org.concord.biologica.ui
Class PedigreeOrganismView

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--org.concord.biologica.ui.UIView
                          |
                          +--org.concord.biologica.ui.OrganismView
                                |
                                +--org.concord.biologica.ui.PedigreeOrganismView

All Implemented Interfaces:

java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.beans.PropertyChangeListener, SelectionPresenter, java.io.Serializable

public final class PedigreeOrganismView

extends OrganismView

implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.beans.PropertyChangeListener, SelectionPresenter

The pedigree organism view of BioLogica.

An object of this class will generate the following property change events:

• org.concord.biologica.ui.UIProp.BACKGROUND - the background color of the view changed
• org.concord.biologica.ui.UIProp.CHARACTERISTICS_TEXT_VISIBLE - the characteristics text visibility boolean changed
• org.concord.biologica.ui.UIProp.CHROMOSOME_TOOL_PICK_ON_ORGANISM - the user clicked on an organism with the chromosome tool
• org.concord.biologica.ui.UIProp.CROSS_SUCCEEDED - the cross succeeded
• org.concord.biologica.ui.UIProp.FIXED_NUMBER_CHILDREN - the fixed number of children from a breeding
• org.concord.biologica.ui.UIProp.FONT - the font of the view changed
• org.concord.biologica.ui.UIProp.FOREGROUND - the foreground color of the view changed
• org.concord.biologica.ui.UIProp.LOCK_SYMBOL_VISIBLE - the lock symbol should or should not be displayed if appropriate
• org.concord.biologica.ui.UIProp.MAXIMUM_NUMBER_CHILDREN - the maximum number of children from a breeding
• org.concord.biologica.ui.UIProp.MINIMUM_NUMBER_CHILDREN - the minimum number of children from a breeding
• org.concord.biologica.ui.UIProp.NAME_TEXT_VISIBLE - the name text visibility boolean changed
• org.concord.biologica.ui.UIProp.NUMBER_FEMALE_CHILDREN - the number of female children in a family when in male / female mode
• org.concord.biologica.ui.UIProp.NUMBER_MALE_CHILDREN - the number of male children in a family when in male / female mode
• org.concord.biologica.ui.UIProp.OFFSPRING_MODE - the pedigree view offspring mode changed
• org.concord.biologica.ui.UIProp.ORGANISM_ADDED_TO_VIEW - an organism has been added to this view
• org.concord.biologica.ui.UIProp.ORGANISM_IMAGE_SIZE - the image size to use for drawing organisms in this view
• org.concord.biologica.ui.UIProp.ORGANISM_REMOVED_FROM_VIEW - an organism has been removed from this view
• org.concord.biologica.ui.UIProp.PEDIGREE_TOOL_PICK_ON_ORGANISM - the user clicked on an organism with the pedigree tool
• org.concord.biologica.ui.UIProp.SEX_TEXT_VISIBLE - the sex text visibility boolean changed
• org.concord.biologica.ui.UIProp.SNIP_TOOL_PICK_ON_FAMILY - the user clicked on an organism with the snip tool with family locked
• org.concord.biologica.ui.UIProp.SNIP_TOOL_PICK_ON_ORGANISM - the user clicked on an organism with the snip tool with organism locked
• org.concord.biologica.ui.UIProp.SPECIES_TEXT_VISIBLE - the species text visibility boolean changed
• org.concord.biologica.ui.UIProp.TEXT_INDENT - the indentation of text from left edge of image
• org.concord.biologica.ui.UIProp.TEXT_LINE_SPACING - the number of pixels between lines of text
• org.concord.biologica.ui.UIProp.TRAIT - the trait to draw, null if should draw whole organism

Version:

$Revision: 1.14 $ $Date: 2002/04/16 19:07:05 $

Author:

$Author: qliao $

See Also:

