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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelBasicIOValidation
biggests.gui.PanelPreProcessing
public class PanelPreProcessing
Title: Preprocessing Panel
Description: Displays options to select and apply different preprocessing techniques on gene expression data matrices.
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 |
|---|
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
| Field Summary | |
|---|---|
static java.lang.String |
DISCRETIZE_ALPHA
'Alpha' discretization parameter name. |
static java.lang.String |
DISCRETIZE_PERCENT
'Percentage for discretization' parameter name. |
static java.lang.String |
DISCRETIZE_SYMBOLS
'Number of symbols' parameter name. |
static java.lang.String |
DISCRETIZE_THRESHOLD
'Threshold' discretization parameter name. |
static java.lang.String |
FILL_NEIGHBORS
'Number of neighbors' parameter name. |
static java.lang.String |
FILL_VALUE
'Value to fill missings' parameter name; |
static java.lang.String |
FILTER_PERCENTAGE
'Percentage of genes to filter' parameter name. |
static java.lang.String |
NORMALIZE_MEAN
'Mean value to normalize expression data' parameter name. |
static java.lang.String |
NORMALIZE_STD
'Std value to normalize expression data' parameter name. |
static java.lang.String |
SMOOTH_WINDOW
'Smoothing window' parameter name. |
| 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 | |
|---|---|
PanelPreProcessing(BiggestsFrame frame)
Creates a new preprocessing panel. |
|
| Method Summary | |
|---|---|
void |
applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks on the apply button. |
javax.swing.JButton |
applyButton()
Returns apply preprocessing options button. |
void |
discretizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the discretize check box. |
void |
discretizeComboBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user changes the selection in the discretize combo box. |
void |
fillAverageRowButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the fill missings with average over the same row radio button. |
void |
fillCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
|
void |
fillKNeighborsButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the fill missings with average over the k-neighbors radio button. |
void |
fillValueButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the fill missings with a given value radio button. |
void |
filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
|
void |
filterPercentGenesButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the filter genes with more than a % of missing values radio button. |
javax.swing.JCheckBox |
getDiscretizeCheckBox()
Returns discretize check box. |
javax.swing.JComboBox |
getDiscretizeComboBox()
Returns discretize combo box. |
javax.swing.JLabel |
getDiscretizeLabel()
Returns discretize label. |
javax.swing.JLabel |
getDiscretizeParameterLabel()
Returns discretize parameter label. |
javax.swing.JTextField |
getDiscretizeParameterTextField()
Returns discretize parameter input text field. |
AbstractExpressionMatrix |
getExpressionMatrix()
Returns the original or preprocessed expression matrix in which preprocessing techniques will be performed. |
javax.swing.JRadioButton |
getFillAverageRowButton()
Returns fill with average over the same row button. |
javax.swing.ButtonGroup |
getFillButtonGroup()
Returns fill options button group. |
javax.swing.JCheckBox |
getFillCheckBox()
Returns fill check box. |
javax.swing.JRadioButton |
getFillKNeighborsButton()
Returns fill with average over the k-neighbors button. |
javax.swing.JLabel |
getFillKNeighborsLabel()
Returns fill with average over the k-neighbors label. |
javax.swing.JTextField |
getFillKNeighborsTextField()
Returns fill with average over the k-neighbors input text field. |
javax.swing.JRadioButton |
getFillValueButton()
Returns fill missings with a certain value button. |
javax.swing.JTextField |
getFillValueTextField()
Returns fill with a certain value input text field. |
javax.swing.JRadioButton |
getFilterAllGenesButton()
Returns filter all genes with missing values button. |
javax.swing.ButtonGroup |
getFilterButtonGroup()
Returns the filter options button group. |
javax.swing.JCheckBox |
getFilterCheckBox()
Returns the filter check box. |
javax.swing.JRadioButton |
getFilterPercentGenesButton()
Returns filter genes with more than a % of missing values button. |
javax.swing.JLabel |
getFilterPercentLabel()
Returns filter percent label. |
javax.swing.JTextField |
