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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelExpression
public class PanelExpression
Title: Expression Panel
Description: Displays expression charts. May contain bicluster time-points, all time-points or bicluster pattern charts. The charts are constructed from either single biclusters or groups 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 int |
ALL_TIME_POINTS
Constant which defines all time-points expression chart type. |
static int |
BICLUSTER_TIME_POINTS
Constant which defines bicluster time-points expression chart type. |
static int |
PATTERN
Constant which defines pattern expression chart 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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PanelExpression(BiggestsFrame frame,
int expressionType)
Creates a new panel to display expression charts. |
Method Summary | |
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void |
clear()
Clears this panel. |
int |
getChartHeight()
Returns the height of the displayed expression chart(s). |
int |
getChartWidth()
Returns the width of the displayed expression chart(s). |
PanelExpressionChart |
getExpressionChart()
Returns single bicluster's expression chart that is being displayed in this panel. |
PanelExpressionChart[] |
getExpressionCharts()
Returns the expression charts of a set of biclusters (which belong to a specific group of biclusters). |
int |
getExpressionType()
Returns the type of expression for this panel's chart. |
BiggestsFrame |
getMainFrame()
Returns the application's main frame, where this panel is being displayed. |
javax.swing.JCheckBox |
getNormalize()
Returns the check box which allows the user to choose between an expression chart with original or normalized data. |
javax.swing.JComboBox |
getOption()
Returns the combo box for the user to choose the number of biclusters to display. |
Bicluster[] |
getSetOfBiclusters()
Returns the set of biclusters retrieved from the group of biclusters to display. |
java.lang.String[] |
getVisualizationOption()
Returns visualization options (number of biclusters to be displayed) to include in a combo box when the expression type is either BICLUSTER_TIME_POINTS or PATTERN and the corresponding object is a group of biclusters. |
void |
normalize_itemStateChanged(java.awt.event.ItemEvent e)
Checks the option selected by the user in the normalize check box. |
void |
option_itemStateChanged(java.awt.event.ItemEvent e)
Checks the option selected by the user in the "number of biclusters to display" combo box. |
void |
paintAllTimePointsChart(NodeInfo nodeInfo,
NodeInfo parentNodeInfo)
Paints an expression chart which data consists of the gene expression values for the genes in a specific nodeInfo matrix object
under all conditions of a specific parentNodeInfo matrix
object. |
void |
paintBiclusterPatternCharts(NodeInfo nodeInfo)
Paints one bicluster / set of bicluster pattern charts. |
void |
paintBiclusterTimePointsCharts(NodeInfo nodeInfo)
Paints one or a set of bicluster time-point charts. |
void |
this_ancestorResized(java.awt.event.HierarchyEvent e)
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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 int BICLUSTER_TIME_POINTS
public static final int ALL_TIME_POINTS
public static final int PATTERN
Constructor Detail |
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public PanelExpression(BiggestsFrame frame, int expressionType)
BICLUSTER_TIME_POINTS
ALL_TIME_POINTS
PATTERN
frame
- the BiggestsFrame
, where this panel is
being displayed.expressionType
- the type of expression chart(s) which is/are
being displayed in this panelMethod Detail |
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public void clear()
public void paintAllTimePointsChart(NodeInfo nodeInfo, NodeInfo parentNodeInfo)
nodeInfo
matrix object
under all conditions of a specific parentNodeInfo
matrix
object.
nodeInfo
- the NodeInfo
with the matrix object to
retrieve the genesparentNodeInfo
- the NodeInfo
with the matrix object
to retrieve all the conditionspublic void paintBiclusterTimePointsCharts(NodeInfo nodeInfo)
NodeInfo
object.
nodeInfo
- the NodeInfo
which contains the matrix
object(s) with the expression valuespublic void paintBiclusterPatternCharts(NodeInfo nodeInfo)
NodeInfo
object.
nodeInfo
- the NodeInfo
which contains the matrix
object(s) with the expression valuespublic void normalize_itemStateChanged(java.awt.event.ItemEvent e)
e
- the ItemEvent
of the check box selected statepublic void option_itemStateChanged(java.awt.event.ItemEvent e)
e
- the ItemEvent
that signals the change of
selection by the user in the combo boxpublic java.lang.String[] getVisualizationOption()
String
optionspublic int getExpressionType()
int
type of expression chart in this panelpublic BiggestsFrame getMainFrame()
BiggestsFrame
public javax.swing.JCheckBox getNormalize()
JCheckBox
public javax.swing.JComboBox getOption()
JComboBox
public PanelExpressionChart getExpressionChart()
PanelExpressionChart
that holds the
chart being displayedpublic PanelExpressionChart[] getExpressionCharts()
PanelExpressionChart
spublic Bicluster[] getSetOfBiclusters()
Bicluster
spublic int getChartWidth()
int
width of expression chart(s)public int getChartHeight()
int
height of expression chart(s)public void this_ancestorResized(java.awt.event.HierarchyEvent e)
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