genomicsnpanalyzer.gui
Class GenomeBrowserPane

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 genomicsnpanalyzer.gui.GenomeBrowserPane
All Implemented Interfaces:
java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible

public class GenomeBrowserPane
extends javax.swing.JPanel
implements java.awt.event.ActionListener, java.awt.event.ItemListener

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
 DisplaySectionSwitch displaySectionSwitch
           
 longTask_genomeBrowse GenomeBrowse
           
 genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPane
           
 genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPaneTop
           
 WindowSequence windowSequence
           
 
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
GenomeBrowserPane(Main para)
           
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent e)
           
 void CallSearchChromosomalRegion(java.lang.String chr, int start, int end)
           
 void CallSearchCNVLociFunction(int sn)
           
 void CallSearchGeneButton(int geneIndex)
           
 void CallSearchLociFunction(int sn)
           
 void CallSearchSNPButton(java.lang.String targetSNP)
           
 void CallSearchSVLociFunction(int sn)
           
 void CallSearchTranscript(java.lang.String genesym, java.lang.String transcriptid)
           
 void DisableAllBrowseButtons()
           
 void EnableAllBrowseButtons()
           
 java.util.ArrayList getGeneList()
           
 void InitiateGenomeBrowser()
           
 void itemStateChanged(java.awt.event.ItemEvent e)
           
 void ReloadImage()
           
 void SetHighlightCNVLociFunction(int sn)
           
 void SetHighlightLociFunction(int sn)
           
 void SetHighlightSVLociFunction(int sn)
           
 void SetHighlightTranscript(java.lang.String transid)
           
 void SimulateKeyPressed(java.lang.String type, boolean left, int prehighidx)
           
 void StartGenomeBrowser()
           
 void updateChrComboList()
           
 void updateGenomeBrowserCoredataStatusLabel()
           
 void updateImage(java.awt.image.BufferedImage par, GenomeBrowserCoord genomeBrowserCoord, GenomeBrowserData genomeBrowserData, int topPartSize)
           
 void UpdateMaxChrLength()
           
 void updateMouseCoord(int mx, int my)
           
 void updateSearchGeneText()
           
 void updateSelectedChrRegion(java.lang.String chr, int start, int end)
           
 
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

plotPane

public genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPane

plotPaneTop

public genomicsnpanalyzer.gui.GenomeBrowserPane.DensityPlotPane plotPaneTop

displaySectionSwitch

public DisplaySectionSwitch displaySectionSwitch

GenomeBrowse

public longTask_genomeBrowse GenomeBrowse

windowSequence

public WindowSequence windowSequence
Constructor Detail

GenomeBrowserPane

public GenomeBrowserPane(Main para)
Method Detail

UpdateMaxChrLength

public void UpdateMaxChrLength()

StartGenomeBrowser

public void StartGenomeBrowser()

InitiateGenomeBrowser

public void InitiateGenomeBrowser()

DisableAllBrowseButtons

public void DisableAllBrowseButtons()

EnableAllBrowseButtons

public void EnableAllBrowseButtons()

updateChrComboList

public void updateChrComboList()

updateSearchGeneText

public void updateSearchGeneText()

updateMouseCoord

public void updateMouseCoord(int mx,
                             int my)

getGeneList

public java.util.ArrayList getGeneList()

updateGenomeBrowserCoredataStatusLabel

public void updateGenomeBrowserCoredataStatusLabel()

updateSelectedChrRegion

public void updateSelectedChrRegion(java.lang.String chr,
                                    int start,
                                    int end)

updateImage

public void updateImage(java.awt.image.BufferedImage par,
                        GenomeBrowserCoord genomeBrowserCoord,
                        GenomeBrowserData genomeBrowserData,
                        int topPartSize)

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)
Specified by:
itemStateChanged in interface java.awt.event.ItemListener

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)
Specified by:
actionPerformed in interface java.awt.event.ActionListener

SimulateKeyPressed

public void SimulateKeyPressed(java.lang.String type,
                               boolean left,
                               int prehighidx)

CallSearchGeneButton

public void CallSearchGeneButton(int geneIndex)

CallSearchSNPButton

public void CallSearchSNPButton(java.lang.String targetSNP)

SetHighlightLociFunction

public void SetHighlightLociFunction(int sn)

SetHighlightCNVLociFunction

public void SetHighlightCNVLociFunction(int sn)

SetHighlightSVLociFunction

public void SetHighlightSVLociFunction(int sn)

SetHighlightTranscript

public void SetHighlightTranscript(java.lang.String transid)

CallSearchLociFunction

public void CallSearchLociFunction(int sn)

CallSearchCNVLociFunction

public void CallSearchCNVLociFunction(int sn)

CallSearchSVLociFunction

public void CallSearchSVLociFunction(int sn)

CallSearchTranscript

public void CallSearchTranscript(java.lang.String genesym,
                                 java.lang.String transcriptid)

CallSearchChromosomalRegion

public void CallSearchChromosomalRegion(java.lang.String chr,
                                        int start,
                                        int end)

ReloadImage

public void ReloadImage()