biggests.gui
Class PanelPostProcessing

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.PanelPostProcessing
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class PanelPostProcessing
extends PanelBasicIOValidation

Title: Post-Processing Panel

Description: Displays options to select and apply post-processing techniques to 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.

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.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
static int FILTER_ACV
          The index of 'filter biclusters with an ACV value below a given threshold' option.
static int FILTER_ACV_ARV
          The index of 'filter trivial biclusters and biclusters with ACV and ARV values below given thresholds' option.
static int FILTER_ARV
          The index of 'filter biclusters with an ARV value below a given threshold' option.
static int FILTER_CONDITIONS
          The index of 'filter biclusters with less than a given number of conditions' option.
static int FILTER_CONDITIONS_GENES_ARV_ACV
          The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV and ACV values below given thresholds' option.
static int FILTER_CONDITIONS_GENES_ARV_ACV_MSR
          The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV, ACV and MSR values below given thresholds' option.
static int FILTER_CONSTANT_PATTERN
          The index of 'filter biclusters with constant pattern' option.
static int FILTER_GENES
          The index of 'filter biclusters with less than a given number of genes' option.
static int FILTER_GENES_CONDITIONS
          The index of 'filter biclusters with less than a given number of genes and less than a given number of conditions' option.
static int FILTER_MSR
          The index of 'filter biclusters with an MSR value below a given threshold' option.
static int FILTER_OVERLAPPING_GENES
          The index of 'filter biclusters with a row similarity below a given threshold' option.
static int FILTER_OVERLAPPING_GENES_CONDITIONS
          The index of 'filter biclusters with row and column similarities below given thresholds' option.
static int FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT
           
static int FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT
           
static int FILTER_SIZE
          The index of 'filter biclusters smaller than a given size' option.
static int FILTER_SIZE_ARV_ACV
          The index of 'filter biclusters smaller than a given size and with ARV and ACV values below given thresholds' option.
static int FILTER_TRIVIAL
          The index of filter trivial biclusters option.
static java.lang.String PARAMETER_ACV
          Average column variance parameter name.
static java.lang.String PARAMETER_ARV
          Average row variance parameter name.
static java.lang.String PARAMETER_CONDITIONS
          Number of conditions parameter name.
static java.lang.String PARAMETER_GENES
          Number of genes parameter name.
static java.lang.String PARAMETER_MARKOV_FILTER
          Markov chain order parameter name.
static java.lang.String PARAMETER_MARKOV_SORT
           
static java.lang.String PARAMETER_MSR
          Mean squared residue parameter name.
static java.lang.String PARAMETER_PVALUE
           
static java.lang.String PARAMETER_SIMILARITY
          Similarity parameter name.
static java.lang.String PARAMETER_SIZE
          Size parameter name.
static int SORT_ACV
          The index of 'sort biclusters by their ACV values' option.
static int SORT_ARV
          The index of 'sort biclusters by their ARV values' option.
static int SORT_ARV_ACV_DIFF
          The index of 'sort biclusters by the differences between their ARV and ACV values' option.
static int SORT_ARV_MSR_DIFF
          The index of 'sort biclusters by the differences between their ARV and MSR values' option.
static int SORT_BEST_GO_BONFERRONI_PVALUE
          The index of 'sort biclusters by their best GO Bonferroni corrected p-value' option.
static int SORT_BEST_GO_PVALUE
          The index of 'sort biclusters by their best GO p-value' option.
static int SORT_CONDITIONS
          The index of 'sort biclusters by their number of conditions' option.
static int SORT_GENES
          The index of 'sort biclusters by their number of genes' option.
static int SORT_MSR
          The index of 'sort biclusters by their MSR values' option.
static int SORT_PATTERN_COLUMNS_PVALUE
          The index of 'sort biclusters by the p-value for their pattern with columns' option.
static int SORT_PATTERN_PVALUE
          The index of 'sort biclusters by their pattern p-value' option.
static int SORT_SIZE
          The index of 'sort biclusters by their size' option.
static int SORT_VARIANCE
          The index of 'sort biclusters by their variance' option.
 
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
PanelPostProcessing(BiggestsFrame frame)
          Creates a new post-processing panel.
 
