org.emboss.jemboss.editor
Class GroutGraphicSequenceCollection

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.emboss.jemboss.editor.GraphicSequenceCollection
                      org.emboss.jemboss.editor.GroutGraphicSequenceCollection

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.event.AdjustmentListener, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, javax.swing.Scrollable, java.io.Serializable

public class GroutGraphicSequenceCollection

extends GraphicSequenceCollection

implements java.awt.event.AdjustmentListener

This class can be used to get a grapical representation of a collection of sequences.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

(package private) java.util.Vector

targets

Fields inherited from class org.emboss.jemboss.editor.GraphicSequenceCollection

colorScheme, drawBlackBox, drawColorBox, drawNumber, drawSequence, graphicName, graphicSequence, jspSequence, MAXSEQLENGTH, numberDraw, seqBox, seqNameBox, seqs

Fields inherited from class javax.swing.JPanel

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.Container

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.print.Printable

NO_SUCH_PAGE, PAGE_EXISTS

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

GroutGraphicSequenceCollection(java.util.Vector seqs, java.util.Hashtable colorScheme, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)

GroutGraphicSequenceCollection(java.util.Vector seqs, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)

GroutGraphicSequenceCollection(java.util.Vector seqs, java.util.Vector indents, java.util.Hashtable colorScheme, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)

GroutGraphicSequenceCollection(java.util.Vector seqs, java.util.Vector indents, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)

Method Summary

void	addGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener listener)
private void	addResidue()
protected void	addSequence(Sequence seq, boolean addToSequences, int ypad, int fontSize) Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.
protected void	addSequence(Sequence seq, boolean addToSequences, int ypad, int fontSize, int index) Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.
void	adjustmentValueChanged(java.awt.event.AdjustmentEvent evt)
void	doIndent(java.util.Vector indents)
protected void	drawNumber()
int	getScrollableBlockIncrement(java.awt.Rectangle r, int orientation, int direction) Override for scrollable interface
int	getScrollableUnitIncrement(java.awt.Rectangle r, int orientation, int direction) Override for scrollable interface
protected void	notifyTargets(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue)
void	removeGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener listener)
void	setPosition(int position) Moves the view position to this residue
int	setSize()

Methods inherited from class org.emboss.jemboss.editor.GraphicSequenceCollection

addAnnotationSequence, deleteConsensusPlot, deleteSequence, drawSequences, drawSequences, findPattern, getColor, getConsensusSequence, getFontSize, getGraphicSequence, getImageableSize, getMaxSeqLength, getName, getNameHeight, getNameViewSize, getNameWidth, getNumberPages, getNumberPages, getNumberSequences, getPanelHeight, getPanelSize, getPanelWidth, getPreferredScrollableViewportSize, getPrettyBackground, getResiduesPerLine, getResiduesPerPage, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getSequenceCollection, getViewPosition, getViewRect, getViewSize, idSort, isPrettyBox, main, moveSequence, print, setColorScheme, setDrawBoxes, setDrawColor, setFontSizeForCollection, setJScrollPaneViewportView, setMatrix, setMaxSeqLength, setMaxSequenceLength, setNamePanelWidth, setNumberOfResiduesPerLine, setNumberSize, setPrettyPlot, setSequenceLock, showConsensusPlot, showConsensusPlot, testUpAndDown

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

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

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

targets

java.util.Vector targets

Constructor Detail

GroutGraphicSequenceCollection

public GroutGraphicSequenceCollection(java.util.Vector seqs,
                                      java.util.Hashtable colorScheme,
                                      javax.swing.JScrollPane jspSequence,
                                      boolean drawSequence,
                                      boolean drawBlackBox,
                                      boolean drawColorBox,
                                      boolean drawNumber,
                                      javax.swing.JTextField statusField)

Parameters:

seqs - vector of sequences

colorScheme - sequence colour scheme

jspSequence - sequence scrollpane

drawSequence - true to draw the sequence

drawBlackBox - true to draw black square around residues

drawColorBox - true to colour residues

drawNumber - true to draw sequence position number

statusField - status field in the editor

GroutGraphicSequenceCollection

public GroutGraphicSequenceCollection(java.util.Vector seqs,
                                      javax.swing.JScrollPane jspSequence,
                                      boolean drawSequence,
                                      boolean drawBlackBox,
                                      boolean drawColorBox,
                                      boolean drawNumber,
                                      javax.swing.JTextField statusField)