getFilterPercentTextField()
Returns the filter percent input text field. |
BiggestsFrame |
getMainFrame()
Returns the application's main frame. |
javax.swing.ButtonGroup |
getNormalizeButtonGroup()
Returns normalize options button group. |
javax.swing.JRadioButton |
getNormalizeByGeneButton()
Returns normalize by gene button. |
javax.swing.JCheckBox |
getNormalizeCheckBox()
Returns normalize check box. |
javax.swing.JRadioButton |
getNormalizeMean0Std1Button()
Returns normalize to mean 0 and std 1 button. |
javax.swing.ButtonGroup |
getNormalizeMeanStdButtonGroup()
Returns normalize to mean and std options button group. |
javax.swing.JRadioButton |
getNormalizeMeanStdValuesButton()
Returns normalize by mean and std values button. |
javax.swing.JLabel |
getNormalizeMeanStdValuesLabel()
Returns normalize to mean and std values label. |
javax.swing.JTextField |
getNormalizeMeanValueTextField()
Return normalize mean input text field. |
javax.swing.JRadioButton |
getNormalizeOverallButton()
Returns normalize overall values button. |
javax.swing.JTextField |
getNormalizeStdValueTextField()
Returns normalize std input text field. |
javax.swing.tree.TreePath |
getSelectionPath()
Returns the path selected on the dataset tree. |
javax.swing.JCheckBox |
getSmoothCheckBox()
Returns smooth check box. |
javax.swing.JLabel |
getSmoothWindowLabel()
Returns smooth window label. |
javax.swing.JTextField |
getSmoothWindowTextField()
Returns smooth window input text field. |
javax.swing.SpringLayout |
getSpringLayout()
Returns the layout of this panel. |
void |
normalizeByGeneButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the normalize by gene radio button. |
void |
normalizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the normalize check box. |
void |
normalizeMean0Std1Button_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the normalize by mean 0 and std 1 radio button. |
void |
normalizeMeanStdValuesButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the normalize by mean and std values radio button. |
void |
normalizeOverallButton_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects the normalize overall values radio button. |
void |
paint(ExpressionMatrix expressionMatrix,
javax.swing.tree.TreePath selectionPath)
Paints this preprocessing panel with the preprocessing options related with a given expressionMatrix. |
java.lang.String |
readParameter(java.lang.String parameterToRead)
Reads the parameter string for its input parameter text field. |
void |
setDiscretizeCheckBoxSelected(boolean selected)
Sets the discretize check box selected/deselected, enabling/disabling the corresponding discretize options. |
void |
setFilterCheckBoxSelected(boolean selected)
Sets the filter check box selected/deselected, enabling/disabling the corresponding filter options. |
void |
setNormalizeCheckBoxSelected(boolean selected)
Sets the normalize check box selected/deselected, enabling/disabling the corresponding normalize options. |
void |
setSmoothCheckBoxSelected(boolean selected)
Sets the smooth check box selected/deselected, enabling/disabling the corresponding smooth options. |
void |
showDiscretizeErrorMessage(java.lang.String algorithmName)
Shows the discretization error message. |
void |
smoothCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the smooth check box. |
| Methods inherited from class biggests.gui.PanelBasicIOValidation |
|---|
readParameterDouble, readParameterDouble, readParameterDouble, readParameterFloat, readParameterFloat, readParameterFloat, readParameterInteger, readParameterInteger, readParameterInteger |
| Methods inherited from class javax.swing.JPanel |
|---|
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 |
|---|
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 |
|---|
public static final java.lang.String FILTER_PERCENTAGE
public static final java.lang.String FILL_VALUE
public static final java.lang.String FILL_NEIGHBORS
public static final java.lang.String NORMALIZE_MEAN
public static final java.lang.String NORMALIZE_STD
public static final java.lang.String SMOOTH_WINDOW
public static final java.lang.String DISCRETIZE_PERCENT
public static final java.lang.String DISCRETIZE_SYMBOLS
public static final java.lang.String DISCRETIZE_ALPHA
public static final java.lang.String DISCRETIZE_THRESHOLD
| Constructor Detail |
|---|
public PanelPreProcessing(BiggestsFrame frame)
frame - the main window| Method Detail |
|---|
public void paint(ExpressionMatrix expressionMatrix,
javax.swing.tree.TreePath selectionPath)
expressionMatrix.