Method Summary
 void addPostProcessedBiclusterGroupToTree(Biclustering bic, java.util.ArrayList<java.lang.String> infoStrings, java.util.ArrayList<java.lang.String> infoStyles, javax.swing.tree.TreePath selectionPath)
          Adds a post-processed biclustering to the dataset tree.
 void applyButton_actionPerformed(java.awt.event.ActionEvent e)
          Applies the post-processing criteria to the current biclusters group.
 void clear()
          Clears post-processing panel.
 void copyFunctionResultFilesForPostProcessedBiclusterGroup(javax.swing.tree.TreePath selectionPath)
          Copies the function result files for a post-processed biclusters' group.
 void displayFilteringErrorMessage(boolean sort)
          Displays a message when some problem occurs while performing filtering operations.
 void filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
          Handles changes on filter check box selection.
 void filterCriteriaList_valueChanged()
          Handles a selection change on filter criteria list.
 void filterCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
          Handles a selection change on filter criteria list.
 javax.swing.JTextField getACVTextField()
          Returns ACV's threshold input text field.
 javax.swing.JTextField getARVTextField()
          Returns ARV's threshold input text field.
 javax.swing.JRadioButton getAscendingButton()
          Returns ascending order option radio button.
 Biclustering getBiclustering()
          Returns the group of biclusters that is being post-processed.
 javax.swing.JTextField getConditionsTextField()
          Returns conditions' number threshold input text field.
 javax.swing.JRadioButton getDescendingButton()
          Returns descending order option radio button.
 javax.swing.JCheckBox getFilterCheckBox()
          Returns enabling/disabling filtering option check box.
 java.lang.String[] getFilterCriteria()
           
 javax.swing.JLabel getFilterCriteriaLabel()
          Returns filtering criteria label.
 javax.swing.JList getFilterCriteriaList()
          Returns filtering criteria list.
 javax.swing.JPanel getFilterPanel()
          Returns the panel with filtering options.
 javax.swing.JTextField getGenesTextField()
          Returns genes' number threshold input text field.
 BiggestsFrame getMainFrame()
          Returns the frame of the application.
 javax.swing.JTextField getMarkovChainOrderFilterTextField()
          Returns Markov chain order input text field.
 javax.swing.JTextField getMarkovChainOrderSortTextField()
          Returns Markov chain order input text field.
 javax.swing.JTextField getMSRTextField()
          Returns MSR threshold input text field.
 javax.swing.tree.TreePath getSelectionPath()
          Rreturns the selected path in the dataset tree.
 javax.swing.JTextField getSimilarityTextField()
          Returns the similarity threshold input text field.
 javax.swing.JTextField getSizeTextField()
          Returns the size threshold input text field.
 javax.swing.JCheckBox getSortCheckBox()
          Returns enabling/disabling sorting option check box.
 java.lang.String[] getSortCriteria()
           
 javax.swing.JLabel getSortCriteriaLabel()
          Returns the sorting criteria label.
 javax.swing.JList getSortCriteriaList()
          Returns sorting criteria list.
 javax.swing.JPanel getSortPanel()
          Returns the panel with the sorting options.
 void paint(Biclustering biclustering, javax.swing.tree.TreePath selectionPath)
          Paints post-processing panel with post-processing options for a specific biclusters group and tree selection path.
 void paintBasic()
           
 void paintDiscrete()
          Paints post-processing object for biclusters groups with discrete data.
 void paintFloat()
           
 java.lang.String readParameter(java.lang.String parameterToRead)
          Reads a filtering/sorting parameter from its input text field box.
 void setFilterCheckBoxSelected(boolean selected)
          Sets filter check box selected/deselected.
 void setSortCheckBoxSelected(boolean selected)
          Sets sort check box selected/deselected.
 void sortCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
          Handles changes on sort check box selection.
 void sortCriteriaList_valueChanged()
          Handles a selection change on sort criteria list.
 void sortCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
          Handles a selection change on sort criteria list.
 
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, 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

FILTER_TRIVIAL

public static final int FILTER_TRIVIAL
The index of filter trivial biclusters option.

See Also:
Constant Field Values

FILTER_GENES

public static final int FILTER_GENES
The index of 'filter biclusters with less than a given number of genes' option.

See Also:
Constant Field Values

FILTER_CONDITIONS

public static final int FILTER_CONDITIONS
The index of 'filter biclusters with less than a given number of conditions' option.

See Also:
Constant Field Values

FILTER_GENES_CONDITIONS

public static final int FILTER_GENES_CONDITIONS
The index of 'filter biclusters with less than a given number of genes and less than a given number of conditions' option.

See Also:
Constant Field Values

FILTER_ACV

public static final int FILTER_ACV
The index of 'filter biclusters with an ACV value below a given threshold' option.

See Also:
Constant Field Values

FILTER_ARV

public static final int FILTER_ARV
The index of 'filter biclusters with an ARV value below a given threshold' option.

See Also:
Constant Field Values

FILTER_ACV_ARV

public static final int FILTER_ACV_ARV
The index of 'filter trivial biclusters and biclusters with ACV and ARV values below given thresholds' option.

