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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
biggests.gui.PanelBasicIOValidation
biggests.gui.PanelBiclustering
public class PanelBiclustering
Title: Biclustering Panel
Description: Displays available biclustering techniques and allows for setting their corresponding parameters and apply them to the gene expression data.
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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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static java.lang.String |
ALPHA
Name of the 'alpha' parameter (CC-TSB-biclustering). |
static java.lang.String |
CC_TSB_BICLUSTERING
CC-TSB-Biclustering algorithm name. |
static java.lang.String |
CCC_BICLUSTERING
CCC-Biclustering algorithm name. |
static java.lang.String |
DELTA
Name of the 'delta' parameter (CC-TSB-biclustering). |
static java.lang.String |
E_CCC_BICLUSTERING
e-CCC-Biclustering algorithm name. |
static java.lang.String |
MAX_ITERATIONS
Name of the 'maximum number of iterations' parameter (CC-TSB-biclustering). |
static java.lang.String |
MAX_TIME_LAG
Maximum time lag. |
static java.lang.String |
NEIGHBORS
Name of the 'neighbors' parameter (e-CCC-Biclustering). |
static java.lang.String |
NUMBER_OF_BICLUSTERS
Name of the 'number of biclusters' parameter (CC-TSB-biclustering). |
static java.lang.String |
NUMBER_OF_ERRORS
Name of the 'number of errors' parameter (e-CCC-Biclustering). |
static java.lang.String |
SHIFTS
Name of the 'shifts' parameter for CCC-Biclustering and e-CCC-Biclustering algorithms. |
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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PanelBiclustering(BiggestsFrame frame)
Creates a new biclustering panel, with biclustering algorithms options. |
Method Summary | |
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void |
addBiclusterGroupToDatasetTree(smadeira.biclustering.Biclustering biclustering,
javax.swing.tree.TreePath selectionPath,
smadeira.ontologizer.GOFrontEnd go)
Adds a bicluster group to the dataset tree. |
void |
algorithmsList_valueChanged(javax.swing.event.ListSelectionEvent e)
Handles a selection change in algorithms' list. |
void |
allowMissingsButton_mouseClicked(java.awt.event.MouseEvent e)
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void |
applyBiclusteringAlgorithm()
Applies biclustering algorithm. |
void |
applyButton_actionPerformed(java.awt.event.ActionEvent e)
Handles the mouse event fired when the user clicks the apply button. |
void |
applyCCCBiclusteringAlgorithm()
Applies CCC-Biclustering algorithm. |
void |
applyCCTSBBiclusteringAlgorithm()
Applies CC-TSB-biclustering algorithm. |
void |
applyECCCBiclusteringAlgorithm()
Applies e-CCC-Biclustering algorithm. |
void |
clear()
Clears this panel's components and other attributes that are no longer needed. |
void |
geneShiftsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles a change in gene shifts check box state. |
javax.swing.JButton |
getApplyButton()
Returns apply button. |
javax.swing.JLabel |
getBiclusteringAlgorithmsLabel()
Returns biclustering algorithms label. |
javax.swing.JPanel |
getBiclusteringPanel()
Returns biclustering panel. |
javax.swing.JLabel |
getErrorsNumberLabel()
Label for the number of errors allowed in e-CCC-Biclustering algorithm. |
javax.swing.JTextField |
getErrorsNumberTextField()
Text field for the input of the number of errors allowed in e-CCC-Biclustering algorithm. |
smadeira.biclustering.NodeObjectInterface |
getExpressionMatrix()
Returns the node object which contains the original, preprocessed or discretized matrix on which biclustering algorithm will be performed. |
javax.swing.JCheckBox |
getGeneShiftsCheckBox()
Returns gene shifts for CCC-Biclustering and e-CCC-Biclustering algorithms check box. |
BiggestsFrame |
getMainFrame()
Returns the application's main frame. |
javax.swing.JLabel |
getNeighborsECCCLabel()
Label for the number of neighbors on e-CCC-Biclustering algorithm. |
javax.swing.JTextField |
getNeighborsECCCTextField()
Text field for the input of number of neighbors for e-CCC-Biclustering algorithm. |
javax.swing.JCheckBox |
getRestrictedErrorsECCCCheckBox()
Returns restricted errors for e-CCC-Biclustering algorithm check box. |
javax.swing.tree.TreePath |
getSelectionPath()
Returns the dataset tree selected path which corresponds to the path of the dataset which in turn leads to the node with the matrix on which biclustering algorithm will be performed. |
javax.swing.JLabel |
getShiftsLabel()
Returns the label for number of shifts for CCC-Biclustering and e-CCC-Biclustering algorithms. |
javax.swing.JTextField |
getShiftsTextField()
Returns the text field for the input of CCC-Biclustering and e-CCC-Biclustering algorithms number of shifts. |
javax.swing.SpringLayout |
getSpringLayout()
Returns the layout of this panel. |
void |
paint(smadeira.biclustering.AbstractExpressionMatrix expressionMatrix,
