org.concord.biologica.ui
Class DNAView

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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.AdjustmentListener, javax.swing.event.ChangeListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.event.KeyListener, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.beans.PropertyChangeListener, java.io.Serializable

public final class DNAView

extends UIView

implements java.awt.image.ImageObserver, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.beans.PropertyChangeListener, java.awt.event.AdjustmentListener, javax.swing.event.ChangeListener, java.awt.event.ActionListener, java.awt.event.KeyListener

The chromosome view of BioLogica.

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

• org.concord.biologica.ui.UIProp.APPLY_BUTTON_PUSHED - apply button was pushed
• org.concord.biologica.ui.UIProp.DEFER_APPLY - the defer apply flag changed
• org.concord.biologica.ui.UIProp.DEFER_REVERT - the defer revert flag changed
• org.concord.biologica.ui.UIProp.ORGANISM_ALLELE - the shown organism allele has changed from one organism allele to another
• org.concord.biologica.ui.UIProp.ORGANISM_ALLELE_PAIR - the shown organism allele pair has changed from one organism allele pair to another
• org.concord.biologica.ui.UIProp.REVERT_BUTTON_PUSHED - revert button was pushed
• org.concord.biologica.ui.UIProp.SELECTED_BASES - the selected bases have changed

Version:

$Revision: 1.2 $ $Date: 2001/06/12 15:30:04 $

Author:

$Author: ed $

See Also:

UIProp.APPLY_BUTTON_PUSHED, UIProp.DEFER_APPLY, UIProp.DEFER_REVERT, UIProp.ORGANISM_ALLELE, UIProp.ORGANISM_ALLELE_PAIR, UIProp.REVERT_BUTTON_PUSHED, UIProp.SELECTED_BASES, 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

Field Summary

static int	BOTTOM_ALLELE
protected java.awt.Color	cursorColor Cursor color
protected java.awt.Color	differentBaseColor Different base color
static int	DNA_AREA_DOUBLE_HEIGHT
static int	DNA_AREA_GAP
static int	DNA_AREA_LEFT DNA area static values, used in drawing and picking on the DNA area
static int	DNA_AREA_SINGLE_HEIGHT
static int	DNA_AREA_TOP
static int	DNA_AREA_WIDTH
static int	DNA_BOTTOM_STRAND
static int	DNA_BOTTOM_STRAND_Y
static java.lang.String	DNA_CMD_APPLY
static java.lang.String	DNA_CMD_REVERT
static int	DNA_CURSOR_HEIGHT
static int	DNA_IMAGE_ARROWS_INDEX
static int	DNA_IMAGE_AT_DARK_INDEX
static int	DNA_IMAGE_AT_DARK_SELECTED_INDEX
static int	DNA_IMAGE_AT_LIGHT_INDEX
static int	DNA_IMAGE_CG_DARK_INDEX
static int	DNA_IMAGE_CG_DARK_SELECTED_INDEX
static int	DNA_IMAGE_CG_LIGHT_INDEX
static int	DNA_IMAGE_GC_DARK_INDEX
static int	DNA_IMAGE_GC_DARK_SELECTED_INDEX
static int	DNA_IMAGE_GC_LIGHT_INDEX
static int	DNA_IMAGE_HEIGHT DNA image values, used to draw base pairs
static int	DNA_IMAGE_MAX_BASES
static int	DNA_IMAGE_TA_DARK_INDEX
static int	DNA_IMAGE_TA_DARK_SELECTED_INDEX
static int	DNA_IMAGE_TA_LIGHT_INDEX
static int	DNA_IMAGE_WIDTH
static int	DNA_SCROLLBAR_AREA_OFFSET
static int	DNA_SCROLLBAR_GARBAGE_WIDTH_IN_BASES
static int	DNA_SCROLLBAR_HEIGHT Scrollbar values
static int	DNA_TOP_STRAND Strand values
static int	DNA_TOP_STRAND_Y
protected java.awt.Color	equalBaseColor Equal base color
static int	TOP_ALLELE Top or bottom allele?