UIProp.BACKGROUND, UIProp.CHARACTERISTICS_TEXT_VISIBLE, UIProp.CHROMOSOME_TOOL_PICK_ON_ORGANISM, UIProp.CROSS_SUCCEEDED, UIProp.FIXED_NUMBER_CHILDREN, UIProp.FONT, UIProp.FOREGROUND, UIProp.LOCK_SYMBOL_VISIBLE, UIProp.MAXIMUM_NUMBER_CHILDREN, UIProp.MINIMUM_NUMBER_CHILDREN, UIProp.NAME_TEXT_VISIBLE, UIProp.NUMBER_FEMALE_CHILDREN, UIProp.NUMBER_MALE_CHILDREN, UIProp.OFFSPRING_MODE, UIProp.ORGANISM_ADDED_TO_VIEW, UIProp.ORGANISM_IMAGE_SIZE, UIProp.ORGANISM_REMOVED_FROM_VIEW, UIProp.PEDIGREE_TOOL_PICK_ON_ORGANISM, UIProp.SEX_TEXT_VISIBLE, UIProp.SNIP_TOOL_PICK_ON_FAMILY, UIProp.SNIP_TOOL_PICK_ON_ORGANISM, UIProp.SPECIES_TEXT_VISIBLE, UIProp.TEXT_INDENT, UIProp.TEXT_LINE_SPACING, UIProp.TRAIT, PropertyChangeListener, Serialized Form

Inner classes inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Inner classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Inner classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent

Fields inherited from class org.concord.biologica.ui.OrganismView

characteristicsTextVisible, highlightColor, hotspotOrganism, hotspotOrganismImage, lockSymbolVisible, nameTextVisible, organismImageSize, selectionColor, sexTextVisible, speciesTextVisible, textIndent, textLineSpacing

Fields inherited from class org.concord.biologica.ui.UIView

changes, fontAscent, fontDescent, fontHeight, fontMetrics, preferredHeight, preferredWidth, scrollPane

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

PedigreeOrganismView()
Creates a pedigree organism view.

Method Summary

void	addFamily(Family aFamily, int xLocation, int yLocation) Add a family to this view.
void	addOrganism(Organism anOrganism, int xLocation, int yLocation) Add an organism to this view without any required ties to a family.
void	addOrganism(Organism anOrganism, int xLocation, int yLocation, java.lang.String aTraitName) Add an organism to this view without any required ties to a family.
boolean	containsOrganism(Organism anOrganism) Returns whether or not the given organism is in this view.
int	findLevelForFamily(PedigreeFamily aPedigreeFamily) Find the level containing the pedigreeFamily
int	findLevelForOrganism(PedigreeOrganism aPedigreeOrganism) Find the level containing the pedigreeOrganism
PedigreeFamily	findPedigreeFamily(Family aFamily) Find the pedigreeFamily corresponding to a given family
PedigreeFamily	findPedigreeFamily(Family aFamily, int[] returnLevel) Find the PedigreeFamily for the given Family
PedigreeOrganism	findPedigreeOrganism(Organism anOrganism) Find the pedigreeOrganism corresponding to a given organism.
int	getActiveTool() Get the active tool.
boolean	getCrossOverTurnOn() Is cross over turn on?
java.util.Enumeration	getFamilies()
Family	getFamilyForParents(Organism parentOne, Organism parentTwo) Get the Family for the given parent Organisms
int	getFixedNumberChildren() Get the fixed number of children from a breeding.
int	getMaximumNumberChildren() Get the maximum number of children from a breeding.
int	getMinimumNumberChildren() Get the minimum number of children from a breeding.
int	getNumberFemaleChildren() Get the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
int	getNumberMaleChildren() Get the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
int	getNumberOfFamilies() Get the number of pedigreeFamilies in this view.
int	getNumberOfOrganisms() Get the number of pedigreeOrganisms in this view.
int	getOffspringMode() Get the offspring mode
java.util.Enumeration	getOrganisms() Get the set of pedigreeOrganisms in this view.
SelectionSet	getSelectionSet() Get the current selection set
Species	getSpecies() Get the current species.
Trait	getTrait() Get the trait for this view.
boolean	isOnlyLiveChildren() Is the Only Live Children flag true?
boolean	isOrganismImagesVisible() Is the organism images visible?
void	mouseClicked(java.awt.event.MouseEvent event) Handle mouse click events
void	mouseDragged(java.awt.event.MouseEvent event) Handle mouse dragged event
void	mouseEntered(java.awt.event.MouseEvent event) Handle mouse entered event
void	mouseExited(java.awt.event.MouseEvent event) Handle mouse exited event
void	mouseMoved(java.awt.event.MouseEvent event) Handle mouse moved event
void	mousePressed(java.awt.event.MouseEvent event) Handle mouse pressed event.
void	mouseReleased(java.awt.event.MouseEvent event) Handle mouse released event.
void	paintComponent(java.awt.Graphics g) Draw the graphics in this view.
void	propertyChange(java.beans.PropertyChangeEvent event) Handle property change events
void	removeAll() Remove all the objects in this view, both organisms and families, without deleting anything.
boolean	removeFamily(Family aFamily) Removes a family from this view.
boolean	removeOrganism(Organism anOrganism) Removes an organism from this view.
void	selectionChanged() Selection changed
void	setActiveTool(int anActiveTool) Set the active tool
void	setCrossOverCheckBox(javax.swing.JCheckBox box)
void	setCrossOverPossibility(double p)
void	setCrossOverTurnOn(boolean on) Set cross over turn on?
void	setFixedNumberChildren(int aFixedNumberChildren) Set the fixed number of children from a breeding.
void	setMaximumNumberChildren(int aMaximumNumberChildren) Set the maximum number of children from a breeding.
void	setMinimumNumberChildren(int aMinimumNumberChildren) Set the minimum number of children from a breeding.
void	setMinMaxNumberChildren(int aMinimumNumberChildren, int aMaximumNumberChildren) Set the minimum and maximum number of children from a breeding.
void	setNumberFemaleChildren(int aNumberFemaleChildren) Set the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
void	setNumberMaleChildren(int aNumberMaleChildren) Set the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
void	setNumberMaleFemaleChildren(int aNumberFemaleChildren, int aNumberMaleChildren) Set the number of female and male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.
void	setOffspringMode(int anOffspringMode) Set the offspring mode
void	setOffspringModePulldown(BioComboBox anOffspringModePulldown) Set the offspring mode pulldown.
void	setOnlyLiveChildren(boolean anOnlyLiveChildren) Set the Only Live Children flag
void	setOrganismImagesVisible(boolean visible) Set the organism images visible
void	setScrollPane(javax.swing.JScrollPane aScrollPane) Tell this view its scroll pane.
void	setSelectionSet(SelectionSet aSelectionSet) Set the current selection set.
void	setSpecies(Species aSpecies) Set the current species.
void	setTrait(java.lang.String aTraitName) Set the trait for this view.
void	setTraitPulldown(BioComboBox aTraitPulldown) Set the trait pulldown.

