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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelAnalyzingFunctionSignificanceGraph
public class PanelAnalyzingFunctionSignificanceGraph
Title: Function Analysis - Significance Graph Panel
Description: Displays a significance graph of a bicluster.
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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static java.lang.String |
GIF
GIF image type. |
static java.lang.String |
PNG
PNG image type. |
static java.lang.String |
SVG
SVG image type. |
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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PanelAnalyzingFunctionSignificanceGraph(BiggestsFrame frame)
Creates a new function analysis - significance graph panel. |
Method Summary | |
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void |
clear()
Clears this panel. |
java.lang.String |
convertDOTtoImage(java.lang.String pathToDotFile,
java.lang.String pathToImgDirectory,
java.lang.String imgFileExtension)
Converts a .dot file to an image file (png, gif, svg). |
BiggestsFrame |
getMainFrame()
Returns the application's main frame. |
java.lang.String |
getPathToImage()
Returns the path to image. |
java.lang.String |
getPathToSvg()
Returns the path to svg. |
org.apache.batik.swing.svg.JSVGComponent |
getSvgGraph()
Returns the swing-based component which holds the svg graph. |
float |
getZoom()
Returns the current zoom scale factor. |
javax.swing.JSlider |
getZoomSlider()
Returns the zoom slider. |
boolean |
isSvgBuilded()
Checks if the gvt tree for the svg document is already built. |
void |
paint(smadeira.biclustering.Bicluster bicluster,
javax.swing.tree.TreePath selectionPath)
Paints this panel with a table of functions for the genes in bicluster . |
void |
saveGraph_actionPerformed(java.awt.event.ActionEvent e)
Handles the user click on the save graph button. |
void |
zoomSlider_stateChanged(javax.swing.event.ChangeEvent e)
Handles changes on the zoom slider. |
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 |
Field Detail |
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public static final java.lang.String PNG
public static final java.lang.String GIF
public static final java.lang.String SVG
Constructor Detail |
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public PanelAnalyzingFunctionSignificanceGraph(BiggestsFrame frame)
frame
- the main BiggestsFrame
Method Detail |
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public void clear()
public void paint(smadeira.biclustering.Bicluster bicluster, javax.swing.tree.TreePath selectionPath)
bicluster
. The path to the given bicluster
datafile is retrieved from the selectionPath
.
bicluster
- the Bicluster
from which the table
of functions will be constructed and shownselectionPath
- the TreePath
holding the necessary
data to find the path to the given
bicluster
graph filepublic java.lang.String convertDOTtoImage(java.lang.String pathToDotFile, java.lang.String pathToImgDirectory, java.lang.String imgFileExtension) throws java.lang.InterruptedException, java.io.IOException, java.lang.Exception
pathToDotFile
- the String
path to dot filepathToImgDirectory
- the String
path to destination directoryimgFileExtension
- the String
image file extension
String
path to the new image file
java.lang.InterruptedException
- if an error occured while waiting for the conversion of the .dot file
java.io.IOException
- if files do not exist or an error occurs in the conversion process
java.lang.Exception
- if it was not possible to convert the .dot filepublic void saveGraph_actionPerformed(java.awt.event.ActionEvent e)
e
- the ActionEvent
fired by the click of the
user in save graph buttonpublic void zoomSlider_stateChanged(javax.swing.event.ChangeEvent e)
e
- ChangeEvent
fired by the user manipulation of the zoom sliderpublic BiggestsFrame getMainFrame()
BiggestsFrame
public java.lang.String getPathToImage()
String
to imagepublic java.lang.String getPathToSvg()
String
to svgpublic javax.swing.JSlider getZoomSlider()
JSlider
public float getZoom()
float
zoom scale factorpublic org.apache.batik.swing.svg.JSVGComponent getSvgGraph()
JSVGComponent
which holds the svg graphpublic boolean isSvgBuilded()
boolean
that indicates if gvt tree for the svg document is already built
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