biggests.gui
Class BiggestsFrame

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Frame
                  extended by javax.swing.JFrame
                      extended by biggests.gui.BiggestsFrame
All Implemented Interfaces:
java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class BiggestsFrame
extends javax.swing.JFrame
implements java.awt.event.ActionListener

Title: BiGGEsTS Frame

Description: The main frame of the application.

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.JFrame
javax.swing.JFrame.AccessibleJFrame
 
Nested classes/interfaces inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
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 SCROLL_BAR_INCREMENT
           
 
Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR
 
Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
 
Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
BiggestsFrame()
          Application's main frame constructor.
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent actionEvent)
           
 void clearAllPanels()
          Clears all application's panels, so that they contain no information.
 void closeOperation(boolean saveWithCancelOption)
          Close operation.
 void colorsRedGreen_actionPerformed(java.awt.event.ActionEvent actionEvent)
           
 void colorsYellowBlue_actionPerformed(java.awt.event.ActionEvent actionEvent)
           
protected  void finishTaskInLabelContext(java.lang.String message)
           
 java.lang.String getGeneAssociationFilesURL()
          Returns gene association files URL.
 java.lang.String getGeneOntologyFilesURL()
          Returns gene ontology files URL.
 javax.swing.JMenu getHelp()
          Returns the about menu.
 javax.swing.JTextField getLabelContext()
          Returns the context label, which displays tips about functionality options to user.
 javax.swing.JMenuBar getMenu()
          Returns the application's menu bar.
 PanelExpression getPanelAnalyzingExpressionAllTimePoints()
          Returns the expression analysis by all time points chart panel.
 PanelAnalyzingFunctionSignificanceGraph getPanelAnalyzingFunctionSignificanceGraph()
          Returns the function analysis - significance graph panel.
 PanelAnalyzingFunctionTable getPanelAnalyzingFunctionTable()
          Returns the function analysis - table panel.
 PanelAnalyzingMatrixTables getPanelAnalyzingMatrixColors()
          Returns the matrix analysis by colors panel.
 PanelAnalyzingMatrixDendrogram getPanelAnalyzingMatrixDendrogram()
          Returns the matrix analysis by dendrogram panel.
 PanelAnalyzingMatrixTables getPanelAnalyzingMatrixSymbols()
          Returns the matrix analysis by symbols panel.
 PanelAnalyzingMatrixTables getPanelAnalyzingMatrixValues()
          Returns the matrix analysis by values panel.
 PanelBiclustering getPanelBiclustering()
          Returns biclustering panel.
 javax.swing.JPanel getPanelContent()
          Returns this frames' content panel.
 PanelExpression getPanelExpressionBiclusterPattern()
          Returns the expression analysis by bicluster pattern chart panel.
 PanelExpression getPanelExpressionBiclusterTimePoints()
          Returns the expression analysis by bicluster time points chart panel.
 PanelLoading getPanelLoading()
          Returns the loading panel.
 PanelPreProcessing getPanelPreProcessing()
          Returns preprocessing panel.
 javax.swing.JPanel getPanelRight()
          Returns the panel on the right, which holds the tabs and visualization panels.
 java.lang.String[] getPathsToFolders()
          Returns the paths to function results, gene ontology files and sessions.
 java.lang.String getPathToDatasets()
          Returns the path to the directory with dataset files.
 java.lang.String getPathToDOT()
          Returns the path to dot binary file.
 java.lang.String getPathToFunctionResults()
          Returns the path to function results' folder/directory.
 java.lang.String getPathToGO_Files()
          Returns the path to gene ontology files folder/directory.
 java.lang.String getPathToSessions()
          Returns the path to stored session files folder/directory.
 javax.swing.JScrollPane getScrollAnalyzingExpressionAllTimePoints()
          Returns the scroll pane which holds the expression analysis - all time points chart panel.
 javax.swing.JScrollPane getScrollAnalyzingExpressionBiclusterPattern()
          Returns the scroll pane which holds the expression analysis - bicluster pattern chart panel.
 javax.swing.JScrollPane getScrollAnalyzingExpressionBiclusterTimePoints()
          Returns the scroll pane which holds the expression analysis - bicluster time points chart panel.
 javax.swing.JScrollPane getScrollAnalyzingFunctionSignificanceGraph()
          Returns the scroll pane which holds the function analysis - significance graph panel.
 javax.swing.JScrollPane getScrollAnalyzingFunctionTable()
          Returns the scroll pane which holds the function analysis - table of functions panel.
 javax.swing.JScrollPane getScrollAnalyzingMatrixColors()
          Returns the scroll pane which holds the matrix analysis by colors panel.
 javax.swing.JScrollPane getScrollAnalyzingMatrixSymbols()
          Returns the scroll pane which holds the matrix analysis by symbols panel.
 javax.swing.JScrollPane getScrollAnalyzingMatrixValues()
          Returns the scroll pane which holds the matrix analysis by values panel.
 javax.swing.JScrollPane getScrollBiclustering()
          Returns the scroll pane which scrolls biclustering panel.
 javax.swing.JScrollPane getScrollInfo()
          Returns the scroll pane which scrolls information text pane.
 javax.swing.JScrollPane getScrollLoading()
          Returns the scroll pane which scrolls loading panel.
 javax.swing.JScrollPane getScrollPreProcessing()
          Returns the scroll pane which scrolls preprocessing panel.
 javax.swing.JScrollPane getScrollTree()
          Returns the scroll pane which scrolls the dataset tree.
 javax.swing.JSplitPane getSplitLeftRight()
          Returns the left-right split pane.
 javax.swing.JSplitPane getSplitTopBottom()
          Returns the top-bottom split pane.
 javax.swing.JTabbedPane getTabbedPane()
          Returns the main tabbed pane.
 javax.swing.JTabbedPane getTabbedPaneAnalyzing()
          Returns the analysis tabbed pane.
 javax.swing.JTabbedPane getTabbedPaneAnalyzingExpression()
          Returns the expression analysis tabbed pane.
 javax.swing.JTabbedPane getTabbedPaneAnalyzingFunction()
          Returns the function analysis tabbed pane.
 javax.swing.JTabbedPane getTabbedPaneAnalyzingMatrix()
          Returns the matrix analysis tabbed pane.
 javax.swing.JTextPane getTextPaneInfo()
          Returns the information text pane, which displays informations about the selected datasets, matrices or biclusters in the tree.
 DatasetTree getTree()
          Returns the dataset tree object.
 void helpAbout_actionPerformed(java.awt.event.ActionEvent actionEvent)
          Handles the event fired when the user clicks Help -> About item menu.
 boolean saveCurrentSession(boolean cancelOption)
          Saves current session to a zip archive file.
 void sessionExit_actionPerformed(java.awt.event.ActionEvent actionEvent)
          Handles the event fired when the user clicks Session -> Exit item menu.
 void sessionLoadDataset_actionPerformed(java.awt.event.ActionEvent actionEvent)
          Handles the event fired when the user clicks the menu item Session -> Load Dataset.
 void sessionLoadSession_actionPerformed(java.awt.event.ActionEvent actionEvent)
          Handles the event fired when the user clicks the menu item Session -> Load Session.
 void sessionSaveSession_actionPerformed(java.awt.event.ActionEvent actionEvent)
          Handles the event fired when the user clicks the menu item Session -> Save Session.
static void setPathToDOT(java.lang.String path)
           
