biggests.gui
Class PanelAnalyzingMatrixDendrogram

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

public class PanelAnalyzingMatrixDendrogram
extends javax.swing.JPanel

Title: Panel for Analyzing Matrix Dendrograms

Description: Allows the user to parameterize and apply hierarchical clustering algorithms to obtain a hierarchical representation of the gene expression data, a dendrogram.

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
static java.lang.String[] clusteringMethods
          Clustering methods (names to display).
static char[] clusteringMethodsAlias
          Clustering methods alias (the arguments to pass to hierarchical methods).
static java.lang.String[] distanceMetrics
          Similarity metrics (names to display).
static char[] distanceMetricsAlias
          Similarity metrics alias (the arguments to pass to hierarchical methods).
static java.lang.String hierarchicalClusteringTempFilesDirectoryPath
           
 
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
PanelAnalyzingMatrixDendrogram(BiggestsFrame frame)
          Creates a new PanelAnalyzingMatrixDendrogram with options to perform hierarchical clustering over a set of expression data.
 
Method Summary
 void applyButton_actionPerformed(java.awt.event.ActionEvent e)
          Handles the event fired when the user clicks apply button.
 void clear()
          Clears this panel.
 void clusterConditionsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
          Handles the event fired when the item state of cluster conditions check box changes.
 void clusterGenesCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
          Handles the event fired when the item state of cluster genes check box changes.
static void deleteTempFilesAndDirectory()
           
 void endTreeViewApp()
           
static int getNumberOfDendrograms()
           
 void paint(IMatrix matrix)
          Paints this panel to perform hierarchical clustering over an expression matrix.
static void setNumberOfDendrograms(int numDend)
           
 void showDendrogram(java.lang.String cdtDirectory, java.lang.String cdtFileName)
           
 
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, 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

hierarchicalClusteringTempFilesDirectoryPath

public static final java.lang.String hierarchicalClusteringTempFilesDirectoryPath
See Also:
Constant Field Values

distanceMetrics

public static final java.lang.String[] distanceMetrics
Similarity metrics (names to display).


distanceMetricsAlias

public static final char[] distanceMetricsAlias
Similarity metrics alias (the arguments to pass to hierarchical methods). Each alias corresponds to the distanceMetrics element with the same index.


clusteringMethods

public static final java.lang.String[] clusteringMethods
Clustering methods (names to display).


clusteringMethodsAlias

public static final char[] clusteringMethodsAlias
Clustering methods alias (the arguments to pass to hierarchical methods). Each alias corresponds to the clusteringMethods element with the same index.

Constructor Detail

PanelAnalyzingMatrixDendrogram

public PanelAnalyzingMatrixDendrogram(BiggestsFrame frame)
Creates a new PanelAnalyzingMatrixDendrogram with options to perform hierarchical clustering over a set of expression data.

Parameters:
frame - the BiggestsFrame
Method Detail

setNumberOfDendrograms

public static void setNumberOfDendrograms(int numDend)

getNumberOfDendrograms

public static int getNumberOfDendrograms()

deleteTempFilesAndDirectory

public static void deleteTempFilesAndDirectory()

endTreeViewApp

public void endTreeViewApp()

clear

public void clear()
Clears this panel. Sets default values for selected options.


paint

public void paint(IMatrix matrix)
Paints this panel to perform hierarchical clustering over an expression matrix.

Overrides:
paint in class javax.swing.JComponent
Parameters:
matrix - the IMatrix to perform hierarchical clustering on

clusterGenesCheckBox_itemStateChanged

public void clusterGenesCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the event fired when the item state of cluster genes check box changes.

Parameters:
e - the ItemEvent fired when the item state of cluster genes check box changes

clusterConditionsCheckBox_itemStateChanged

public void clusterConditionsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the event fired when the item state of cluster conditions check box changes.

Parameters:
e - the ItemEvent fired when the item state of cluster conditions check box changes

applyButton_actionPerformed

public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the event fired when the user clicks apply button. Performs hierarchical clustering over the expression data with the selected options and opens a new Java Treeview window with the resulting dendrogram. If no clustering (genes or conditions) is selected, hierarchical clustering won't be performed.

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

showDendrogram

public void showDendrogram(java.lang.String cdtDirectory,
                           java.lang.String cdtFileName)