Parameters:

seqs - vector of sequences

jspSequence - sequence scrollpane

drawSequence - true to draw the sequence

drawBlackBox - true to draw black square around residues

drawColorBox - true to colour residues

drawNumber - true to draw sequence position number

statusField - status field in the editor

GroutGraphicSequenceCollection

public GroutGraphicSequenceCollection(java.util.Vector seqs,
                                      java.util.Vector indents,
                                      java.util.Hashtable colorScheme,
                                      javax.swing.JScrollPane jspSequence,
                                      boolean drawSequence,
                                      boolean drawBlackBox,
                                      boolean drawColorBox,
                                      boolean drawNumber,
                                      javax.swing.JTextField statusField)

Parameters:

seqs - vector of sequences

indents - vector of indents

colorScheme - sequence colour scheme

jspSequence - sequence scrollpane

drawSequence - true to draw the sequence

drawBlackBox - true to draw black square around residues

drawColorBox - true to colour residues

drawNumber - true to draw sequence position number

statusField - status field in the editor

GroutGraphicSequenceCollection

public GroutGraphicSequenceCollection(java.util.Vector seqs,
                                      java.util.Vector indents,
                                      javax.swing.JScrollPane jspSequence,
                                      boolean drawSequence,
                                      boolean drawBlackBox,
                                      boolean drawColorBox,
                                      boolean drawNumber,
                                      javax.swing.JTextField statusField)

Parameters:

seqs - vector of sequences

indents - vector of indents

jspSequence - sequence scrollpane

drawSequence - true to draw the sequence

drawBlackBox - true to draw black square around residues

drawColorBox - true to colour residues

drawNumber - true to draw sequence position number

statusField - status field in the editor

Method Detail

doIndent

public void doIndent(java.util.Vector indents)

addSequence

protected void addSequence(Sequence seq,
                           boolean addToSequences,
                           int ypad,
                           int fontSize,
                           int index)

Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

Overrides:

addSequence in class GraphicSequenceCollection

Parameters:

seq - sequence to add to the editor display

addToSequences - true to add seq to the vector of sequences

ypad - sequence panel height padding

fontSize - font size

index - sequence index

addSequence

protected void addSequence(Sequence seq,
                           boolean addToSequences,
                           int ypad,
                           int fontSize)

Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding.

Overrides:

addSequence in class GraphicSequenceCollection

Parameters:

seq - sequence to add to the editor display

addToSequences - true to add seq to the vector of sequences

ypad - sequence panel height padding

fontSize - font size

setPosition

public void setPosition(int position)

Moves the view position to this residue

Parameters:

position - the position to view

addResidue

private void addResidue()

getScrollableBlockIncrement

public int getScrollableBlockIncrement(java.awt.Rectangle r,
                                       int orientation,
                                       int direction)

Override for scrollable interface

Specified by:

getScrollableBlockIncrement in interface javax.swing.Scrollable

Overrides:

getScrollableBlockIncrement in class GraphicSequenceCollection

getScrollableUnitIncrement

public int getScrollableUnitIncrement(java.awt.Rectangle r,
                                      int orientation,
                                      int direction)

Override for scrollable interface

Specified by:

getScrollableUnitIncrement in interface javax.swing.Scrollable

Overrides:

getScrollableUnitIncrement in class GraphicSequenceCollection

addGroutGraphicSequenceCollectionListener

public void addGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener listener)

removeGroutGraphicSequenceCollectionListener

public void removeGroutGraphicSequenceCollectionListener(GroutGraphicSequenceCollectionListener listener)

notifyTargets

protected void notifyTargets(java.lang.String propertyName,
                             java.lang.Object oldValue,
                             java.lang.Object newValue)

adjustmentValueChanged

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

Specified by:

adjustmentValueChanged in interface java.awt.event.AdjustmentListener

drawNumber

protected void drawNumber()

Overrides:

drawNumber in class GraphicSequenceCollection

setSize

public int setSize()