViewerStub - class org.concord.pedagogica.ui.ViewerStub.
 
ViewerStub(Applet) - Constructor for class org.concord.pedagogica.ui.ViewerStub
 
viewFormat - Variable in class org.concord.pedagogica.engine.Logging
 
viewPanel - Variable in class org.concord.pedagogica.ui.LogView
 
viewText - Variable in class org.concord.pedagogica.engine.ActivityScript
 
VISIBLE - Static variable in class org.concord.biologica.engine.EngineProp
Visible flag.
VISIBLE_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
VISIBLE_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
visibleToScripts(String) - Method in class org.concord.util.script.Script.ScriptSecuritySupport
Return true iff the Java class with the given name should be exposed to scripts.
vx - Variable in class org.concord.collisions.engine.JWorldElement
 
vx - Variable in class org.concord.collisions.ui.PassiveElement
 
vx - Variable in class org.concord.collisions.ui.DataCrossPanel
 
vy - Variable in class org.concord.collisions.engine.JWorldElement
 
vy - Variable in class org.concord.collisions.ui.PassiveElement
 
vy - Variable in class org.concord.collisions.ui.DataCrossPanel
 

W

waitForPause() - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
waitingThread - Variable in class org.concord.util.script.Script
 
WALL_TEMP_CONST - Static variable in class org.concord.collisions.engine.JWall
 
WALL_TEMP_NONE - Static variable in class org.concord.collisions.engine.JWall
 
WARNING - Static variable in class org.concord.util.Debug
 
WARNING - Static variable in class org.concord.biologica.engine.Debug
 
WARNING - Static variable in class org.concord.biologica.engine.EngineStrings
 
wasCollision() - Method in class org.concord.collisions.engine.JWorldElement
 
wasLastStepCollision - Variable in class org.concord.collisions.engine.JWorldElement
 
WATCH_MODE_CROSS - Static variable in class org.concord.collisions.ui.GUIPanel
 
WATCH_MODE_LEFT_BOTTOM - Static variable in class org.concord.collisions.ui.GUIPanel
 
WATCH_MODE_LEFT_TOP - Static variable in class org.concord.collisions.ui.GUIPanel
 
WATCH_MODE_RIGHT_BOTTOM - Static variable in class org.concord.collisions.ui.GUIPanel
 
WATCH_MODE_RIGHT_TOP - Static variable in class org.concord.collisions.ui.GUIPanel
 
WATSONIUM - Static variable in class org.concord.molecular.ui.MolecularView
 
WEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
Weight changed.
WEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
WEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
WelcomeView - class org.concord.biologica.ui.WelcomeView.
The welcome view of BioLogica.
WelcomeView() - Constructor for class org.concord.biologica.ui.WelcomeView
Creates a large view with the given name and colors.
when - Variable in class org.concord.collisions.event.AreaEvent
 
when - Variable in class org.concord.collisions.event.CollisionsEvent
 
width - Variable in class org.concord.util.LineGraph
 
width - Variable in class org.concord.biologica.ui.PedigreeObject
The width of the pedigree object as drawn
width - Variable in class org.concord.collisions.event.AreaEvent
 
width - Variable in class org.concord.flash.player.fill.FImage
 
width - Variable in class org.concord.pedagogica.ui.ChoiceQuestion
 
WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
Width changed.
WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
widthr - Variable in class org.concord.collisions.engine.JAtom
 
WINDOW_CLOSED - Static variable in class org.concord.biologica.ui.UIProp
A window has closed.
WINDOW_MODE_EXPORT_SPECIES_FILE - Static variable in class org.concord.biologica.ui.AllInOneView
Export Species window mode, meaning the file chooser is shown for choosing a species file to export.
WINDOW_MODE_IMPORT_SPECIES_FILE - Static variable in class org.concord.biologica.ui.AllInOneView
Import Species window mode, meaning the file chooser is shown for choosing a species file to import.
WINDOW_MODE_NORMAL - Static variable in class org.concord.biologica.ui.AllInOneView
Normal window mode, meaning we have a world open and the normal views can be seen.
WINDOW_MODE_OPEN_WORLD_FILE - Static variable in class org.concord.biologica.ui.AllInOneView
Open window mode, meaning the file chooser is shown for choosing a world file to open.
WINDOW_MODE_SAVE_WORLD_FILE_AS - Static variable in class org.concord.biologica.ui.AllInOneView
Save As window mode, meaning the file chooser is shown for choosing a world file to save to.
WINDOW_MODE_STARTUP - Static variable in class org.concord.biologica.ui.AllInOneView
Startup window mode, meaning we want ALL views visible so they all get the proper look and feel.
WINDOW_MODE_WELCOME - Static variable in class org.concord.biologica.ui.AllInOneView
Welcome window mode, meaning no world is currently open and we want some text on the screen telling the user to choose New or Open...
windowActivated(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowClosed(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowClosing(WindowEvent) - Method in class org.concord.biologica.test.TestWindow.WindowCloser
 
