biggests.gui
Class PanelPreProcessing

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by biggests.gui.PanelBasicIOValidation
                      extended by biggests.gui.PanelPreProcessing
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class PanelPreProcessing
extends PanelBasicIOValidation

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.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, 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.
 smadeira.biclustering.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(smadeira.biclustering.ExpressionMatrix expressionMatrix, javax.swing.tree.TreePath selectionPath)
          Paints this preprocessing panel with the preprocessing options related with a given expressionMatrix.
 void paint(smadeira.biclustering.PreProcessedExpressionMatrix preProcessedExpMat, 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
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
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

FILTER_PERCENTAGE

public static final java.lang.String FILTER_PERCENTAGE
'Percentage of genes to filter' parameter name.

See Also:
Constant Field Values

FILL_VALUE

public static final java.lang.String FILL_VALUE
'Value to fill missings' parameter name;

See Also:
Constant Field Values

FILL_NEIGHBORS

public static final java.lang.String FILL_NEIGHBORS
'Number of neighbors' parameter name.

See Also:
Constant Field Values

NORMALIZE_MEAN

public static final java.lang.String NORMALIZE_MEAN
'Mean value to normalize expression data' parameter name.

See Also:
Constant Field Values

NORMALIZE_STD

public static final java.lang.String NORMALIZE_STD
'Std value to normalize expression data' parameter name.

See Also:
Constant Field Values

SMOOTH_WINDOW

public static final java.lang.String SMOOTH_WINDOW
'Smoothing window' parameter name.

See Also:
Constant Field Values

DISCRETIZE_PERCENT

public static final java.lang.String DISCRETIZE_PERCENT
'Percentage for discretization' parameter name.

See Also:
Constant Field Values

DISCRETIZE_SYMBOLS

public static final java.lang.String DISCRETIZE_SYMBOLS
'Number of symbols' parameter name.

See Also:
Constant Field Values

DISCRETIZE_ALPHA

public static final java.lang.String DISCRETIZE_ALPHA
'Alpha' discretization parameter name.

See Also:
Constant Field Values

DISCRETIZE_THRESHOLD

public static final java.lang.String DISCRETIZE_THRESHOLD
'Threshold' discretization parameter name.

See Also:
Constant Field Values
Constructor Detail

PanelPreProcessing

public PanelPreProcessing(BiggestsFrame frame)
Creates a new preprocessing panel.

Parameters:
frame - the main window
Method Detail

paint

public void paint(smadeira.biclustering.ExpressionMatrix expressionMatrix,
                  javax.swing.tree.TreePath selectionPath)
Paints this preprocessing panel with the preprocessing options related with a given expressionMatrix.

Parameters:
expressionMatrix - the ExpressionMatrix in which preprocessing options will be performed
selectionPath - the TreePath selected in the dataset tree; corresponds to the path from the root node to the node that contains the expressionMatrix

paint

public void paint(smadeira.biclustering.PreProcessedExpressionMatrix preProcessedExpMat,
                  javax.swing.tree.TreePath selectionPath)
Paints this preprocessing panel with the preprocessing options related with a given expressionMatrix.

Parameters:
preProcessedExpMat - the PreProcessedExpressionMatrix in which preprocessing options will be performed
selectionPath - the TreePath selected in the dataset tree; corresponds to the path from the root node to the node that contains the preProcessedExpMat

setFilterCheckBoxSelected

public void setFilterCheckBoxSelected(boolean selected)
Sets the filter check box selected/deselected, enabling/disabling the corresponding filter options.

Parameters:
selected - boolean true if the filter check box is to select; false otherwise

setNormalizeCheckBoxSelected

public void setNormalizeCheckBoxSelected(boolean selected)
Sets the normalize check box selected/deselected, enabling/disabling the corresponding normalize options.

Parameters:
selected - boolean true if the normalize check box is to select; false otherwise

setSmoothCheckBoxSelected

public void setSmoothCheckBoxSelected(boolean selected)
Sets the smooth check box selected/deselected, enabling/disabling the corresponding smooth options.

Parameters:
selected - boolean true if the smooth check box is to select; false otherwise

setDiscretizeCheckBoxSelected

public void setDiscretizeCheckBoxSelected(boolean selected)
Sets the discretize check box selected/deselected, enabling/disabling the corresponding discretize options.