 void setTabbedPaneAnalyzingEnabledTabs(boolean matrix, boolean expression, boolean function)
          Enables/disables tabs on the analyzing tabbed pane.
 void setTabbedPaneAnalyzingMatrixEnabledTabs(boolean values, boolean colors, boolean symbols, boolean dendrogram)
          Enables/disables tabs on the matrix analysis tabbed pane.
 void setTabbedPaneEnabledTabs(boolean loading, boolean preprocessing, boolean biclustering, boolean analyzing, boolean postprocessing, boolean comparing)
          Enables/disables tabs on the main tabbed pane.
 void setTree(DatasetTree t)
          Sets a new dataset tree.
protected  void startTaskInLabelContext(java.lang.String message)
           
 void this_componentResized(java.awt.event.ComponentEvent e)
          Handles the event fired when the user resizes the main window.
 void this_windowClosing(java.awt.event.WindowEvent e)
          Handles the event fired when the main window of the application is closing.
 void this_windowStateChanged(java.awt.event.WindowEvent e)
          Handles the event fired when the state of the main window changes.
 void tree_valueChanged(javax.swing.event.TreeSelectionEvent e)
          Handles a change in dataset tree's selection.
 
Methods inherited from class javax.swing.JFrame
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update
 
Methods inherited from class java.awt.Frame
addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, toBack, toFront
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

SCROLL_BAR_INCREMENT

public static int SCROLL_BAR_INCREMENT
Constructor Detail

BiggestsFrame

public BiggestsFrame()
Application's main frame constructor.

Method Detail

setPathToDOT

public static void setPathToDOT(java.lang.String path)

getHelp

public javax.swing.JMenu getHelp()
Returns the about menu.

Returns:
JMenu the application's about menu

getLabelContext

public javax.swing.JTextField getLabelContext()
Returns the context label, which displays tips about functionality options to user.

Returns:
JTextField the context label

getMenu

public javax.swing.JMenuBar getMenu()
Returns the application's menu bar.