windowClosing(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowDeactivated(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowDeiconified(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowIconified(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
windowOpened(WindowEvent) - Method in class org.concord.flash.util.ApplicationFrame
 
within(int, int, int, int) - Method in class org.concord.biologica.ui.PedigreeObject
Is this organism within the given rectangle? We'll consider a organism within the rectangle if the rectangle contains some portion of the organism.
within(int, int, int, int) - Method in class org.concord.biologica.ui.PedigreeFamily
Is this family within the given rectangle? We'll consider a family within the rectangle if the rectangle contains some portion of the child bar, parent bar or vertical bar.
wordsInAnswers - Variable in class org.concord.util.LogProcess
 
World - class org.concord.biologica.engine.World.
This class represents a BioLogica world.
WORLD_ADDED - Static variable in class org.concord.biologica.engine.EngineProp
World added.
WORLD_COLON - Static variable in class org.concord.biologica.engine.EngineStrings
 
WORLD_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
WORLD_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
WORLD_ID_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
WORLD_ID_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
WORLD_NODE_TYPE - Static variable in class org.concord.biologica.ui.TreeViewNode
Node types, assuming the tree looks like world | +- species 1 | | | +- chromosome 1 of species 1 | | | | | +- gene 1 of species 1 on chromosome 1 | | | | | | | +- allele 1 of gene 1 of species 1 on chromosome 1 | | | +- allele 2 of gene 1 of species 1 on chromosome 1 | | | | | +- gene 2 of species 1 on chromosome 1 | | | | | +- allele 1 of gene 2 of species 1 on chromosome 1 | | +- allele 2 of gene 2 of species 1 on chromosome 1 | | | +- chromosome 2 of species 1 | | | | | +- gene 3 of species 1 on chromosome 2 | | | | | | | +- allele 1 of gene 3 of species 1 on chromosome 2 | | | +- allele 2 of gene 3 of species 1 on chromosome 2 | | | | | +- gene 4 of species 1 on chromosome 2 | | | | | +- allele 1 of gene 4 of species 1 on chromosome 2 | | +- allele 2 of gene 4 of species 1 on chromosome 2 | | | +- other chromosomes ...
WORLD_REMOVED - Static variable in class org.concord.biologica.engine.EngineProp
World removed.
World() - Constructor for class org.concord.biologica.engine.World
Creates a new world, as when creating a new world that has no associated file yet.
World(File) - Constructor for class org.concord.biologica.engine.World
Creates a new world with by opening the given file and retrieving the contents of the file.
World(String) - Constructor for class org.concord.biologica.engine.World
Creates a new world with by opening the given url and retrieving the contents of the url file.
WorldFileFilter - class org.concord.biologica.ui.WorldFileFilter.
 
WorldFileFilter() - Constructor for class org.concord.biologica.ui.WorldFileFilter
 
worldLock - Static variable in class org.concord.collisions.engine.JPartWorld
 
worldTime - Variable in class org.concord.collisions.event.StepEvent
 
write(byte[]) - Method in class org.concord.util.TextOutputStream
 
write(byte[]) - Method in class org.concord.util.script.ScriptFileOutputStream
 
write(byte[], int, int) - Method in class org.concord.util.TextOutputStream
 
write(byte[], int, int) - Method in class org.concord.util.script.ScriptFileOutputStream
 
write(char[]) - Method in class org.concord.util.TextWriter
 
write(char[], int, int) - Method in class org.concord.util.TextWriter
 
write(int) - Method in class org.concord.util.TextWriter
 
write(int) - Method in class org.concord.util.TextOutputStream
 
write(int) - Method in class org.concord.util.script.ScriptFileOutputStream
 
write(String) - Method in class org.concord.util.TextWriter
 
write(String, int, int) - Method in class org.concord.util.TextWriter
 
writeExpression(Expression) - Method in class org.concord.util.beans.Encoder
The implementation first checks to see if an expression with this value has already been written.
writeExpression(Expression) - Method in class org.concord.util.beans.XMLEncoder
This method calls the superclass's implementation and records oldExp so that it can produce the actual output when the stream is flushed.
writeExternal(DataStream) - Method in class org.concord.pedagogica.graph.GenericDataSource
 
writeExternal(DataStream) - Method in class org.concord.pedagogica.graph.ArrayDataSource
 