See Also:
Constant Field Values

FILTER_MSR

public static final int FILTER_MSR
The index of 'filter biclusters with an MSR value below a given threshold' option.

See Also:
Constant Field Values

FILTER_SIZE

public static final int FILTER_SIZE
The index of 'filter biclusters smaller than a given size' option.

See Also:
Constant Field Values

FILTER_SIZE_ARV_ACV

public static final int FILTER_SIZE_ARV_ACV
The index of 'filter biclusters smaller than a given size and with ARV and ACV values below given thresholds' option.

See Also:
Constant Field Values

FILTER_CONDITIONS_GENES_ARV_ACV

public static final int FILTER_CONDITIONS_GENES_ARV_ACV
The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV and ACV values below given thresholds' option.

See Also:
Constant Field Values

FILTER_CONDITIONS_GENES_ARV_ACV_MSR

public static final int FILTER_CONDITIONS_GENES_ARV_ACV_MSR
The index of 'filter biclusters with less than given numbers of genes and conditions and with ARV, ACV and MSR values below given thresholds' option.

See Also:
Constant Field Values

FILTER_OVERLAPPING_GENES

public static final int FILTER_OVERLAPPING_GENES
The index of 'filter biclusters with a row similarity below a given threshold' option.

See Also:
Constant Field Values

FILTER_OVERLAPPING_GENES_CONDITIONS

public static final int FILTER_OVERLAPPING_GENES_CONDITIONS
The index of 'filter biclusters with row and column similarities below given thresholds' option.

See Also:
Constant Field Values

FILTER_CONSTANT_PATTERN

public static final int FILTER_CONSTANT_PATTERN
The index of 'filter biclusters with constant pattern' option.

See Also:
Constant Field Values

FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT

public static final int FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT
See Also:
Constant Field Values

FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT

public static final int FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT
See Also:
Constant Field Values

SORT_ACV

public static final int SORT_ACV
The index of 'sort biclusters by their ACV values' option.

See Also:
Constant Field Values

SORT_ARV

public static final int SORT_ARV
The index of 'sort biclusters by their ARV values' option.

See Also:
Constant Field Values

SORT_MSR

public static final int SORT_MSR
The index of 'sort biclusters by their MSR values' option.

See Also:
Constant Field Values

SORT_ARV_ACV_DIFF

public static final int SORT_ARV_ACV_DIFF
The index of 'sort biclusters by the differences between their ARV and ACV values' option.

See Also:
Constant Field Values

SORT_ARV_MSR_DIFF

public static final int SORT_ARV_MSR_DIFF
The index of 'sort biclusters by the differences between their ARV and MSR values' option.

See Also:
Constant Field Values

SORT_GENES

public static final int SORT_GENES
The index of 'sort biclusters by their number of genes' option.

See Also:
Constant Field Values

SORT_CONDITIONS

public static final int SORT_CONDITIONS
The index of 'sort biclusters by their number of conditions' option.

See Also:
Constant Field Values

SORT_SIZE

public static final int SORT_SIZE
The index of 'sort biclusters by their size' option.

See Also:
Constant Field Values

SORT_VARIANCE

public static final int SORT_VARIANCE
The index of 'sort biclusters by their variance' option.

See Also:
Constant Field Values

SORT_BEST_GO_PVALUE

public static final int SORT_BEST_GO_PVALUE
The index of 'sort biclusters by their best GO p-value' option.

See Also:
Constant Field Values

SORT_BEST_GO_BONFERRONI_PVALUE

public static final int SORT_BEST_GO_BONFERRONI_PVALUE
The index of 'sort biclusters by their best GO Bonferroni corrected p-value' option.

See Also:
Constant Field Values

SORT_PATTERN_PVALUE

public static final int SORT_PATTERN_PVALUE
The index of 'sort biclusters by their pattern p-value' option.

See Also:
Constant Field Values

SORT_PATTERN_COLUMNS_PVALUE

public static final int SORT_PATTERN_COLUMNS_PVALUE
The index of 'sort biclusters by the p-value for their pattern with columns' option.

See Also:
Constant Field Values

PARAMETER_GENES

public static final java.lang.String PARAMETER_GENES
Number of genes parameter name.

See Also:
Constant Field Values

PARAMETER_CONDITIONS

public static final java.lang.String PARAMETER_CONDITIONS
Number of conditions parameter name.

See Also:
Constant Field Values

PARAMETER_SIZE

public static final java.lang.String PARAMETER_SIZE
Size parameter name.

See Also:
Constant Field Values

PARAMETER_SIMILARITY

public static final java.lang.String PARAMETER_SIMILARITY
Similarity parameter name.