Methods inherited from class org.concord.biologica.ui.OrganismView

getDefaultHighlightColor, getDefaultSelectionColor, getHighlightColor, getOrganismCellDimensions, getOrganismImageSize, getSelectionColor, getTextIndent, getTextLineSpacing, imageUpdate, isCharacteristicsTextVisible, isLockSymbolVisible, isNameTextVisible, isSexTextVisible, isSpeciesTextVisible, preloadSpeciesImages, setCharacteristicsTextVisible, setDefaultHighlightColor, setDefaultSelectionColor, setHighlightColor, setLockSymbolVisible, setNameTextVisible, setOrganismImageSize, setSelectionColor, setSexTextVisible, setSpeciesTextVisible, setTextIndent, setTextLineSpacing, updateHotspotOnMousePress, updateHotspotOnMouseReleased

Methods inherited from class org.concord.biologica.ui.UIView

addPropertyChangeListener, getLocalImage, getPreferredSize, paintBackground, removePropertyChangeListener, setBackground, setFont, setForeground, toolChanged, updateFont

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getUIClassID, getVerifyInputWhenFocusTarget, getVisibleRect, getWidth, getX, getY, grabFocus, hasFocus, hide, isDoubleBuffered, isFocusCycleRoot, isFocusTraversable, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processFocusEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBorder, setDebugGraphicsOptions, setDoubleBuffered, setEnabled, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update, updateUI

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getLayout, insets, invalidate, isAncestorOf, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeContainerListener, setLayout, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, getBackground, getBounds, getColorModel, getComponentOrientation, getCursor, getDropTarget, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getInputContext, getInputMethodRequests, getLocale, getLocation, getLocationOnScreen, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, inside, isDisplayable, isEnabled, isLightweight, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

PedigreeOrganismView

public PedigreeOrganismView()

Creates a pedigree organism view.

Method Detail

setScrollPane

public void setScrollPane(javax.swing.JScrollPane aScrollPane)

Tell this view its scroll pane.

Overrides:

setScrollPane in class UIView

Parameters:

aScrollPane - JScrollPane - the scroll pane containing this view

getOffspringMode

public int getOffspringMode()

Get the offspring mode

Returns:

int - the offspring mode

setOffspringMode

public void setOffspringMode(int anOffspringMode)

Set the offspring mode

Parameters:

anOffspringMode - int - the new offspring mode

Throws:

java.lang.IllegalArgumentException - - input offspring mode illegal

getSelectionSet

public SelectionSet getSelectionSet()

Get the current selection set

Specified by:

getSelectionSet in interface SelectionPresenter

Returns:

SelectionSet - the current selection set

setSelectionSet

public void setSelectionSet(SelectionSet aSelectionSet)

Set the current selection set.