writeObject(Object) - Method in class org.concord.util.beans.CCXMLEncoder
 
writeObject(Object) - Method in class org.concord.util.beans.Encoder
Write the specified object to the output stream.
writeObject(Object) - Method in class org.concord.util.beans.XMLEncoder
Write an XML representation of the specified object to the output.
writeObject(Object, Encoder) - Method in class org.concord.util.beans.PersistenceDelegate
The writeObject is a single entry point to the persistence and is used by a Encoder in the traditional mode of delegation.
writer - Variable in class org.concord.util.TextOutputStream
 
writeStatement(Statement) - Method in class org.concord.util.beans.Encoder
Writes statement oldStm to the stream.
writeStatement(Statement) - Method in class org.concord.util.beans.XMLEncoder
This method calls the superclass's implementation and records oldStm so that it can produce the actual output when the stream is flushed.
writeString(String, Object) - Method in class org.concord.util.Debug
Send a string to our print stream for debugging purposes.
writeString(String, Object) - Method in class org.concord.biologica.engine.Debug
Send a string to our print stream for debugging purposes.
writeText(OutputStream) - Method in class org.concord.pedagogica.engine.ActivityScript
 
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.EngineObject
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.World
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.SpeciesChromosome
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.OrganismAllele
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.AlgorithmicNucleicAcid
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.SpeciesImageColumn
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Environment
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.SpeciesImage
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Species
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.NucleicAcid
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.SpeciesAllele
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Organism
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Family
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.OrganismImage
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.GenotypeToPhenotypeRule
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Characteristic
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.OrganismChromosomePair
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in interface org.concord.biologica.engine.INucleicAcid
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.OrganismChromosome
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Gene
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Trait
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.OrganismAllelePair
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.SpeciesImageRow
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.Terrain
Writes this object to the given stream in XML format.
writeToStream(PrintWriter) - Method in class org.concord.biologica.engine.RawNucleicAcid
Writes this object to the given stream in XML format.
wsize - Static variable in class org.concord.biologica.datasupport.SpecieFileDesc
 

X

x - Static variable in class org.concord.biologica.engine.EngineStrings
 
x - Variable in class org.concord.collisions.engine.CCPoint
 
x - Variable in class org.concord.collisions.event.AreaEvent
 
x - Variable in class org.concord.collisions.event.CollisionsEvent
 
x - Variable in class org.concord.collisions.ui.PassiveElement
 
x - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
X - Static variable in class org.concord.biologica.engine.EngineStrings
 
X_BLUE_CHROMOSOME - Static variable in class org.concord.biologica.ui.ChromosomeView
 
X_BLUE_CHROMOSOME - Static variable in class org.concord.biologica.ui.ObjectPropertiesView
 
X_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
X chromosome - used as a "number type".
X_CHROMOSOME_STRING - Static variable in interface org.concord.biologica.engine.IChromosome
 
X_COMBO_BOX_OFFSET - Static variable in class org.concord.biologica.ui.ChromosomeView
 
X_LEFT_IMAGE - Static variable in class org.concord.biologica.ui.ChromosomeView
 
X_RIGHT_IMAGE - Static variable in class org.concord.biologica.ui.ChromosomeView
 
X_YELLOW_CHROMOSOME - Static variable in class org.concord.biologica.ui.ChromosomeView
 
X_YELLOW_CHROMOSOME - Static variable in class org.concord.biologica.ui.ObjectPropertiesView
 
x1 - Variable in class org.concord.collisions.engine.JWall
x coordinate of first wall's side
x2 - Variable in class org.concord.collisions.engine.JWall
x coordinate of second wall's side
XLARGE_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
XLarge hotspot location.
XLARGE_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
XLarge image column width of a Species object.
XLARGE_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
XLarge image row height of a Species object.
XLARGE_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XLARGE_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
xLeftLimit - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
xLeftLimit - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
xLeftLimit - Static variable in class org.concord.collisions.ui.IngridProblem
 