javax.swing.tree.TreePath selectionPath)
Paints this biclustering panel with options to perform biclustering and function analysis on AbstractExpressionMatrix objects
(ExpressionMatrix and
PreProcessedExpressionMatrix ). |
void |
paint(smadeira.biclustering.DiscretizedExpressionMatrix discretizedExpressionMatrix,
javax.swing.tree.TreePath selectionPath)
Paints this biclustering panel with options to perform biclustering on the discretizedExpressionMatrix and options to
perform function analysis. |
void |
paintBiclusteringAlgorithmPanelWithCCC()
Paints biclustering algorithm panel with CCC-Biclustering algorithm. |
void |
paintBiclusteringAlgorithmPanelWithCCTSB()
Paints biclustering algorithm panel with CC-TSB-Biclustering algorithm. |
void |
paintBiclusteringAlgorithmPanelWithECCC()
Paints biclustering algorithm panel with E-CCC-Biclustering algorithm. |
java.lang.String |
readParameter(java.lang.String parameterToRead)
Reads a parameter from its input text field box. |
int |
readParameterInteger(int min,
int max,
java.lang.String parameterToRead)
Reads parameterToRead entered by the user, converts
it to an integer value and checks if the resulting value is in
[min , max ] range. |
void |
restrictedErrorsECCCCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
Handles the item state changed event fired when the user selects/deselects restricted errors for e-CCC-Biclustering algorithm check box. |
void |
setGeneShiftsCheckBoxSelected(boolean selected)
Sets gene shifts check box selected/deselected, along with the corresponding enabling/disabling of shifts label and input text field. |
void |
setRestrictedErrorsECCCCheckBoxSelected(boolean selected)
Sets restricted errors for e-CCC-Biclustering algorithm check box selected/deselected, along with the corresponding enabling/disabling of neighbors label and text field. |
void |
setStringsAndStyles(smadeira.biclustering.Biclustering biclustering)
Sets strings and styles attributes according to the type and parameters of biclustering object. |
void |
setStringsAndStylesCCC(smadeira.biclustering.CCC_Biclustering biclustering)
Sets strings and styles attributes according to the parameters of the CCC_Biclustering object. |
void |
setStringsAndStylesCCTSB(smadeira.biclustering.CC_TSB_Biclustering biclustering)
Sets strings and styles attributes according to the parameters of the CC_TSB_Biclustering object. |
void |
setStringsAndStylesECCC(smadeira.biclustering.E_CCC_Biclustering biclustering)
Sets strings and styles attributes according to the parameters of the E_CCC_Biclustering object. |
void |
signChangesCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
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void |
timeLagsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
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Methods inherited from class biggests.gui.PanelBasicIOValidation |
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readParameterDouble, readParameterDouble, readParameterDouble, readParameterFloat, readParameterFloat, readParameterFloat, 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, 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 |
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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 java.lang.String NUMBER_OF_ERRORS
public static final java.lang.String SHIFTS
public static final java.lang.String NEIGHBORS
public static final java.lang.String DELTA
public static final java.lang.String ALPHA
public static final java.lang.String NUMBER_OF_BICLUSTERS
public static final java.lang.String MAX_ITERATIONS
public static final java.lang.String MAX_TIME_LAG
public static final java.lang.String CCC_BICLUSTERING
public static final java.lang.String E_CCC_BICLUSTERING
public static final java.lang.String CC_TSB_BICLUSTERING
Constructor Detail |
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public PanelBiclustering(BiggestsFrame frame)
frame
- the main BiggestsFrame
, in which this
panel is being displayedMethod Detail |
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public void paintBiclusteringAlgorithmPanelWithCCC()
public void paintBiclusteringAlgorithmPanelWithECCC()
public void paintBiclusteringAlgorithmPanelWithCCTSB()
public void paint(smadeira.biclustering.DiscretizedExpressionMatrix discretizedExpressionMatrix, javax.swing.tree.TreePath selectionPath)
discretizedExpressionMatrix
and options to
perform function analysis.
discretizedExpressionMatrix
- the DiscretizedExpressionMatrix
to which biclustering algorithm and function analysis will
be applied.selectionPath
- the TreePath
selected on the dataset
tree; corresponds to the node that contains the
discretizedExpressionMatrix
public void paint(smadeira.biclustering.AbstractExpressionMatrix expressionMatrix, javax.swing.tree.TreePath selectionPath)
AbstractExpressionMatrix
objects
(ExpressionMatrix
and
PreProcessedExpressionMatrix
).