Specified by:

setSelectionSet in interface SelectionPresenter

Parameters:

aSelectionSet - SelectionSet - a new selection set

isOrganismImagesVisible

public boolean isOrganismImagesVisible()

Is the organism images visible?

Returns:

boolean - organism images visible?

setOrganismImagesVisible

public void setOrganismImagesVisible(boolean visible)

Set the organism images visible

Parameters:

visible - boolean - visible?

isOnlyLiveChildren

public boolean isOnlyLiveChildren()

Is the Only Live Children flag true?

Returns:

boolean - onlyLiveChildren

setOnlyLiveChildren

public void setOnlyLiveChildren(boolean anOnlyLiveChildren)

Set the Only Live Children flag

Parameters:

anOnlyLiveChildren - boolean - only live children?

getActiveTool

public int getActiveTool()

Get the active tool.

Returns:

int - the active tool

setActiveTool

public void setActiveTool(int anActiveTool)

Set the active tool

Parameters:

anActiveTool - int - the new active tool

addFamily

public void addFamily(Family aFamily,
                      int xLocation,
                      int yLocation)

Add a family to this view. If the parents or children are not already in the view, this method will create and arbitrarily place them in the view.

If neither parent is in the view, the given x, y coordinates are used to place the mother organism and then the father and children positions are calculated relative to the mother's position.

Parameters:

aFamily - Family - a family to add, may not be null nor already in the view

xLocation - int - x location of first parent organism, ignored if a parent already in view

yLocation - int - y location of first parent organism, ignored if a parent already in view

Throws:

java.lang.IllegalArgumentException - - input organism null

removeFamily

public boolean removeFamily(Family aFamily)

Removes a family from this view. This method returns false if aFamily is null.

Parameters:

aFamily - Family - a family, may be null

Returns:

boolean indicating whether or not the family was found and removed

getNumberOfFamilies

public int getNumberOfFamilies()

Get the number of pedigreeFamilies in this view.

Returns:

int - number of pedigreeFamilies in this view (0 or greater)

addOrganism

public void addOrganism(Organism anOrganism,
                        int xLocation,
                        int yLocation,
                        java.lang.String aTraitName)

Add an organism to this view without any required ties to a family. The trait name specified will be used to set the trait ONLY IF THIS IS THE FIRST ORGANISM ADDED TO THE VIEW. Otherwise, aTraitName is ignored.

Note: X and Y locations are now ignored. Placement is done via new PedigreeLevel class. This interface should be changed to take a level number instead of X and Y coordinates.

Parameters:

anOrganism - Organism - an organism to add, may not be null

xLocation - int - x location of organism

yLocation - int - y location of organism

aTraitName - String - a trait name, if null then full organism images will be shown

Throws:

java.lang.IllegalArgumentException - - input organism null

addOrganism

public void addOrganism(Organism anOrganism,
                        int xLocation,
                        int yLocation)

Add an organism to this view without any required ties to a family.

Note: X and Y locations are now ignored. Placement is done via new PedigreeLevel class. This interface should be changed to take a level number instead of X and Y coordinates.

Parameters:

anOrganism - Organism - an organism to add, may not be null

xLocation - int - x location of organism

yLocation - int - y location of organism

Throws:

java.lang.IllegalArgumentException - - input organism null

removeOrganism

public boolean removeOrganism(Organism anOrganism)

Removes an organism from this view. This method returns false if anOrganism is null.

Parameters:

anOrganism - Organism - an organism, may be null

Returns:

boolean indicating whether or not the organism was found and removed

getNumberOfOrganisms

public int getNumberOfOrganisms()

Get the number of pedigreeOrganisms in this view.

Returns:

int - number of pedigreeOrganisms in this view (0 or greater)

getOrganisms

public java.util.Enumeration getOrganisms()

Get the set of pedigreeOrganisms in this view.

Returns:

Enumeration - enumeration over the set of pedigreeOrganisms in this view

getFamilies

public java.util.Enumeration getFamilies()

removeAll

public void removeAll()

Remove all the objects in this view, both organisms and families, without deleting anything.

Remove all the listeners and then the objects.

