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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelAnalyzingFunctionTable
public class PanelAnalyzingFunctionTable
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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javax.swing.JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class javax.swing.JComponent |
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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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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PanelAnalyzingFunctionTable(BiggestsFrame frame)
Creates a new PanelAnalyzingFunctionTable . |
Method Summary | |
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void |
applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks the apply button. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.Bicluster bicluster)
Calculates the GO frontend for the given bicluster. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.Biclustering biclustering)
Calculates the GO frontend for the given biclusters' group. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.Biclustering biclustering,
java.lang.String pathTo_GeneOntologyFile,
java.lang.String pathTo_GeneAssociationFile)
Calculates the GO frontend for the given biclusters' group. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.Bicluster bicluster,
java.lang.String pathTo_GeneOntologyFile,
java.lang.String pathTo_GeneAssociationFile)
Calculates the GO frontend for the given bicluster. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.IMatrix matrix)
Calculates the GO frontend for the given expression matrix. |
smadeira.ontologizer.GOFrontEnd |
calculateGOFrontEnd(smadeira.biclustering.IMatrix matrix,
java.lang.String pathTo_GeneOntologyFile,
java.lang.String pathTo_GeneAssociationFile)
Calculates the GO frontend for the given biclusters' group. |
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. |
smadeira.ontologizer.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 . |
smadeira.biclustering.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()
|
smadeira.ontologizer.GeneSetResult |
paint(smadeira.biclustering.Bicluster bicluster,
smadeira.ontologizer.GeneSetResult goProperties,
float pvalue,
javax.swing.tree.TreePath selectionPath)
Paints the functions table in this panel, with data retrieved from bicluster object. |
void |
paint(smadeira.biclustering.Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary)
Paints this panel with a table of faunctions for the given biclustering (biclusters' group). |
void |
paint(smadeira.ontologizer.GeneSetResult goProperties,
smadeira.ontologizer.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(smadeira.biclustering.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,
smadeira.ontologizer.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(smadeira.ontologizer.GeneSetResult goProperties,
float pvalue)
Repaints function analysis panel after recalculating biological relevance of a bicluster. |
void |
repaintPanelAnalyzingFunctionTable(java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary)
Repaints function analysis panel after recalculating biological relevance of a biclusters' group. |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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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 |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public PanelAnalyzingFunctionTable(BiggestsFrame frame)
PanelAnalyzingFunctionTable
.
frame
- the main BiggestsFrame
Method Detail |
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public void initializeGOFrontEnds()
public PanelFunctionAnalysis getFunctionAnalysisPanel()
public javax.swing.tree.TreePath getSelectionPath()
public smadeira.biclustering.NodeObjectInterface getNodeObject()
public void clear()
public void paint(smadeira.biclustering.IMatrix expressionMatrix, javax.swing.tree.TreePath selectionPath)
expressionMatrix
.
expressionMatrix
- the IMatrix
with the
function informationselectionPath
- TreePath
selected in the
dataset tree, whose node contains the given
expressionMatrix
public void paint(smadeira.ontologizer.GeneSetResult goProperties, smadeira.ontologizer.GOFrontEnd go, java.lang.String[] genesNames, float pvalue)
goProperties
- GeneSetResult
with GO termsgo
- the GOFrontEnd
genesNames
- String[]
the set of genes' namespvalue
- float
the pvalue thresholdpublic smadeira.ontologizer.GeneSetResult paint(smadeira.biclustering.Bicluster bicluster, smadeira.ontologizer.GeneSetResult goProperties, float pvalue, javax.swing.tree.TreePath selectionPath)
bicluster
object.
bicluster
- the Bicluster
object which contains the
function analysis to present in the functions tablegoProperties
- the GeneSetResult
for the given
bicluster
pvalue
- the p-value threshold for significanceselectionPath
- the TreePath
selected in the
dataset treepublic void paint(smadeira.biclustering.Biclustering biclustering, javax.swing.tree.TreePath selectionPath, java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary)
biclustering
(biclusters' group).
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)public void putGOFrontEnd(javax.swing.tree.TreePath selectionPath, smadeira.ontologizer.GOFrontEnd go)
selectionPath
- the selection TreePath
go
- the GOFrontEnd
for the given
selectionPath/code>
public java.lang.String getGOFrontEndHashKeyForSelectionPath(javax.swing.tree.TreePath selectionPath)
GOFrontEnd
of
the given selectionPath
.
selectionPath
- the selection TreePath
public smadeira.ontologizer.GOFrontEnd getGOFrontEndForSelectionPath(javax.swing.tree.TreePath selectionPath)
GOFrontEnd
for the given
selectionPath
, if it exists, otherwise returns null.
selectionPath
- TreePath
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.Bicluster bicluster, java.lang.String pathTo_GeneOntologyFile, java.lang.String pathTo_GeneAssociationFile)
bicluster
- the Bicluster
pathTo_GeneOntologyFile
- String
the path to gene
ontology filepathTo_GeneAssociationFile
- String
the path to
organism's specific gene association file
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.Bicluster bicluster)
bicluster
- the Bicluster
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.IMatrix matrix, java.lang.String pathTo_GeneOntologyFile, java.lang.String pathTo_GeneAssociationFile)
matrix
- the expression IMatrix
pathTo_GeneOntologyFile
- String
the path to gene
ontology filepathTo_GeneAssociationFile
- String
the path to
organism's specific gene association file
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.IMatrix matrix)
matrix
- the expression IMatrix
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.Biclustering biclustering, java.lang.String pathTo_GeneOntologyFile, java.lang.String pathTo_GeneAssociationFile)
biclustering
- Biclustering
(the biclusters' group)pathTo_GeneOntologyFile
- String
the path to gene
ontology filepathTo_GeneAssociationFile
- String
the path to
organism's specific gene association file
public smadeira.ontologizer.GOFrontEnd calculateGOFrontEnd(smadeira.biclustering.Biclustering biclustering)
biclustering
- Biclustering
(the biclusters' group)
public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
e
- the ActionEvent
fired when the user clicks
the apply buttonpublic void repaintPanelAnalyzingFunctionTable(smadeira.ontologizer.GeneSetResult goProperties, float pvalue)
ThreadFunctionAnalysis
.
goProperties
- the GeneSetResult
for the biclusterpvalue
- float
the p-value user's thresholdpublic void repaintPanelAnalyzingFunctionTable(java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary)
ThreadFunctionAnalysis
.
biologicalRelevanceSummary
- Hashtablepublic void repaintPanelAnalyzingFunctionTable()
ThreadFunctionAnalysis
.
public void recalculate_actionPerformed(java.awt.event.ActionEvent e)
e
- the ActionEvent
fired when the user clicks on
recalculate functions buttonpublic void functionGroupTable_mouseClicked(java.awt.event.MouseEvent e)
e
- the MouseEvent
fired with the mouse's click
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