Parameters:
selected - boolean true if the discretize check box is to select; false otherwise

readParameter

public java.lang.String readParameter(java.lang.String parameterToRead)
                               throws java.lang.Exception
Reads the parameter string for its input parameter text field.

Specified by:
readParameter in class PanelBasicIOValidation
Parameters:
parameterToRead - String the name of the parameter to read
Returns:
the parameter String read from the discretize parameter text field
Throws:
java.lang.Exception - if there is no parameter written in the text field

showDiscretizeErrorMessage

public void showDiscretizeErrorMessage(java.lang.String algorithmName)
Shows the discretization error message.

Parameters:
algorithmName - String the name of the discretization algorithm that was applied

filterPercentGenesButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the filter genes with more than a % of missing values radio button

normalizeOverallButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the normalize overall values radio button

normalizeByGeneButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the normalize by gene radio button

normalizeCheckBox_itemStateChanged

public void normalizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the normalize check box.

Parameters:
e - ItemEvent fired when the user selects/deselects the normalize option check box

smoothCheckBox_itemStateChanged

public void smoothCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the smooth check box.

Parameters:
e - ItemEvent fired when the user selects/deselects the smooth option check box

discretizeCheckBox_itemStateChanged

public void discretizeCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects the discretize check box.

Parameters:
e - ItemEvent fired when the user selects/deselects the discretize option check box

discretizeComboBox_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user changes the selection in the discretize combo box

applyButton_actionPerformed

public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks on the apply button.

Parameters:
e - ActionEvent fired when the user clicks on the apply button

normalizeMeanStdValuesButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the normalize by mean and std values radio button

normalizeMean0Std1Button_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the normalize by mean 0 and std 1 radio button

fillValueButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the fill missings with a given value radio button

fillKNeighborsButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the fill missings with average over the k-neighbors radio button

fillAverageRowButton_itemStateChanged

public 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.

Parameters:
e - ItemEvent fired when the user selects the fill missings with average over the same row radio button

getMainFrame

public BiggestsFrame getMainFrame()
Returns the application's main frame.

Returns:
the main window

getExpressionMatrix

public smadeira.biclustering.AbstractExpressionMatrix getExpressionMatrix()
Returns the original or preprocessed expression matrix in which preprocessing techniques will be performed.

Returns:
original or preprocessed AbstractExpressionMatrix in which preprocessing techniques will be performed

getSelectionPath

public javax.swing.tree.TreePath getSelectionPath()
Returns the path selected on the dataset tree. Corresponds to the path in the tree from the root node to the node that contains the original or preprocessed matrix to apply preprocessing techniques.

Returns:
TreePath selected on the dataset tree

getSpringLayout

public javax.swing.SpringLayout getSpringLayout()
Returns the layout of this panel.

Returns:
SpringLayout

getFilterCheckBox

public javax.swing.JCheckBox getFilterCheckBox()
Returns the filter check box.

Returns:
the filter JCheckBox

getFilterButtonGroup

public javax.swing.ButtonGroup getFilterButtonGroup()
Returns the filter options button group.

Returns:
the filter options ButtonGroup

getFilterAllGenesButton

public javax.swing.JRadioButton getFilterAllGenesButton()
Returns filter all genes with missing values button.

Returns:
filter all genes with missing values JRadioButton

getFilterPercentGenesButton

public javax.swing.JRadioButton getFilterPercentGenesButton()
Returns filter genes with more than a % of missing values button.

Returns:
filter genes with more than a % of missing values JRadioButton

getFilterPercentTextField

public javax.swing.JTextField getFilterPercentTextField()
Returns the filter percent input text field.

Returns:
the filter percent input JTextField

getFilterPercentLabel

public javax.swing.JLabel getFilterPercentLabel()
Returns filter percent label.

Returns:
filter percent JLabel

getFillCheckBox

public javax.swing.JCheckBox getFillCheckBox()
Returns fill check box.

Returns:
fill check JCheckBox

getFillButtonGroup

public javax.swing.ButtonGroup getFillButtonGroup()
Returns fill options button group.

Returns:
fill options ButtonGroup

getFillValueButton

public javax.swing.JRadioButton getFillValueButton()
Returns fill missings with a certain value button.

Returns:
fill missings with a certain value JRadioButton

getFillKNeighborsButton

public javax.swing.JRadioButton getFillKNeighborsButton()
Returns fill with average over the k-neighbors button.