expressionMatrix
- the AbstractExpressionMatrix
to which biclustering algorithm and function analysis will
be appliedselectionPath
- the TreePath
selected on the dataset
tree; corresponds to the node that contains the
expressionMatrix
public void clear()
public void setGeneShiftsCheckBoxSelected(boolean selected)
selected
- boolean
true
if
gene shifts check box should be selected and false
otherwisepublic void setRestrictedErrorsECCCCheckBoxSelected(boolean selected)
selected
- boolean
value true
if
the check box should get selected; false
otherwisepublic void restrictedErrorsECCCCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e
- the ItemEvent
fired when the user
selects/deselects restricted errors for e-CCC-Biclustering
algorithm check boxpublic void applyButton_actionPerformed(java.awt.event.ActionEvent e)
e
- the ActionEvent
fired when the user clicks
the apply buttonpublic void applyBiclusteringAlgorithm()
public void applyCCTSBBiclusteringAlgorithm() throws java.lang.Exception
java.lang.Exception
public void applyCCCBiclusteringAlgorithm() throws java.lang.Exception
java.lang.Exception
public void applyECCCBiclusteringAlgorithm() throws java.lang.Exception
java.lang.Exception
public void setStringsAndStyles(smadeira.biclustering.Biclustering biclustering)
biclustering
object.
biclustering
- Biclustering
public void setStringsAndStylesCCTSB(smadeira.biclustering.CC_TSB_Biclustering biclustering)
CC_TSB_Biclustering
object.
biclustering
- CC_TSB_Biclustering
public void setStringsAndStylesCCC(smadeira.biclustering.CCC_Biclustering biclustering)
CCC_Biclustering
object.
biclustering
- CCC_Biclustering
public void setStringsAndStylesECCC(smadeira.biclustering.E_CCC_Biclustering biclustering)
E_CCC_Biclustering
object.
biclustering
- E_CCC_Biclustering
public void addBiclusterGroupToDatasetTree(smadeira.biclustering.Biclustering biclustering, javax.swing.tree.TreePath selectionPath, smadeira.ontologizer.GOFrontEnd go)
biclustering
- Biclustering
- biclusters' groupselectionPath
- TreePathgo
- the GOFrontEnd
for the biclusters' grouppublic int readParameterInteger(int min, int max, java.lang.String parameterToRead) throws java.lang.Exception
PanelBasicIOValidation
parameterToRead
entered by the user, converts
it to an integer value and checks if the resulting value is in
[min
, max
] range. Displays an error
message if parameter could not be read, could not be converted
to integer or if it's under the minimum (min
) or
over the maximum (max
) given thresholds. Also
throws an exception in these cases.
readParameterInteger
in class PanelBasicIOValidation
min
- int
minimum thresholdmax
- int
maximum thresholdparameterToRead
- String
the name of the parameter
to read
java.lang.Exception
- if parameter could not be read, could not be
converted to an integer value or if its under the minimum
or over the maximum valuepublic 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 BiggestsFrame getMainFrame()
BiggestsFrame
public smadeira.biclustering.NodeObjectInterface getExpressionMatrix()
NodeObjectInterface
which contains a gene
expression matrix (real valued or discretized)public javax.swing.tree.TreePath getSelectionPath()
TreePath
selected in the dataset treepublic javax.swing.SpringLayout getSpringLayout()
SpringLayout
public javax.swing.JLabel getBiclusteringAlgorithmsLabel()
JLabel
public javax.swing.JCheckBox getGeneShiftsCheckBox()
JCheckBox
public javax.swing.JLabel getShiftsLabel()
JLabel
for number of shifts for
CCC-Biclustering and e-CCC-Biclustering algorithmpublic javax.swing.JTextField getShiftsTextField()
JTextField
for the input of
CCC-Biclustering and e-CCC-Biclustering algorithms
number of shiftspublic javax.swing.JCheckBox getRestrictedErrorsECCCCheckBox()
JCheckBox
public javax.swing.JLabel getNeighborsECCCLabel()
JLabel
for the number of neighbors on
e-CCC-Biclustering algorithmpublic javax.swing.JTextField getNeighborsECCCTextField()
JTextField
for the input of number
of neighbors for e-CCC-Biclustering algorithmpublic javax.swing.JLabel getErrorsNumberLabel()
JLabel
for the number of errors allowed
in e-CCC-Biclustering algorithmpublic javax.swing.JTextField getErrorsNumberTextField()
JTextField
for the input of the number
of errors allowed in e-CCC-Biclustering algorithmpublic javax.swing.JPanel getBiclusteringPanel()
public javax.swing.JButton getApplyButton()
JButton
public void algorithmsList_valueChanged(javax.swing.event.ListSelectionEvent e)
e
- ListSelectionEvent
public void geneShiftsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
e
- ItemEvent
public void signChangesCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
public void timeLagsCheckBox_itemStateChanged(java.awt.event.ItemEvent e)
public void allowMissingsButton_mouseClicked(java.awt.event.MouseEvent e)
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