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

DNAView()
Creates a chromosome view.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) React to actions
void	addActionListener(java.awt.event.ActionListener listener)
void	adjustmentValueChanged(java.awt.event.AdjustmentEvent event) Handle adjustment event
void	allelesEdited() Alleles edited
void	applyPendingChanges() Apply pending changes made to DNA
protected void	callActionListeners(java.awt.event.ActionEvent e)
java.lang.String	getAllelePendingTextSymbol(int topOrBottomAllele) Get the text symbol of the top or bottom allele if the pending changes are made to that allele.
java.awt.Color	getCursorColor() Get the cursor color
static java.awt.Color	getDefaultCursorColor() Get the default cursor color
static java.awt.Color	getDefaultDifferentBaseColor() Get the default different base color
static java.awt.Color	getDefaultEqualBaseColor() Get the default equal base color
boolean	getDeferApply() Get the defer apply setting.
boolean	getDeferRevert() Get the defer revert setting.
java.awt.Color	getDifferentBaseColor() Get the different base color
java.awt.Color	getEqualBaseColor() Get the equal base color
OrganismAllele	getOrganismAllele() Get the shown organism allele for this view.
OrganismAllelePair	getOrganismAllelePair() Get the shown organism allele pair for this view.
java.awt.Dimension	getPreferredSize() Return the preferred size of this canvas
boolean	imageUpdate(java.awt.Image anImage, int infoFlags, int x, int y, int width, int height) ImageObserver method
void	keyPressed(java.awt.event.KeyEvent e) Handle key pressed event
void	keyReleased(java.awt.event.KeyEvent e) Handle key released event
void	keyTyped(java.awt.event.KeyEvent e) Handle key typed event
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	paintAllele(java.awt.Graphics g, OrganismAllele allele, OrganismAllele comparisonAllele, int xTopLeft, int yTopLeft) Paint a single allele
void	paintBase(java.awt.Graphics g, byte base, int xInView, int yInView, boolean inAllele, boolean selected) Paint a single base pair
void	paintComponent(java.awt.Graphics g) Draw the graphics in this view.
void	propertyChange(java.beans.PropertyChangeEvent event) Handle property change events
void	removeActionListener(java.awt.event.ActionListener listener)
void	revertPendingChanges() Revert pending changes to DNA
void	setApplyVisible(boolean visible)
void	setCursorColor(java.awt.Color aColor) Set the cursor color.
static void	setDefaultCursorColor(java.awt.Color aColor) Set the default cursor color.
static void	setDefaultDifferentBaseColor(java.awt.Color aColor) Set the default different base color.
static void	setDefaultEqualBaseColor(java.awt.Color aColor) Set the default equal base color.
void	setDeferApply(boolean trueOrFalse) Set the defer apply setting.
void	setDeferRevert(boolean trueOrFalse) Set the defer revert setting.
void	setDifferentBaseColor(java.awt.Color aColor) Set the different base color.
void	setEqualBaseColor(java.awt.Color aColor) Set the equal base color.
void	setOrganismAllele(OrganismAllele anOrganismAllele) Set the shown organism allele for this view.
void	setOrganismAllelePair(OrganismAllelePair anOrganismAllelePair) Set the shown organism allele pair for this view.
void	setRevertVisible(boolean visible)
void	startMouseMotionListener(int startIndex, int endIndex) Start mouse motion listener given the start and end index of any current selection.
void	stateChanged(javax.swing.event.ChangeEvent event) Handle change event

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

addPropertyChangeListener, getLocalImage, paintBackground, removePropertyChangeListener, setBackground, setFont, setForeground, setScrollPane, 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, removeAll, 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