xLocation - Variable in class org.concord.biologica.ui.PedigreeObject
The X location of the top left corner of object
XML_FILE - Static variable in class org.concord.biologica.engine.EngineProp
XML file simple property name.
XML_FILENAME - Static variable in class org.concord.biologica.engine.EngineProp
XML filename simple property name.
XMLDecoder - class org.concord.util.beans.XMLDecoder.
The XMLDecoder class is used to read XML documents created using the XMLEncoder and is used just like the ObjectInputStream.
XMLDecoder(InputStream) - Constructor for class org.concord.util.beans.XMLDecoder
Creates a new input stream for reading archives created by the XMLEncoder class.
XMLDecoder(InputStream, Object) - Constructor for class org.concord.util.beans.XMLDecoder
Creates a new input stream for reading archives created by the XMLEncoder class.
XMLDecoder(InputStream, Object, ExceptionListener) - Constructor for class org.concord.util.beans.XMLDecoder
Creates a new input stream for reading archives created by the XMLEncoder class.
xmlElementContext - Variable in class org.concord.biologica.engine.EngineObject
XML Element context used when reading an element this object from a file.
XMLEncoder - class org.concord.util.beans.XMLEncoder.
The XMLEncoder class is a complementary alternative to the ObjectOutputStream and can used to generate a textual representation of a JavaBean in the same way that the ObjectOutputStream can be used to create binary representation of Serializable objects.
XMLEncoder(OutputStream) - Constructor for class org.concord.util.beans.XMLEncoder
Creates a new output stream for sending JavaBeans to the stream out using an XML encoding.
XMLFileFilter - class org.concord.biologica.ui.XMLFileFilter.
 
XMLFileFilter() - Constructor for class org.concord.biologica.ui.XMLFileFilter
 
xNumb - Variable in class org.concord.biologica.datasupport.ShortImageDescription
 
xRightLimit - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
xRightLimit - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
xRightLimit - Static variable in class org.concord.collisions.ui.IngridProblem
 
XSMALL_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
XSmall hotspot location.
XSMALL_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
XSmall image column width of a Species object.
XSMALL_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
XSmall image row height of a Species object.
XSMALL_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XSMALL_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 
XXSMALL_HOTSPOT - Static variable in class org.concord.biologica.engine.EngineProp
XXSmall hotspot location.
XXSMALL_HOTSPOT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_HOTSPOT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_IMAGE_COLUMN_WIDTH - Static variable in class org.concord.biologica.engine.EngineProp
XXSmall image column width of a Species object.
XXSMALL_IMAGE_COLUMN_WIDTH_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_IMAGE_COLUMN_WIDTH_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_IMAGE_ROW_HEIGHT - Static variable in class org.concord.biologica.engine.EngineProp
XXSmall image row height of a Species object.
XXSMALL_IMAGE_ROW_HEIGHT_ELEMENT_ID - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_IMAGE_ROW_HEIGHT_ELEMENT_NAME - Static variable in class org.concord.biologica.engine.Elements
 
XXSMALL_IMAGE_SIZE - Static variable in class org.concord.biologica.engine.SpeciesImage
 

Y

y - Static variable in class org.concord.biologica.engine.EngineStrings
 
y - Variable in class org.concord.collisions.engine.CCPoint
 
y - Variable in class org.concord.collisions.event.AreaEvent
 
y - Variable in class org.concord.collisions.event.CollisionsEvent
 
y - Variable in class org.concord.collisions.ui.PassiveElement
 
y - Variable in class org.concord.flash.player.FMovieBuilder.TextBuilder
 
Y - Static variable in class org.concord.biologica.engine.EngineStrings
 
Y_CHROMOSOME - Static variable in interface org.concord.biologica.engine.IChromosome
Y chromosome - used as a "number type".
Y_CHROMOSOME_STRING - Static variable in interface org.concord.biologica.engine.IChromosome
 
Y_IMAGE_OFFSET - Static variable in class org.concord.biologica.ui.ChromosomeView
 
Y_TOP_IMAGE - Static variable in class org.concord.biologica.ui.ChromosomeView
 
y1 - Variable in class org.concord.collisions.engine.JWall
y coordinate of first wall's side
y2 - Variable in class org.concord.collisions.engine.JWall
y coordinate of second wall's side
yDownLimit - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
yDownLimit - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
yDownLimit - Static variable in class org.concord.collisions.ui.IngridProblem
 
yLocation - Variable in class org.concord.biologica.ui.PedigreeObject
The Y location of the top left corner of the object
yMax - Variable in class org.concord.util.LineGraph
 
yOrigin - Variable in class org.concord.util.LineGraph
 
yUpLimit - Static variable in class org.concord.collisions.ui.GUIElementsFrame
 
yUpLimit - Static variable in class org.concord.collisions.ui.GUITestIngrid
 
yUpLimit - Static variable in class org.concord.collisions.ui.IngridProblem
 

Z

zeroAllCharges(Atom[]) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
zeroAllRestraints(Atom[]) - Method in class org.concord.molecular.engine.DefaultAtomicModel
 
zipEntry - Variable in class org.concord.util.script.ScriptFile
 
zipFile - Variable in class org.concord.util.script.ScriptFile
 

_

_currentframe - Variable in class org.concord.flash.player.FMovieClip
 

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