Overrides:

removeAll in class java.awt.Container

getSpecies

public Species getSpecies()

Get the current species.

Returns:

Species - the current species, may be null

setSpecies

public void setSpecies(Species aSpecies)

Set the current species.

Parameters:

aSpecies - Species - new current species, may be null

setTraitPulldown

public void setTraitPulldown(BioComboBox aTraitPulldown)

Set the trait pulldown. This method exists so the containing pedigree view can tell this view the pulldown and this view can keep the items in thee pulldown current as the species of this view changes.

Parameters:

aTraitPulldown - BioComboBox - a trait pulldown, may be null

setCrossOverCheckBox

public void setCrossOverCheckBox(javax.swing.JCheckBox box)

setOffspringModePulldown

public void setOffspringModePulldown(BioComboBox anOffspringModePulldown)

Set the offspring mode pulldown. This method exists so the containing pedigree view can tell this view the pulldown and this view can keep the selected item in the pulldown current as the offspring mode of this view changes.

Parameters:

anOffspringPulldown - BioComboBox - an offspring pulldown, may be null

getTrait

public Trait getTrait()

Get the trait for this view.

Returns:

Trait - the trait to draw, null if whole organism

setTrait

public void setTrait(java.lang.String aTraitName)

Set the trait for this view. If aTrait is null, the whole organism's phenotype will be drawn.

Parameters:

aTraitName - String - the name of the trait to draw, may be null to cause whole organisms to be drawn

getFixedNumberChildren

public int getFixedNumberChildren()

Get the fixed number of children from a breeding.

Returns:

int - fixed number of children from a breeding

setFixedNumberChildren

public void setFixedNumberChildren(int aFixedNumberChildren)

Set the fixed number of children from a breeding.

Parameters:

aFixedNumberChildren - int - fixed number of children from a breeding

Throws:

java.lang.IllegalArgumentException - - new fixed number illegal

getMaximumNumberChildren

public int getMaximumNumberChildren()

Get the maximum number of children from a breeding.

Returns:

int - maximum number of children from a breeding

setMaximumNumberChildren

public void setMaximumNumberChildren(int aMaximumNumberChildren)

Set the maximum number of children from a breeding. This must be higher than the minimum or else an exception is thrown.

Parameters:

aMaximumNumberChildren - int - maximum number of children from a breeding

Throws:

java.lang.IllegalArgumentException - - new maximum illegal, may be less than minimum

getMinimumNumberChildren

public int getMinimumNumberChildren()

Get the minimum number of children from a breeding.

Returns:

int - minimum number of children from a breeding

setMinimumNumberChildren

public void setMinimumNumberChildren(int aMinimumNumberChildren)

Set the minimum number of children from a breeding. This must be less than the maximum or else an exception is thrown.

Parameters:

aMinimumNumberChildren - int - minimum number of children from a breeding

Throws:

java.lang.IllegalArgumentException - - new minimum illegal, may be more than maximum

setMinMaxNumberChildren

public void setMinMaxNumberChildren(int aMinimumNumberChildren,
                                    int aMaximumNumberChildren)

Set the minimum and maximum number of children from a breeding. The minimum must be less than or equal to the maximum or else an exception is thrown.

Parameters:

aMinimumNumberChildren - int - minimum number of children from a breeding

aMaximumNumberChildren - int - maximum number of children from a breeding

Throws:

java.lang.IllegalArgumentException - - new minimum illegal, may be more than maximum

getNumberFemaleChildren

public int getNumberFemaleChildren()

Get the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.

Returns:

int - number of female children

setNumberFemaleChildren

public void setNumberFemaleChildren(int aNumberFemaleChildren)

Set the number of female children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.

Parameters:

aNumberFemaleChildren - int - new number of female children, must be >= 0

Throws:

java.lang.IllegalArgumentException - - new value illegal

getNumberMaleChildren

public int getNumberMaleChildren()

Get the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.

Returns:

int - number of male children

setNumberMaleChildren

public void setNumberMaleChildren(int aNumberMaleChildren)

Set the number of male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.

Parameters:

aNumberMaleChildren - int - new number of male children, must be >= 0

Throws:

java.lang.IllegalArgumentException - - new value illegal

setNumberMaleFemaleChildren

public void setNumberMaleFemaleChildren(int aNumberFemaleChildren,
                                        int aNumberMaleChildren)

Set the number of female and male children to create in a family when the view is in PedigreeView.OFFSPRING_MODE_MALE_FEMALE mode.