Field Detail

DNA_CMD_APPLY

public static final java.lang.String DNA_CMD_APPLY

DNA_CMD_REVERT

public static final java.lang.String DNA_CMD_REVERT

DNA_AREA_LEFT

public static final int DNA_AREA_LEFT

DNA area static values, used in drawing and picking on the DNA area

DNA_AREA_TOP

public static final int DNA_AREA_TOP

DNA_AREA_WIDTH

public static final int DNA_AREA_WIDTH

DNA_AREA_SINGLE_HEIGHT

public static final int DNA_AREA_SINGLE_HEIGHT

DNA_AREA_DOUBLE_HEIGHT

public static final int DNA_AREA_DOUBLE_HEIGHT

DNA_AREA_GAP

public static final int DNA_AREA_GAP

DNA_IMAGE_HEIGHT

public static final int DNA_IMAGE_HEIGHT

DNA image values, used to draw base pairs

DNA_IMAGE_WIDTH

public static final int DNA_IMAGE_WIDTH

DNA_IMAGE_MAX_BASES

public static final int DNA_IMAGE_MAX_BASES

DNA_IMAGE_ARROWS_INDEX

public static final int DNA_IMAGE_ARROWS_INDEX

DNA_IMAGE_GC_DARK_INDEX

public static final int DNA_IMAGE_GC_DARK_INDEX

DNA_IMAGE_CG_DARK_INDEX

public static final int DNA_IMAGE_CG_DARK_INDEX

DNA_IMAGE_TA_DARK_INDEX

public static final int DNA_IMAGE_TA_DARK_INDEX

DNA_IMAGE_AT_DARK_INDEX

public static final int DNA_IMAGE_AT_DARK_INDEX

DNA_IMAGE_GC_LIGHT_INDEX

public static final int DNA_IMAGE_GC_LIGHT_INDEX

DNA_IMAGE_CG_LIGHT_INDEX

public static final int DNA_IMAGE_CG_LIGHT_INDEX

DNA_IMAGE_TA_LIGHT_INDEX

public static final int DNA_IMAGE_TA_LIGHT_INDEX

DNA_IMAGE_AT_LIGHT_INDEX

public static final int DNA_IMAGE_AT_LIGHT_INDEX

DNA_IMAGE_GC_DARK_SELECTED_INDEX

public static final int DNA_IMAGE_GC_DARK_SELECTED_INDEX

DNA_IMAGE_CG_DARK_SELECTED_INDEX

public static final int DNA_IMAGE_CG_DARK_SELECTED_INDEX

DNA_IMAGE_TA_DARK_SELECTED_INDEX

public static final int DNA_IMAGE_TA_DARK_SELECTED_INDEX

DNA_IMAGE_AT_DARK_SELECTED_INDEX

public static final int DNA_IMAGE_AT_DARK_SELECTED_INDEX

DNA_TOP_STRAND_Y

public static final int DNA_TOP_STRAND_Y

DNA_BOTTOM_STRAND_Y

public static final int DNA_BOTTOM_STRAND_Y

DNA_CURSOR_HEIGHT

public static final int DNA_CURSOR_HEIGHT

DNA_SCROLLBAR_HEIGHT

public static final int DNA_SCROLLBAR_HEIGHT

Scrollbar values

DNA_SCROLLBAR_AREA_OFFSET

public static final int DNA_SCROLLBAR_AREA_OFFSET

DNA_SCROLLBAR_GARBAGE_WIDTH_IN_BASES

public static final int DNA_SCROLLBAR_GARBAGE_WIDTH_IN_BASES

DNA_TOP_STRAND

public static final int DNA_TOP_STRAND

Strand values

DNA_BOTTOM_STRAND

public static final int DNA_BOTTOM_STRAND

TOP_ALLELE

public static final int TOP_ALLELE

Top or bottom allele?

BOTTOM_ALLELE

public static final int BOTTOM_ALLELE

cursorColor

protected java.awt.Color cursorColor

Cursor color

equalBaseColor

protected java.awt.Color equalBaseColor

Equal base color

differentBaseColor

protected java.awt.Color differentBaseColor

Different base color

Constructor Detail

DNAView

public DNAView()

Creates a chromosome view.

Method Detail

getDefaultCursorColor

public static java.awt.Color getDefaultCursorColor()

Get the default cursor color

Returns:

Color - default cursor color, never null

setDefaultCursorColor

public static void setDefaultCursorColor(java.awt.Color aColor)

Set the default cursor color. This will be used as the default cursor color for views created after calling this method.

