org.geworkbench.util.promoter
Class SequencePatternDisplayPanel

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
                      extended by org.geworkbench.util.promoter.SequencePatternDisplayPanel
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class SequencePatternDisplayPanel
extends SequenceViewWidget

Version:
$Id: SequencePatternDisplayPanel.java,v 1.20 2009-01-15 19:26:36 jiz Exp $
Author:
See Also:
Serialized Form

Nested Class Summary
 
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
 
Fields inherited from class org.geworkbench.util.sequences.SequenceViewWidget
activatedMarkers, activeSequenceDB, jToolBar1, NONBASIC, patternLocationsMatches, selectedPatterns, seqViewWPanel, subsetMarkerOn
 
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
SequencePatternDisplayPanel()
           
 
Method Summary
 void addAPattern(DSPattern<DSSequence,CSSeqRegistration> pt, Display dis, java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>> matches)
           
 void addMenuItem(javax.swing.JMenuItem saveItem)
           
 void addToolBarButton(javax.swing.AbstractButton jbutton)
           
 java.util.Hashtable<DSPattern<DSSequence,CSSeqRegistration>,java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>>> getPatternMatches()
           
 java.util.HashMap getPatternTFMatches()
           
 void initialize(DSSequenceSet seqDB)
           
 void paintComponent(java.awt.Graphics g)
           
 void removePattern(DSPattern<DSSequence,CSSeqRegistration> pt)
           
 void setDisplaySeqPattern(boolean displaySeqPattern)
           
 void setDisplayTF(boolean displayTF)
           
 void setPatternDisplay(java.util.HashMap patternDisplay)
           
 void setPatternMatches(java.util.Hashtable patternMatches)
           
 void setPatternTFMatches(java.util.HashMap patternTFMatches)
           
 void updatePatternSeqMatches()
          Transform the patterns to patternsUtil class.
 
Methods inherited from class org.geworkbench.util.sequences.SequenceViewWidget
fireModelChangedEvent, getDataSetView, getSequenceDB, getSeqViewWPanel, initPanelView, isDirection, jAllSequenceCheckBox_actionPerformed, jViewComboBox_actionPerformed, patternSelectionHasChanged, receive, refreshMaSetView, removeButtons, sequenceDBUpdate, seqViewWPanel_mouseMoved, setDirection, setPatterns, setSequenceDB, updateBottomPanel
 
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, 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
 

Constructor Detail

SequencePatternDisplayPanel

public SequencePatternDisplayPanel()
Method Detail

addToolBarButton

public void addToolBarButton(javax.swing.AbstractButton jbutton)

addMenuItem

public void addMenuItem(javax.swing.JMenuItem saveItem)

updatePatternSeqMatches

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

Overrides:
updatePatternSeqMatches in class SequenceViewWidget

initialize

public void initialize(DSSequenceSet seqDB)

paintComponent

public void paintComponent(java.awt.Graphics g)
Overrides:
paintComponent in class javax.swing.JComponent

addAPattern

public void addAPattern(DSPattern<DSSequence,CSSeqRegistration> pt,
                        Display dis,
                        java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>> matches)

removePattern

public void removePattern(DSPattern<DSSequence,CSSeqRegistration> pt)

getPatternMatches

public java.util.Hashtable<DSPattern<DSSequence,CSSeqRegistration>,java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>>> getPatternMatches()

getPatternTFMatches

public java.util.HashMap getPatternTFMatches()

setPatternDisplay

public void setPatternDisplay(java.util.HashMap patternDisplay)

setPatternMatches

public void setPatternMatches(java.util.Hashtable patternMatches)

setDisplaySeqPattern

public void setDisplaySeqPattern(boolean displaySeqPattern)

setDisplayTF

public void setDisplayTF(boolean displayTF)

setPatternTFMatches

public void setPatternTFMatches(java.util.HashMap patternTFMatches)