Parameters:

aNumberFemaleChildren - int - new number of female children, must be >= 0

aNumberMaleChildren - int - new number of male children, must be >= 0

Throws:

java.lang.IllegalArgumentException - - new value illegal

containsOrganism

public boolean containsOrganism(Organism anOrganism)

Returns whether or not the given organism is in this view.

Parameters:

anOrganism - Organism - the organism to find

Returns:

boolean true (in view) or false (not in view)

findPedigreeOrganism

public PedigreeOrganism findPedigreeOrganism(Organism anOrganism)

Find the pedigreeOrganism corresponding to a given organism.

Parameters:

anOrganism - Organism - the organism to find

Returns:

PedigreeOrganism - the pedigree organism for the given organism

findPedigreeFamily

public PedigreeFamily findPedigreeFamily(Family aFamily)

Find the pedigreeFamily corresponding to a given family

Parameters:

aFamily - Family - the family to find

Returns:

PedigreeFamily - the pedigree family for the given family

findPedigreeFamily

public PedigreeFamily findPedigreeFamily(Family aFamily,
                                         int[] returnLevel)

Find the PedigreeFamily for the given Family

Parameters:

aFamily - Family - the Family to find

returnLevel - int[] - the resulting level (in the first array element)

Returns:

PedgireeLevel - the resulting PedigreeFamily or null.

findLevelForOrganism

public int findLevelForOrganism(PedigreeOrganism aPedigreeOrganism)

Find the level containing the pedigreeOrganism

Parameters:

aPedigreeOrganism - PedigreeOrganism - the pedigree organism to find

Returns:

int - the level containing it or -1 if not found.

findLevelForFamily

public int findLevelForFamily(PedigreeFamily aPedigreeFamily)

Find the level containing the pedigreeFamily

Parameters:

aPedigreeFamily - PedigreeFamily - the pedigree organism to find

Returns:

int - the level containing it or -1 if not found.

getFamilyForParents

public Family getFamilyForParents(Organism parentOne,
                                  Organism parentTwo)

Get the Family for the given parent Organisms

Parameters:

parentOne - Organism - the first parent Organism

parentTwo - Organism - the second parent Organism

Returns:

Family - the resulting Family or null.

setCrossOverTurnOn

public void setCrossOverTurnOn(boolean on)

Set cross over turn on?

Returns:

on boolean --Turn on?

getCrossOverTurnOn

public boolean getCrossOverTurnOn()

Is cross over turn on?

Returns:

boolean --Turn on?

paintComponent

public void paintComponent(java.awt.Graphics g)

Draw the graphics in this view. First paint the connections and then the families and organisms so to ensure that the organisms are drawn on top of the connections. Draw the rubberbanding for crossing and for the selection rectangle.

Overrides:

paintComponent in class javax.swing.JComponent

Parameters:

g - Graphics - the given graphics to use in drawing

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent event)

Handle mouse click events

Specified by:

mouseClicked in interface java.awt.event.MouseListener

Parameters:

event - MouseEvent - the event object

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent event)

Handle mouse entered event

Specified by:

mouseEntered in interface java.awt.event.MouseListener

Parameters:

event - MouseEvent - the event object

mouseExited

public void mouseExited(java.awt.event.MouseEvent event)

Handle mouse exited event

Specified by:

mouseExited in interface java.awt.event.MouseListener

Parameters:

event - MouseEvent - the event object

mousePressed

public void mousePressed(java.awt.event.MouseEvent event)

Handle mouse pressed event. Handles Snipping, Chromosome and Pedigree tools. Assists in handling Selection.

Specified by:

mousePressed in interface java.awt.event.MouseListener

Parameters:

event - MouseEvent - the event object

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent event)

Handle mouse released event. Handles Crossing and assists in handling Selection.

Specified by:

mouseReleased in interface java.awt.event.MouseListener

Parameters:

event - MouseEvent - the event object

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent event)

Handle mouse dragged event

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener

Parameters:

event - MouseEvent - the event object

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent event)

Handle mouse moved event

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

Parameters:

event - MouseEvent - the event object

selectionChanged

public void selectionChanged()

Selection changed

Specified by:

selectionChanged in interface SelectionPresenter

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent event)

Handle property change events

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

Parameters:

event - PropertyChangeEvent - the property change event

setCrossOverPossibility

public void setCrossOverPossibility(double p)