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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelFunctionAnalysis
public class PanelFunctionAnalysis
Title: Function Analysis Panel
Description: This panel displays function analysis options to apply to a given 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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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static java.lang.String |
OBO_FILE_NAME
|
static java.lang.String[] |
organisms
Set of organisms to display in organism combo box. |
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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PanelFunctionAnalysis(BiggestsFrame frame)
Creates a new PanelFunctionAnalysis . |
Method Summary | |
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void |
browseGeneAssociationFilesPathButton_actionPerformed(java.awt.event.ActionEvent e)
Handles event fired when the user clicks on browse gene association file path button. |
void |
browseGOFilesPathButton_actionPerformed(java.awt.event.ActionEvent e)
Handles event fired when the user clicks browse gene ontology file path button. |
de.schlichtherle.io.File[] |
checkGOFiles(boolean biclustering_function)
Checks the existence of the required gene ontology files (the gene ontology file and the specific gene association file for the specified organism) in the GO Files directory. |
float |
checkPValue()
Checks the input of the p-value on pvalueTextField |
void |
clear()
Clears this panel. |
void |
downloadGeneAssociationFileButton_actionPerformed(java.awt.event.ActionEvent e)
Handles a mouse click event on download gene association file button. |
void |
downloadGeneOntologyFileButton_actionPerformed(java.awt.event.ActionEvent e)
Handles a mouse click event on download gene ontology file button. |
static java.lang.String |
findAnnotationFileExtensionForOrganism(java.lang.String organism)
Finds and returns the corresponding annotation file extension for a given organism. |
static java.lang.String |
findGeneAssociationFileName(java.lang.String organism,
boolean filename_extension)
Finds a specific filename or extension for a given organism. |
javax.swing.JButton |
getBrowseGeneAssociationFilePathButton()
Returns browse gene association file path button. |
javax.swing.JButton |
getBrowseGeneOntologyFilePathButton()
Returns browse gene ontology file path button. |
javax.swing.JLabel |
getFilesFunctionAnalysisLabel()
Returns label of files to use on function analysis. |
javax.swing.JLabel |
getFunctionAnalysisLabel()
Returns function analysis label. |
javax.swing.JLabel |
getGeneAssociationFilePathLabel()
Returns gene association file path label. |
javax.swing.JTextField |
getGeneAssociationFilePathTextField()
Returns gene association file path text field. |
javax.swing.JLabel |
getGeneOntologyFilePathLabel()
Returns gene ontology file path label. |
javax.swing.JTextField |
getGeneOntologyFilePathTextField()
Returns gene ontology file path text field. |
BiggestsFrame |
getMainFrame()
Returns the application's main frame. |
java.lang.String |
getOrganism()
Returns the organism related with this function analysis. |
javax.swing.JLabel |
getOrganismLabel()
Returns the organism label. |
javax.swing.JLabel |
getPvalueLabel()
Returns p-value label. |
javax.swing.JTextField |
getPvalueTextField()
Returns text field for the input of a p-value. |
javax.swing.tree.TreePath |
getSelectionPath()
Returns the dataset tree selected path which corresponds to the path of the dataset which in turn leads to the node with the matrix on which biclustering algorithm will be performed. |
void |
goFrontEndCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
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void |
paint(javax.swing.tree.TreePath selectionPath)
Paints the panel with information from the given selectionPath . |
javax.swing.SpringLayout |
springLayout()
Returns the layout for this panel. |
GOFrontEnd |
useGOFrontEnd()
Check if GO frontend can be used for function analysis. |
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, 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 |
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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 |
Field Detail |
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public static final java.lang.String OBO_FILE_NAME
public static final java.lang.String[] organisms
Constructor Detail |
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public PanelFunctionAnalysis(BiggestsFrame frame)
PanelFunctionAnalysis
.
frame
- the main BiggestsFrame
Method Detail |
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public void clear()
public void paint(javax.swing.tree.TreePath selectionPath)
selectionPath
.
selectionPath
- the TreePath
selected in a dataset treepublic static java.lang.String findGeneAssociationFileName(java.lang.String organism, boolean filename_extension)
organism
- String
with the organism to find a
gene association file forfilename_extension
- boolean
true
if
the String to return is the filename of the
corresponding organism gene association file;
false
if the String to return is the
file extension of the corresponding organism gene
association file
String
the filename/extension of the corresponding
organism gene association filepublic static java.lang.String findAnnotationFileExtensionForOrganism(java.lang.String organism)
organism
- String
the name of the organism to find
the annotation file extension for
String
the annotation file extension for the
given organismpublic float checkPValue()
pvalueTextField
float
entered by the userpublic de.schlichtherle.io.File[] checkGOFiles(boolean biclustering_function)
In case the gene ontology files are correct, returns:
File[0] - containing the gene ontology file.
File[1] - containing the gene association file.
Returns null
if there was some error on the input
(p-value or file paths are not valid) and the user wants to ignore it.
Returns File[0]
if there was some error on the input
(p-value or file paths are not valid) and the user wants to correct it.
biclustering_function
- boolean
that indicates if
this panel is being used in biclustering (true) or in
function panel (false)
File[]
list of filespublic GOFrontEnd useGOFrontEnd()
public void browseGOFilesPathButton_actionPerformed(java.awt.event.ActionEvent e)
e
- ActionEvent
fired when the user clicks
browse gene ontology file path buttonpublic void browseGeneAssociationFilesPathButton_actionPerformed(java.awt.event.ActionEvent e)
e
- ActionEvent
fired when the user clicks
on browse gene association file path buttonpublic BiggestsFrame getMainFrame()
BiggestsFrame
public javax.swing.tree.TreePath getSelectionPath()
TreePath
selected in the dataset treepublic java.lang.String getOrganism()
String
organismpublic javax.swing.JLabel getFunctionAnalysisLabel()
JLabel
public javax.swing.JLabel getPvalueLabel()
JLabel
public javax.swing.JTextField getPvalueTextField()
JTextField
for the input of a p-valuepublic javax.swing.JLabel getOrganismLabel()
JLabel
public javax.swing.JLabel getFilesFunctionAnalysisLabel()
public javax.swing.JLabel getGeneOntologyFilePathLabel()
JLabel
public javax.swing.JTextField getGeneOntologyFilePathTextField()
JTextField
public javax.swing.JButton getBrowseGeneOntologyFilePathButton()
JButton
public javax.swing.JLabel getGeneAssociationFilePathLabel()
JLabel
public javax.swing.JTextField getGeneAssociationFilePathTextField()
JTextField
public javax.swing.JButton getBrowseGeneAssociationFilePathButton()
JButton
public javax.swing.SpringLayout springLayout()
SpringLayout
public void downloadGeneOntologyFileButton_actionPerformed(java.awt.event.ActionEvent e)
e
- ActionEventpublic void downloadGeneAssociationFileButton_actionPerformed(java.awt.event.ActionEvent e)
e
- ActionEventpublic void goFrontEndCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
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