org.geworkbench.util.sequences
Class SequenceViewWidget

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by org.geworkbench.util.sequences.SequenceViewWidget
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class SequenceViewWidget
extends javax.swing.JPanel

Widget provides all GUI services for sequence panel displays. Widget is controlled by its associated component, SequenceViewAppComponent Copyright: Copyright (c) 2003 Company: Califano Lab

Version:
$Id: SequenceViewWidget.java 9522 2012-06-05 16:18:23Z zji $
Author:
See Also:
Serialized Form

Nested Class Summary
protected  class SequenceViewWidget.JDetailPanel
           
 
Nested classes/interfaces inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
protected  DSPanel<? extends DSGeneMarker> activatedMarkers
           
protected  CSSequenceSet<DSSequence> activeSequenceDB
           
protected  DSSequenceSet<DSSequence> displaySequenceDB
           
protected  boolean isLineView
           
protected  javax.swing.JCheckBox jAllSequenceCheckBox
           
 javax.swing.JToolBar jToolBar1
           
protected  javax.swing.JComboBox jViewComboBox
           
protected static java.lang.String LINEVIEW
           
protected  DSSequenceSet<?> orgSequenceDB
           
protected  java.util.HashMap<CSSequence,PatternSequenceDisplayUtil> patternLocationsMatches
           
protected  java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> selectedPatterns
           
protected  javax.swing.JScrollPane seqScrollPane
           
protected  DSSequenceSet<DSSequence> sequenceDB
           
protected  SequenceViewWidget.JDetailPanel sequencedetailPanel
           
protected  SequenceViewWidgetPanel seqViewWPanel
           
protected  javax.swing.JCheckBox showAllBtn
           
protected  boolean subsetMarkerOn
           
protected  int xStartPoint
           
 
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
SequenceViewWidget()
           
 
Method Summary
protected  DSSequence getSelectedSequence()
           
 SequenceViewWidgetPanel getSeqViewWPanel()
           
 void initPanelView()
          Initiate the Panel, which should be used as the entry point.
 void patternSelectionHasChanged(java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> patterns)
           
 void sequenceDBUpdate(GeneSelectorEvent e)
          geneSelectorAction
 void setPatterns(java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> matches)
           
 void setSequenceDB(DSSequenceSet<?> db)
           
protected  void updateBottomPanel()
           
protected  void updatePatternSeqMatches()
          Transform the patterns to patternsUtil class.
 
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, 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, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, 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, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, 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, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, 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

patternLocationsMatches

protected java.util.HashMap<CSSequence,PatternSequenceDisplayUtil> patternLocationsMatches

selectedPatterns

protected java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> selectedPatterns

jToolBar1

public javax.swing.JToolBar jToolBar1

seqViewWPanel

protected SequenceViewWidgetPanel seqViewWPanel

activeSequenceDB

protected CSSequenceSet<DSSequence> activeSequenceDB

subsetMarkerOn

protected boolean subsetMarkerOn

activatedMarkers

protected DSPanel<? extends DSGeneMarker> activatedMarkers

sequenceDB

protected DSSequenceSet<DSSequence> sequenceDB

orgSequenceDB

protected DSSequenceSet<?> orgSequenceDB

displaySequenceDB

protected DSSequenceSet<DSSequence> displaySequenceDB

sequencedetailPanel

protected SequenceViewWidget.JDetailPanel sequencedetailPanel

seqScrollPane

protected javax.swing.JScrollPane seqScrollPane

showAllBtn

protected javax.swing.JCheckBox showAllBtn

jAllSequenceCheckBox

protected javax.swing.JCheckBox jAllSequenceCheckBox

jViewComboBox

protected javax.swing.JComboBox jViewComboBox

LINEVIEW

protected static final java.lang.String LINEVIEW
See Also:
Constant Field Values

isLineView

protected boolean isLineView

xStartPoint

protected int xStartPoint
Constructor Detail

SequenceViewWidget

public SequenceViewWidget()
Method Detail

sequenceDBUpdate

public void sequenceDBUpdate(GeneSelectorEvent e)
geneSelectorAction

Parameters:
e - GeneSelectorEvent

patternSelectionHasChanged

public void patternSelectionHasChanged(java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> patterns)

updateBottomPanel

protected void updateBottomPanel()

setSequenceDB

public void setSequenceDB(DSSequenceSet<?> db)

getSeqViewWPanel

public SequenceViewWidgetPanel getSeqViewWPanel()

setPatterns

public void setPatterns(java.util.List<DSMatchedPattern<DSSequence,CSSeqRegistration>> matches)

updatePatternSeqMatches

protected void updatePatternSeqMatches()
Transform the patterns to patternsUtil class. Child class should override this method.


initPanelView

public void initPanelView()
Initiate the Panel, which should be used as the entry point.


getSelectedSequence

protected DSSequence getSelectedSequence()