See Also:
Constant Field Values

PARAMETER_ACV

public static final java.lang.String PARAMETER_ACV
Average column variance parameter name.

See Also:
Constant Field Values

PARAMETER_ARV

public static final java.lang.String PARAMETER_ARV
Average row variance parameter name.

See Also:
Constant Field Values

PARAMETER_MSR

public static final java.lang.String PARAMETER_MSR
Mean squared residue parameter name.

See Also:
Constant Field Values

PARAMETER_MARKOV_FILTER

public static final java.lang.String PARAMETER_MARKOV_FILTER
Markov chain order parameter name.

See Also:
Constant Field Values

PARAMETER_MARKOV_SORT

public static final java.lang.String PARAMETER_MARKOV_SORT
See Also:
Constant Field Values

PARAMETER_PVALUE

public static final java.lang.String PARAMETER_PVALUE
See Also:
Constant Field Values
Constructor Detail

PanelPostProcessing

public PanelPostProcessing(BiggestsFrame frame)
Creates a new post-processing panel.

Parameters:
frame - the main BiggestsFrame
Method Detail

clear

public void clear()
Clears post-processing panel. Removes graphical components and sets biclusters group and selection path to null.


paint

public void paint(Biclustering biclustering,
                  javax.swing.tree.TreePath selectionPath)
Paints post-processing panel with post-processing options for a specific biclusters group and tree selection path.

Parameters:
biclustering - Biclustering the biclusters group to post-process
selectionPath - the TreePath to biclusters group object

paintDiscrete

public void paintDiscrete()
Paints post-processing object for biclusters groups with discrete data.


paintFloat

public void paintFloat()

paintBasic

public void paintBasic()

getFilterCriteria

public java.lang.String[] getFilterCriteria()

getSortCriteria

public java.lang.String[] getSortCriteria()

setFilterCheckBoxSelected

public void setFilterCheckBoxSelected(boolean selected)
Sets filter check box selected/deselected. Also other components are set to enabled/disabled according to the state of filter check box.

Parameters:
selected - boolean true if check box should be turn to selected state, false otherwise

setSortCheckBoxSelected

public void setSortCheckBoxSelected(boolean selected)
Sets sort check box selected/deselected. Also other components are set to enabled/disabled according to the state of sort check box.

Parameters:
selected - boolean true if check box should be turn to selected state, false otherwise

getMainFrame

public BiggestsFrame getMainFrame()
Returns the frame of the application.

Returns:
BiggestsFrame

getACVTextField

public javax.swing.JTextField getACVTextField()
Returns ACV's threshold input text field.

Returns:
JTextField

getARVTextField

public javax.swing.JTextField getARVTextField()
Returns ARV's threshold input text field.

Returns:
JTextField

getAscendingButton

public javax.swing.JRadioButton getAscendingButton()
Returns ascending order option radio button.

Returns:
JTextField

getConditionsTextField

public javax.swing.JTextField getConditionsTextField()
Returns conditions' number threshold input text field.

Returns:
JTextField

getDescendingButton

public javax.swing.JRadioButton getDescendingButton()
Returns descending order option radio button.

Returns:
JTextField

getFilterCheckBox

public javax.swing.JCheckBox getFilterCheckBox()
Returns enabling/disabling filtering option check box.

Returns:
JCheckBox

getFilterCriteriaLabel

public javax.swing.JLabel getFilterCriteriaLabel()
Returns filtering criteria label.

Returns:
JLabel

getFilterCriteriaList

public javax.swing.JList getFilterCriteriaList()
Returns filtering criteria list.

Returns:
JList

getGenesTextField

public javax.swing.JTextField getGenesTextField()
Returns genes' number threshold input text field.

Returns:
JTextField

getMarkovChainOrderFilterTextField

public javax.swing.JTextField getMarkovChainOrderFilterTextField()
Returns Markov chain order input text field.

Returns:
JTextField

getMarkovChainOrderSortTextField

public javax.swing.JTextField getMarkovChainOrderSortTextField()
Returns Markov chain order input text field.

Returns:
JTextField

getMSRTextField

public javax.swing.JTextField getMSRTextField()
Returns MSR threshold input text field.

Returns:
JTextField

getSortCheckBox

public javax.swing.JCheckBox getSortCheckBox()
Returns enabling/disabling sorting option check box.

Returns:
JCheckBox

getSortCriteriaList

public javax.swing.JList getSortCriteriaList()
Returns sorting criteria list.

Returns:
JList

getBiclustering

public Biclustering getBiclustering()
Returns the group of biclusters that is being post-processed.

