biggests.gui
Class PanelAnalyzingFunctionTable

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 biggests.gui.PanelAnalyzingFunctionTable
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class PanelAnalyzingFunctionTable
extends javax.swing.JPanel

Title: Panel for Analyzing Tables of Functions

Description: Displays a table of functions of a bicluster or group of biclusters.

Copyright: Copyright (C) 2007 Joana Gonçalves This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
 
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
PanelAnalyzingFunctionTable(BiggestsFrame frame)
          Creates a new PanelAnalyzingFunctionTable.
 
Method Summary
 void applyButton_actionPerformed(java.awt.event.ActionEvent e)
          Handles the mouse event fired when the user clicks the apply button.
 GOFrontEnd calculateGOFrontEnd(Bicluster bicluster)
          Calculates the GO frontend for the given bicluster.
 GOFrontEnd calculateGOFrontEnd(Bicluster bicluster, java.lang.String pathTo_GeneOntologyFile, java.lang.String pathTo_GeneAssociationFile)
          Calculates the GO frontend for the given bicluster.
 void clear()
          Clears this panel's components.
 void functionGroupTable_mouseClicked(java.awt.event.MouseEvent e)
          Handles the event fired when the mouse is clicked on a function group table's row.
 PanelFunctionAnalysis getFunctionAnalysisPanel()
          Returns function analysis panel.
 GOFrontEnd getGOFrontEndForSelectionPath(javax.swing.tree.TreePath selectionPath)
          Returns the GOFrontEnd for the given selectionPath, if it exists, otherwise returns null.
 java.lang.String getGOFrontEndHashKeyForSelectionPath(javax.swing.tree.TreePath selectionPath)
          Returns the hashtable key for the GOFrontEnd of the given selectionPath.
 NodeObjectInterface getNodeObject()
          Returns the bicluster group that is being processed.
 javax.swing.tree.TreePath getSelectionPath()
          Returns the tree selection path that corresponds to the bicluster or bicluster group that is being processed.
 void initializeGOFrontEnds()
           
 GeneSetResult paint(Bicluster bicluster, GeneSetResult goProperties, float pvalue, javax.swing.tree.TreePath selectionPath)
          Paints the functions table in this panel, with data retrieved from bicluster object.
 void paint(Biclustering biclustering, javax.swing.tree.TreePath selectionPath, java.util.Hashtable<java.lang.Integer,BiologicalRelevanceSummary> biologicalRelevanceSummary)
          Paints this panel with a table of faunctions for the given biclustering (biclusters' group).
 void paint(GeneSetResult goProperties, GOFrontEnd go, java.lang.String[] genesNames, float pvalue)
          Paints a function table with the GO terms annotated for all the genes of the experiment.
 void paint(IMatrix expressionMatrix, javax.swing.tree.TreePath selectionPath)
          Paints a table of functions with data retrieved from the given expressionMatrix.
 void putGOFrontEnd(javax.swing.tree.TreePath selectionPath, GOFrontEnd go)
          Puts a new GO frontend in the GO frontends hashtable.
 void recalculate_actionPerformed(java.awt.event.ActionEvent e)
          Handles the mouse event fired when the user clicks on recalculate functions button.
 void repaintPanelAnalyzingFunctionTable()
          Repaints function analysis panel after recalculating biological relevance of an expression matrix (original, preprocessed or discretized one).
 void repaintPanelAnalyzingFunctionTable(GeneSetResult goProperties, float pvalue)
          Repaints function analysis panel after recalculating biological relevance of a bicluster.
 void repaintPanelAnalyzingFunctionTable(java.util.Hashtable<java.lang.Integer,BiologicalRelevanceSummary> biologicalRelevanceSummary)
          Repaints function analysis panel after recalculating biological relevance of a biclusters' group.
 
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, 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, 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
 

Constructor Detail

PanelAnalyzingFunctionTable

public PanelAnalyzingFunctionTable(BiggestsFrame frame)
Creates a new PanelAnalyzingFunctionTable.

Parameters:
frame - the main BiggestsFrame
Method Detail

initializeGOFrontEnds

public void initializeGOFrontEnds()

getFunctionAnalysisPanel

public PanelFunctionAnalysis getFunctionAnalysisPanel()
Returns function analysis panel.

Returns:
PanelFunctionAnalysis the panel that holds function analysis options

getSelectionPath

public javax.swing.tree.TreePath getSelectionPath()
Returns the tree selection path that corresponds to the bicluster or bicluster group that is being processed.

Returns:
TreePath the selection path that corresponds to the bicluster or bicluster group being processed in this panel.

getNodeObject

public NodeObjectInterface getNodeObject()
Returns the bicluster group that is being processed.
Null if the object being processed is not a bicluster group (it is a single bicluster instead).

Returns:
Biclustering the bicluster group that is being processed

clear

public void clear()
Clears this panel's components.


paint

public void paint(IMatrix expressionMatrix,
                  javax.swing.tree.TreePath selectionPath)
Paints a table of functions with data retrieved from the given expressionMatrix.