Returns:
fill with average over the k-neighbors JRadioButton

getFillAverageRowButton

public javax.swing.JRadioButton getFillAverageRowButton()
Returns fill with average over the same row button.

Returns:
fill with average over the same row JRadioButton

getFillValueTextField

public javax.swing.JTextField getFillValueTextField()
Returns fill with a certain value input text field.

Returns:
fill with a certain value input JTextField

getFillKNeighborsTextField

public javax.swing.JTextField getFillKNeighborsTextField()
Returns fill with average over the k-neighbors input text field.

Returns:
fill with average over the k-neighbors input JTextField

getFillKNeighborsLabel

public javax.swing.JLabel getFillKNeighborsLabel()
Returns fill with average over the k-neighbors label.

Returns:
fill with average over the k-neighbors JLabel

getNormalizeCheckBox

public javax.swing.JCheckBox getNormalizeCheckBox()
Returns normalize check box.

Returns:
normalize JCheckBox

getNormalizeButtonGroup

public javax.swing.ButtonGroup getNormalizeButtonGroup()
Returns normalize options button group.

Returns:
normalize options ButtonGroup

getNormalizeOverallButton

public javax.swing.JRadioButton getNormalizeOverallButton()
Returns normalize overall values button.

Returns:
normalize overall values JRadioButton

getNormalizeByGeneButton

public javax.swing.JRadioButton getNormalizeByGeneButton()
Returns normalize by gene button.

Returns:
normalize by gene JRadioButton

getNormalizeMean0Std1Button

public javax.swing.JRadioButton getNormalizeMean0Std1Button()
Returns normalize to mean 0 and std 1 button.

Returns:
normalize to mean 0 and std 1 JRadioButton

getNormalizeMeanStdValuesButton

public javax.swing.JRadioButton getNormalizeMeanStdValuesButton()
Returns normalize by mean and std values button.

Returns:
normalize by mean and std values JRadioButton

getNormalizeMeanValueTextField

public javax.swing.JTextField getNormalizeMeanValueTextField()
Return normalize mean input text field.

Returns:
normalize mean input JTextField

getNormalizeStdValueTextField

public javax.swing.JTextField getNormalizeStdValueTextField()
Returns normalize std input text field.

Returns:
normalize std input JTextField

getNormalizeMeanStdValuesLabel

public javax.swing.JLabel getNormalizeMeanStdValuesLabel()
Returns normalize to mean and std values label.

Returns:
normalize to mean and std values JLabel

getNormalizeMeanStdButtonGroup

public javax.swing.ButtonGroup getNormalizeMeanStdButtonGroup()
Returns normalize to mean and std options button group.

Returns:
normalize to mean and std options ButtonGroup

getSmoothCheckBox

public javax.swing.JCheckBox getSmoothCheckBox()
Returns smooth check box.

Returns:
smooth JCheckBox

getSmoothWindowLabel

public javax.swing.JLabel getSmoothWindowLabel()
Returns smooth window label.

Returns:
smooth window JLabel

getSmoothWindowTextField

public javax.swing.JTextField getSmoothWindowTextField()
Returns smooth window input text field.

Returns:
smooth window input JTextField

getDiscretizeCheckBox

public javax.swing.JCheckBox getDiscretizeCheckBox()
Returns discretize check box.

Returns:
discretize JCheckBox

getDiscretizeLabel

public javax.swing.JLabel getDiscretizeLabel()
Returns discretize label.

Returns:
discretize JLabel

getDiscretizeComboBox

public javax.swing.JComboBox getDiscretizeComboBox()
Returns discretize combo box.

Returns:
discretize JComboBox

getDiscretizeParameterTextField

public javax.swing.JTextField getDiscretizeParameterTextField()
Returns discretize parameter input text field.

Returns:
discretize parameter input JTextField

getDiscretizeParameterLabel

public javax.swing.JLabel getDiscretizeParameterLabel()
Returns discretize parameter label.

Returns:
discretize parameter JLabel

applyButton

public javax.swing.JButton applyButton()
Returns apply preprocessing options button.

Returns:
apply preprocessing options JButton

fillCheckBox_itemStateChanged

public void fillCheckBox_itemStateChanged(java.awt.event.ItemEvent e)

filterCheckBox_itemStateChanged

public void filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)