Returns:
Biclustering

getFilterPanel

public javax.swing.JPanel getFilterPanel()
Returns the panel with filtering options.

Returns:
JPanel

getSimilarityTextField

public javax.swing.JTextField getSimilarityTextField()
Returns the similarity threshold input text field.

Returns:
JTextField

getSelectionPath

public javax.swing.tree.TreePath getSelectionPath()
Rreturns the selected path in the dataset tree.

Returns:
TreePath

getSizeTextField

public javax.swing.JTextField getSizeTextField()
Returns the size threshold input text field.

Returns:
JTextField

getSortCriteriaLabel

public javax.swing.JLabel getSortCriteriaLabel()
Returns the sorting criteria label.

Returns:
JLabel

getSortPanel

public javax.swing.JPanel getSortPanel()
Returns the panel with the sorting options.

Returns:
JPanel

filterCriteriaList_valueChanged

public void filterCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
Handles a selection change on filter criteria list. Displays information about selected filter criteria and text fields for the user to input filtering parameters.

Parameters:
e - the ListSelectionEvent

filterCriteriaList_valueChanged

public void filterCriteriaList_valueChanged()
Handles a selection change on filter criteria list. Displays information about selected filter criteria and text fields for the user to input filtering parameters.

Parameters:
e - the ListSelectionEvent

sortCriteriaList_valueChanged

public void sortCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
Handles a selection change on sort criteria list. Displays information about selected sort criteria and text fields for the user to input sorting parameters.

Parameters:
e - the ListSelectionEvent

sortCriteriaList_valueChanged

public void sortCriteriaList_valueChanged()
Handles a selection change on sort criteria list. Displays information about selected sort criteria and text fields for the user to input sorting parameters.

Parameters:
e - the ListSelectionEvent

filterCheckBox_itemStateChanged

public void filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles changes on filter check box selection.

Parameters:
e - ItemEvent the change on the state of the filter check box

sortCheckBox_itemStateChanged

public void sortCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles changes on sort check box selection.

Parameters:
e - ItemEvent the change on the state of the sort check box

readParameter

public java.lang.String readParameter(java.lang.String parameterToRead)
                               throws java.lang.Exception
Reads a filtering/sorting parameter from its input text field box. Valid parameter names: PanelPostProcessing.PARAMETER_GENES PanelPostProcessing.PARAMETER_CONDITIONS PanelPostProcessing.PARAMETER_ACV PanelPostProcessing.PARAMETER_ARV PanelPostProcessing.PARAMETER_MSR PanelPostProcessing.PARAMETER_SIZE PanelPostProcessing.PARAMETER_SIMILARITY PanelPostProcessing.PARAMETER_MARKOV

Specified by:
readParameter in class PanelBasicIOValidation
Parameters:
parameterToRead - String the name of the parameter to read
Returns:
String the parameter read from the input text field
Throws:
java.lang.Exception - if parameter could not be read
See Also:
PanelBasicIOValidation.readParameter(String parameterToRead)

applyButton_actionPerformed

public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
Applies the post-processing criteria to the current biclusters group.

Parameters:
e - ActionEvent the click on apply button

copyFunctionResultFilesForPostProcessedBiclusterGroup

public void copyFunctionResultFilesForPostProcessedBiclusterGroup(javax.swing.tree.TreePath selectionPath)
                                                           throws java.lang.Exception
Copies the function result files for a post-processed biclusters' group.

Parameters:
bic - Biclustering the post-processed group of biclusters to add to the dataset tree
infoStrings - the ArrayList with the set of information strings
infoStyles - the ArrayList with the set of formatting styles for infoStrings
selectionPath - the dataset tree selected TreePath
Throws:
java.lang.Exception

addPostProcessedBiclusterGroupToTree

public void addPostProcessedBiclusterGroupToTree(Biclustering bic,
                                                 java.util.ArrayList<java.lang.String> infoStrings,
                                                 java.util.ArrayList<java.lang.String> infoStyles,
                                                 javax.swing.tree.TreePath selectionPath)
                                          throws java.lang.Exception
Adds a post-processed biclustering to the dataset tree.

Parameters:
bic - Biclustering the post-processed bicluster group to add to the dataset tree
infoStrings - ArrayList the set of information strings
infoStyles - ArrayList the set of styles for the information strings
selectionPath - the selected TreePath in the dataset tree, which contains the biclusters' group from which this post-processed group of biclusters was derived
Throws:
java.lang.Exception

displayFilteringErrorMessage

public void displayFilteringErrorMessage(boolean sort)
Displays a message when some problem occurs while performing filtering operations.

Parameters:
sort - the boolean value that states if sort option was enabled (true) or not (false)