Parameters:
expressionMatrix - the IMatrix with the function information
selectionPath - TreePath selected in the dataset tree, whose node contains the given expressionMatrix

paint

public void paint(GeneSetResult goProperties,
                  GOFrontEnd go,
                  java.lang.String[] genesNames,
                  float pvalue)
Paints a function table with the GO terms annotated for all the genes of the experiment.

Parameters:
goProperties - GeneSetResult with GO terms
go - the GOFrontEnd
genesNames - String[] the set of genes' names
pvalue - float the pvalue threshold

paint

public GeneSetResult paint(Bicluster bicluster,
                           GeneSetResult goProperties,
                           float pvalue,
                           javax.swing.tree.TreePath selectionPath)
Paints the functions table in this panel, with data retrieved from bicluster object.

Parameters:
bicluster - the Bicluster object which contains the function analysis to present in the functions table
goProperties - the GeneSetResult for the given bicluster
pvalue - the p-value threshold for significance
selectionPath - the TreePath selected in the dataset tree

paint

public void paint(Biclustering biclustering,
                  javax.swing.tree.TreePath selectionPath,
                  java.util.Hashtable<java.lang.Integer,BiologicalRelevanceSummary> biologicalRelevanceSummary)
Paints this panel with a table of faunctions for the given biclustering (biclusters' group).

Parameters:
biclustering - the Biclustering (biclusters' group)
selectionPath - the selection TreePath
biologicalRelevanceSummary - the Hashtable which contains the actual table's info (a BiologicalRelevanceSummary for each bicluster in the biclusters' group; the hash key is the bicluster id)

putGOFrontEnd

public void putGOFrontEnd(javax.swing.tree.TreePath selectionPath,
                          GOFrontEnd go)
Puts a new GO frontend in the GO frontends hashtable.

Parameters:
selectionPath - the selection TreePath
go - the GOFrontEnd for the given selectionPath/code>

getGOFrontEndHashKeyForSelectionPath

public java.lang.String getGOFrontEndHashKeyForSelectionPath(javax.swing.tree.TreePath selectionPath)
Returns the hashtable key for the GOFrontEnd of the given selectionPath.

Parameters:
selectionPath - the selection TreePath
Returns:
String the hashtable's GO frontend key

getGOFrontEndForSelectionPath

public GOFrontEnd getGOFrontEndForSelectionPath(javax.swing.tree.TreePath selectionPath)
Returns the GOFrontEnd for the given selectionPath, if it exists, otherwise returns null.

Parameters:
selectionPath - TreePath
Returns:
GOFrontEnd

calculateGOFrontEnd

public GOFrontEnd calculateGOFrontEnd(Bicluster bicluster,
                                      java.lang.String pathTo_GeneOntologyFile,
                                      java.lang.String pathTo_GeneAssociationFile)
Calculates the GO frontend for the given bicluster.

Parameters:
bicluster - the Bicluster
pathTo_GeneOntologyFile - String the path to gene ontology file
pathTo_GeneAssociationFile - String the path to organism's specific gene association file
Returns:
GOFrontEnd the GO frontend for the given bicluster

calculateGOFrontEnd

public GOFrontEnd calculateGOFrontEnd(Bicluster bicluster)
Calculates the GO frontend for the given bicluster.

Parameters:
bicluster - the Bicluster
Returns:
GOFrontEnd the GO frontend for the given bicluster

applyButton_actionPerformed

public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks the apply button.

Parameters:
e - the ActionEvent fired when the user clicks the apply button

repaintPanelAnalyzingFunctionTable

public void repaintPanelAnalyzingFunctionTable(GeneSetResult goProperties,
                                               float pvalue)
Repaints function analysis panel after recalculating biological relevance of a bicluster. Mainly to be called by ThreadFunctionAnalysis.

Parameters:
goProperties - the GeneSetResult for the bicluster
pvalue - float the p-value user's threshold

repaintPanelAnalyzingFunctionTable

public void repaintPanelAnalyzingFunctionTable(java.util.Hashtable<java.lang.Integer,BiologicalRelevanceSummary> biologicalRelevanceSummary)
Repaints function analysis panel after recalculating biological relevance of a biclusters' group. Mainly to be called by ThreadFunctionAnalysis.

Parameters:
biologicalRelevanceSummary - Hashtable

repaintPanelAnalyzingFunctionTable

public void repaintPanelAnalyzingFunctionTable()
Repaints function analysis panel after recalculating biological relevance of an expression matrix (original, preprocessed or discretized one). Mainly to be called by ThreadFunctionAnalysis.


recalculate_actionPerformed

public void recalculate_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks on recalculate functions button.

Parameters:
e - the ActionEvent fired when the user clicks on recalculate functions button

functionGroupTable_mouseClicked

public void functionGroupTable_mouseClicked(java.awt.event.MouseEvent e)
Handles the event fired when the mouse is clicked on a function group table's row. Each row corresponds to a bicluster. When the user clicks a given row, the application redirects him/her to the corresponding bicluster object.

Parameters:
e - the MouseEvent fired with the mouse's click