expressionMatrix - the ExpressionMatrix in which
preprocessing options will be performedselectionPath - the TreePath selected in the
dataset tree; corresponds to the path from the root node to
the node that contains the expressionMatrixpublic void setFilterCheckBoxSelected(boolean selected)
selected - boolean true if the
filter check box is to select; false otherwisepublic void setNormalizeCheckBoxSelected(boolean selected)
selected - boolean true if the
normalize check box is to select; false otherwisepublic void setSmoothCheckBoxSelected(boolean selected)
selected - boolean true if the
smooth check box is to select; false otherwisepublic void setDiscretizeCheckBoxSelected(boolean selected)
selected - boolean true if the
discretize check box is to select; false otherwise
public java.lang.String readParameter(java.lang.String parameterToRead)
throws java.lang.Exception
readParameter in class PanelBasicIOValidationparameterToRead - String the name of the parameter
to read
String read from the
discretize parameter text field
java.lang.Exception - if there is no parameter written in the text fieldpublic void showDiscretizeErrorMessage(java.lang.String algorithmName)
algorithmName - String the name of the
discretization algorithm that was appliedpublic void filterPercentGenesButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the filter genes with more than a % of missing values radio buttonpublic void normalizeOverallButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the normalize overall values radio buttonpublic void normalizeByGeneButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the normalize by gene radio buttonpublic void normalizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects/deselects
the normalize option check boxpublic void smoothCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects/deselects
the smooth option check boxpublic void discretizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects/deselects
the discretize option check boxpublic void discretizeComboBox_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user changes
the selection in the discretize combo boxpublic void applyButton_actionPerformed(java.awt.event.ActionEvent e)
e - ActionEvent fired when the user clicks on
the apply buttonpublic void normalizeMeanStdValuesButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the normalize by mean and std values radio buttonpublic void normalizeMean0Std1Button_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the normalize by mean 0 and std 1 radio buttonpublic void fillValueButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the fill missings with a given value radio buttonpublic void fillKNeighborsButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the fill missings with average over the k-neighbors radio buttonpublic void fillAverageRowButton_itemStateChanged(java.awt.event.ItemEvent e)
e - ItemEvent fired when the user selects
the fill missings with average over the same row radio buttonpublic BiggestsFrame getMainFrame()
public AbstractExpressionMatrix getExpressionMatrix()
AbstractExpressionMatrix
in which preprocessing techniques will be performedpublic javax.swing.tree.TreePath getSelectionPath()
TreePath selected on the dataset treepublic javax.swing.SpringLayout getSpringLayout()
SpringLayoutpublic javax.swing.JCheckBox getFilterCheckBox()
JCheckBoxpublic javax.swing.ButtonGroup getFilterButtonGroup()
ButtonGrouppublic javax.swing.JRadioButton getFilterAllGenesButton()
JRadioButtonpublic javax.swing.JRadioButton getFilterPercentGenesButton()
JRadioButtonpublic javax.swing.JTextField getFilterPercentTextField()
JTextFieldpublic javax.swing.JLabel getFilterPercentLabel()
JLabelpublic javax.swing.JCheckBox getFillCheckBox()
JCheckBoxpublic javax.swing.ButtonGroup getFillButtonGroup()
ButtonGrouppublic javax.swing.JRadioButton getFillValueButton()
JRadioButtonpublic javax.swing.JRadioButton getFillKNeighborsButton()
JRadioButtonpublic javax.swing.JRadioButton getFillAverageRowButton()
JRadioButtonpublic javax.swing.JTextField getFillValueTextField()
JTextFieldpublic javax.swing.JTextField getFillKNeighborsTextField()
JTextFieldpublic javax.swing.JLabel getFillKNeighborsLabel()
JLabelpublic javax.swing.JCheckBox getNormalizeCheckBox()
JCheckBoxpublic javax.swing.ButtonGroup getNormalizeButtonGroup()
ButtonGrouppublic javax.swing.JRadioButton getNormalizeOverallButton()
JRadioButtonpublic javax.swing.JRadioButton getNormalizeByGeneButton()
JRadioButtonpublic javax.swing.JRadioButton getNormalizeMean0Std1Button()
JRadioButtonpublic javax.swing.JRadioButton getNormalizeMeanStdValuesButton()
JRadioButtonpublic javax.swing.JTextField getNormalizeMeanValueTextField()
JTextFieldpublic javax.swing.JTextField getNormalizeStdValueTextField()
JTextFieldpublic javax.swing.JLabel getNormalizeMeanStdValuesLabel()
JLabelpublic javax.swing.ButtonGroup getNormalizeMeanStdButtonGroup()
ButtonGrouppublic javax.swing.JCheckBox getSmoothCheckBox()
JCheckBoxpublic javax.swing.JLabel getSmoothWindowLabel()
JLabelpublic javax.swing.JTextField getSmoothWindowTextField()
JTextFieldpublic javax.swing.JCheckBox getDiscretizeCheckBox()
JCheckBoxpublic javax.swing.JLabel getDiscretizeLabel()
JLabelpublic javax.swing.JComboBox getDiscretizeComboBox()
JComboBoxpublic javax.swing.JTextField getDiscretizeParameterTextField()
JTextFieldpublic javax.swing.JLabel getDiscretizeParameterLabel()
JLabelpublic javax.swing.JButton applyButton()
JButtonpublic void fillCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
public void filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
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