Parameters:

aColor - Color - a default cursor color, may not be null

Throws:

java.lang.IllegalArgumentException - - input argument illegal (null)

getDefaultEqualBaseColor

public static java.awt.Color getDefaultEqualBaseColor()

Get the default equal base color

Returns:

Color - default equal base color, never null

setDefaultEqualBaseColor

public static void setDefaultEqualBaseColor(java.awt.Color aColor)

Set the default equal base color. This will be used as the default equal base color for views created after calling this method.

Parameters:

aColor - Color - a default equal base color, may not be null

Throws:

java.lang.IllegalArgumentException - - input argument illegal (null)

getDefaultDifferentBaseColor

public static java.awt.Color getDefaultDifferentBaseColor()

Get the default different base color

Returns:

Color - default different base color, never null

setDefaultDifferentBaseColor

public static void setDefaultDifferentBaseColor(java.awt.Color aColor)

Set the default different base color. This will be used as the default different base color for views created after calling this method.

Parameters:

aColor - Color - a default different base color, may not be null

Throws:

java.lang.IllegalArgumentException - - input argument illegal (null)

getCursorColor

public java.awt.Color getCursorColor()

Get the cursor color

Returns:

Color - cursor color for this

setCursorColor

public void setCursorColor(java.awt.Color aColor)

Set the cursor color. If null is input, the color reverts back to the default cursor color.

Parameters:

aColor - Color - a new cursor color, may be null

getEqualBaseColor

public java.awt.Color getEqualBaseColor()

Get the equal base color

Returns:

Color - equal base color for this view

setEqualBaseColor

public void setEqualBaseColor(java.awt.Color aColor)

Set the equal base color. If null is input, the color reverts back to the default equal base color.

Parameters:

aColor - Color - a new equal base color, may be null

getDifferentBaseColor

public java.awt.Color getDifferentBaseColor()

Get the different base color

Returns:

Color - different base color for this view

setDifferentBaseColor

public void setDifferentBaseColor(java.awt.Color aColor)

Set the different base color. If null is input, the color reverts back to the default different base color.

Parameters:

aColor - Color - a new different base color, may be null

getDeferApply

public boolean getDeferApply()

Get the defer apply setting.

Returns:

boolean - defer apply setting

setDeferApply

public void setDeferApply(boolean trueOrFalse)

Set the defer apply setting. If true, then the apply will not happen when the user pushes on the apply button. Instead, only notification that the user pushed the button will be done and it is up to a listener to apply the pending changes (or revert them or do nothing with them).

Parameters:

trueOrFalse - boolean - true or false

getDeferRevert

public boolean getDeferRevert()

Get the defer revert setting.

Returns:

boolean - defer revert setting

setDeferRevert

public void setDeferRevert(boolean trueOrFalse)

Set the defer revert setting. If true, then the revert will not happen when the user pushes on the revert button. Instead, only notification that the user pushed the revert button will be done and it is up to a listener to revert the pending changes (or apply them or do nothing with them).

Parameters:

trueOrFalse - boolean - true or false

paintComponent

public void paintComponent(java.awt.Graphics g)

Draw the graphics in this view. Note that we are NOT overriding the paint method, as that would mean we're also responsible for painting the border and children, which we would rather leave to standard JFC code.

Overrides:

paintComponent in class javax.swing.JComponent

Parameters:

g - Graphics - the given graphics to use in drawing

paintAllele

public void paintAllele(java.awt.Graphics g,
                        OrganismAllele allele,
                        OrganismAllele comparisonAllele,
                        int xTopLeft,
                        int yTopLeft)

Paint a single allele

paintBase

public void paintBase(java.awt.Graphics g,
                      byte base,
                      int xInView,
                      int yInView,
                      boolean inAllele,
                      boolean selected)

Paint a single base pair

getPreferredSize

public java.awt.Dimension getPreferredSize()

Return the preferred size of this canvas

Overrides:

getPreferredSize in class UIView

Returns:

Dimension - preferred size of canvas

imageUpdate

public boolean imageUpdate(java.awt.Image anImage,
                           int infoFlags,
                           int x,
                           int y,
                           int width,
                           int height)

