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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelBasicIOValidation
biggests.gui.PanelPostProcessing
public class PanelPostProcessing
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.
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 |
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 |
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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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PanelPostProcessing(BiggestsFrame frame)
Creates a new post-processing panel. |
Method Summary | |
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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 |
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readParameterDouble, readParameterDouble, readParameterDouble, readParameterFloat, readParameterFloat, readParameterFloat, readParameterInteger, readParameterInteger, readParameterInteger |
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 FILTER_TRIVIAL
public static final int FILTER_GENES
public static final int FILTER_CONDITIONS
public static final int FILTER_GENES_CONDITIONS
public static final int FILTER_ACV
public static final int FILTER_ARV
public static final int FILTER_ACV_ARV
public static final int FILTER_MSR
public static final int FILTER_SIZE
public static final int FILTER_SIZE_ARV_ACV
public static final int FILTER_CONDITIONS_GENES_ARV_ACV
public static final int FILTER_CONDITIONS_GENES_ARV_ACV_MSR
public static final int FILTER_OVERLAPPING_GENES
public static final int FILTER_OVERLAPPING_GENES_CONDITIONS
public static final int FILTER_CONSTANT_PATTERN
public static final int FILTER_PATTERN_PVALUE_NOT_SIGNIFICANT
public static final int FILTER_PATTERN_COLUMNS_PVALUE_NOT_SIGNIFICANT
public static final int SORT_ACV
public static final int SORT_ARV
public static final int SORT_MSR
public static final int SORT_ARV_ACV_DIFF
public static final int SORT_ARV_MSR_DIFF
public static final int SORT_GENES
public static final int SORT_CONDITIONS
public static final int SORT_SIZE
public static final int SORT_VARIANCE
public static final int SORT_BEST_GO_PVALUE
public static final int SORT_BEST_GO_BONFERRONI_PVALUE
public static final int SORT_PATTERN_PVALUE
public static final int SORT_PATTERN_COLUMNS_PVALUE
public static final java.lang.String PARAMETER_GENES
public static final java.lang.String PARAMETER_CONDITIONS
public static final java.lang.String PARAMETER_SIZE
public static final java.lang.String PARAMETER_SIMILARITY
public static final java.lang.String PARAMETER_ACV
public static final java.lang.String PARAMETER_ARV
public static final java.lang.String PARAMETER_MSR
public static final java.lang.String PARAMETER_MARKOV_FILTER
public static final java.lang.String PARAMETER_MARKOV_SORT
public static final java.lang.String PARAMETER_PVALUE
Constructor Detail |
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public PanelPostProcessing(BiggestsFrame frame)
frame
- the main BiggestsFrame
Method Detail |
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public void clear()
public void paint(Biclustering biclustering, javax.swing.tree.TreePath selectionPath)
biclustering
- Biclustering
the biclusters group
to post-processselectionPath
- the TreePath
to biclusters group objectpublic void paintDiscrete()
public void paintFloat()
public void paintBasic()
public java.lang.String[] getFilterCriteria()
public java.lang.String[] getSortCriteria()
public void setFilterCheckBoxSelected(boolean selected)
selected
- boolean
true
if check
box should be turn to selected state, false
otherwisepublic void setSortCheckBoxSelected(boolean selected)
selected
- boolean
true
if check
box should be turn to selected state, false
otherwisepublic BiggestsFrame getMainFrame()
public javax.swing.JTextField getACVTextField()
public javax.swing.JTextField getARVTextField()
public javax.swing.JRadioButton getAscendingButton()
public javax.swing.JTextField getConditionsTextField()
public javax.swing.JRadioButton getDescendingButton()
public javax.swing.JCheckBox getFilterCheckBox()
public javax.swing.JLabel getFilterCriteriaLabel()
public javax.swing.JList getFilterCriteriaList()
public javax.swing.JTextField getGenesTextField()
public javax.swing.JTextField getMarkovChainOrderFilterTextField()
public javax.swing.JTextField getMarkovChainOrderSortTextField()
public javax.swing.JTextField getMSRTextField()
public javax.swing.JCheckBox getSortCheckBox()
public javax.swing.JList getSortCriteriaList()
public Biclustering getBiclustering()
public javax.swing.JPanel getFilterPanel()
public javax.swing.JTextField getSimilarityTextField()
public javax.swing.tree.TreePath getSelectionPath()
public javax.swing.JTextField getSizeTextField()
public javax.swing.JLabel getSortCriteriaLabel()
public javax.swing.JPanel getSortPanel()
public void filterCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
e
- the ListSelectionEvent
public void filterCriteriaList_valueChanged()
e
- the ListSelectionEvent
public void sortCriteriaList_valueChanged(javax.swing.event.ListSelectionEvent e)
e
- the ListSelectionEvent
public void sortCriteriaList_valueChanged()
e
- the ListSelectionEvent
public void filterCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e
- ItemEvent
the change on the state of the filter check boxpublic void sortCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e
- ItemEvent
the change on the state of the sort check boxpublic java.lang.String readParameter(java.lang.String parameterToRead) throws java.lang.Exception
readParameter
in class PanelBasicIOValidation
parameterToRead
- String
the name of the
parameter to read
java.lang.Exception
- if parameter could not be readPanelBasicIOValidation.readParameter(String parameterToRead)
public void applyButton_actionPerformed(java.awt.event.ActionEvent e)
e
- ActionEvent
the click on apply buttonpublic void copyFunctionResultFilesForPostProcessedBiclusterGroup(javax.swing.tree.TreePath selectionPath) throws java.lang.Exception
bic
- Biclustering
the post-processed
group of biclusters to add to the dataset treeinfoStrings
- the ArrayList
with the set of
information stringsinfoStyles
- the ArrayList
with the set of
formatting styles for infoStrings
selectionPath
- the dataset tree selected TreePath
java.lang.Exception
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
bic
- Biclustering
the post-processed
bicluster group to add to the dataset treeinfoStrings
- ArrayList
the set of information stringsinfoStyles
- ArrayList
the set of styles for the
information stringsselectionPath
- the selected TreePath
in the
dataset tree, which contains the biclusters' group from which
this post-processed group of biclusters was derived
java.lang.Exception
public void displayFilteringErrorMessage(boolean sort)
sort
- the boolean
value that states if sort
option was enabled (true
) or not (false
)
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