ImageObserver method

Specified by:

imageUpdate in interface java.awt.image.ImageObserver

Overrides:

imageUpdate in class java.awt.Component

mouseClicked

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

Handle mouse click events

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

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

Handle mouse entered event

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

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

Handle mouse exited event

Specified by:

mouseExited in interface java.awt.event.MouseListener

mousePressed

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

Handle mouse pressed event

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseReleased

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

Handle mouse released event

Specified by:

mouseReleased in interface java.awt.event.MouseListener

mouseDragged

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

Handle mouse dragged event

Specified by:

mouseDragged in interface java.awt.event.MouseMotionListener

mouseMoved

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

Handle mouse moved event

Specified by:

mouseMoved in interface java.awt.event.MouseMotionListener

startMouseMotionListener

public void startMouseMotionListener(int startIndex,
                                     int endIndex)

Start mouse motion listener given the start and end index of any current selection. If there is no current selection, then startIndex and endIndex should be the same.

getOrganismAllele

public OrganismAllele getOrganismAllele()

Get the shown organism allele for this view.

Returns:

OrganismAllele - the shown organism allele in this view, may be null

setOrganismAllele

public void setOrganismAllele(OrganismAllele anOrganismAllele)

Set the shown organism allele for this view. This will result in the given organism allele's base pairs being shown in the view. No particular base pair is selected initially.

Parameters:

anOrganismAllele - OrganismAllele - the organism allele whose base pairs to show, may be null

getOrganismAllelePair

public OrganismAllelePair getOrganismAllelePair()

Get the shown organism allele pair for this view.

Returns:

OrganismAllelePair - the shown organism allele pair in this view, may be null

setOrganismAllelePair

public void setOrganismAllelePair(OrganismAllelePair anOrganismAllelePair)

Set the shown organism allele pair for this view. This will result in the given organism allele pair's base pairs being shown in the view. No particular base pair is selected initially.

Parameters:

anOrganismAllelePair - OrganismAllelePair - the organism allele pair whose base pairs to show, may be null

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

adjustmentValueChanged

public void adjustmentValueChanged(java.awt.event.AdjustmentEvent event)

Handle adjustment event

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

stateChanged

public void stateChanged(javax.swing.event.ChangeEvent event)

Handle change event

Specified by:

stateChanged in interface javax.swing.event.ChangeListener

setRevertVisible

public void setRevertVisible(boolean visible)

setApplyVisible

public void setApplyVisible(boolean visible)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

React to actions

Specified by:

actionPerformed in interface java.awt.event.ActionListener

keyTyped

public void keyTyped(java.awt.event.KeyEvent e)

Handle key typed event

Specified by:

keyTyped in interface java.awt.event.KeyListener

keyPressed

public void keyPressed(java.awt.event.KeyEvent e)

Handle key pressed event

Specified by:

keyPressed in interface java.awt.event.KeyListener

keyReleased

public void keyReleased(java.awt.event.KeyEvent e)

Handle key released event

Specified by:

keyReleased in interface java.awt.event.KeyListener

allelesEdited

public void allelesEdited()

Alleles edited

getAllelePendingTextSymbol

public java.lang.String getAllelePendingTextSymbol(int topOrBottomAllele)

Get the text symbol of the top or bottom allele if the pending changes are made to that allele.

Parameters:

topOrBottomAllele - int - DNAView.TOP_ALLELE or DNAView.BOTTOM_ALLELE

Returns:

textSymbol String - text symbol of allele, null if no strands are shown

Throws:

java.lang.IllegalArgumentException - - input topOrBottomAllele argument illegal

applyPendingChanges

public void applyPendingChanges()

Apply pending changes made to DNA

revertPendingChanges

public void revertPendingChanges()

Revert pending changes to DNA

addActionListener

public void addActionListener(java.awt.event.ActionListener listener)

removeActionListener

public void removeActionListener(java.awt.event.ActionListener listener)

callActionListeners

protected void callActionListeners(java.awt.event.ActionEvent e)