Returns:
JMenuBar the application's menu bar

getPanelAnalyzingExpressionAllTimePoints

public PanelExpression getPanelAnalyzingExpressionAllTimePoints()
Returns the expression analysis by all time points chart panel.

Returns:
PanelExpression the expression analysis by all time points panel

getPanelExpressionBiclusterPattern

public PanelExpression getPanelExpressionBiclusterPattern()
Returns the expression analysis by bicluster pattern chart panel.

Returns:
PanelExpression the expression analysis by bicluster pattern

getPanelExpressionBiclusterTimePoints

public PanelExpression getPanelExpressionBiclusterTimePoints()
Returns the expression analysis by bicluster time points chart panel.

Returns:
PanelExpression the expression analysis by bicluster time points chart panel

getPanelAnalyzingFunctionSignificanceGraph

public PanelAnalyzingFunctionSignificanceGraph getPanelAnalyzingFunctionSignificanceGraph()
Returns the function analysis - significance graph panel.

Returns:
PanelAnalyzingFunctionSignificanceGraph

getPanelAnalyzingFunctionTable

public PanelAnalyzingFunctionTable getPanelAnalyzingFunctionTable()
Returns the function analysis - table panel.

Returns:
PanelAnalyzingFunctionTable

getPanelAnalyzingMatrixColors

public PanelAnalyzingMatrixTables getPanelAnalyzingMatrixColors()
Returns the matrix analysis by colors panel.

Returns:
PanelAnalyzingMatrixTables the matrix analysis by colors panel

getPanelAnalyzingMatrixSymbols

public PanelAnalyzingMatrixTables getPanelAnalyzingMatrixSymbols()
Returns the matrix analysis by symbols panel.

Returns:
PanelAnalyzingMatrixTables the matrix analysis by symbols panel

getPanelAnalyzingMatrixValues

public PanelAnalyzingMatrixTables getPanelAnalyzingMatrixValues()
Returns the matrix analysis by values panel.

Returns:
PanelAnalyzingMatrixTables the matrix analysis by values panel

getPanelAnalyzingMatrixDendrogram

public PanelAnalyzingMatrixDendrogram getPanelAnalyzingMatrixDendrogram()
Returns the matrix analysis by dendrogram panel.

Returns:
PanelAnalyzingMatrixDendrogram

getPanelBiclustering

public PanelBiclustering getPanelBiclustering()
Returns biclustering panel.

Returns:
PanelBiclustering

getPanelContent

public javax.swing.JPanel getPanelContent()
Returns this frames' content panel.

Returns:
this frame's content JPanel

getPanelLoading

public PanelLoading getPanelLoading()
Returns the loading panel.

Returns:
PanelLoading

getPanelPreProcessing

public PanelPreProcessing getPanelPreProcessing()
Returns preprocessing panel.

Returns:
PanelPreProcessing

getPanelRight

public javax.swing.JPanel getPanelRight()
Returns the panel on the right, which holds the tabs and visualization panels.

Returns:
the JPanel on the right

getTextPaneInfo

public javax.swing.JTextPane getTextPaneInfo()
Returns the information text pane, which displays informations about the selected datasets, matrices or biclusters in the tree.

Returns:
JTextPane the information text pane

getTree

public DatasetTree getTree()
Returns the dataset tree object.

Returns:
DatasetTree the dataset tree

getPathToFunctionResults

public java.lang.String getPathToFunctionResults()
Returns the path to function results' folder/directory.

Returns:
the String path

getPathToGO_Files

public java.lang.String getPathToGO_Files()
Returns the path to gene ontology files folder/directory.

Returns:
String path

getPathToSessions

public java.lang.String getPathToSessions()
Returns the path to stored session files folder/directory.

Returns:
String path

getPathToDatasets

public java.lang.String getPathToDatasets()
Returns the path to the directory with dataset files.

Returns:
String path

getPathsToFolders

public java.lang.String[] getPathsToFolders()
Returns the paths to function results, gene ontology files and sessions.

Returns:
the String[] array with paths to function results, gene ontology files and sessions

getPathToDOT

public java.lang.String getPathToDOT()
Returns the path to dot binary file.

Returns:
String the path to dot binary file

getGeneOntologyFilesURL

public java.lang.String getGeneOntologyFilesURL()
Returns gene ontology files URL.

Returns:
String the gene ontology files URL

getGeneAssociationFilesURL

public java.lang.String getGeneAssociationFilesURL()
Returns gene association files URL.

Returns:
String the gene association files URL

getScrollAnalyzingExpressionAllTimePoints

public javax.swing.JScrollPane getScrollAnalyzingExpressionAllTimePoints()
Returns the scroll pane which holds the expression analysis - all time points chart panel.

Returns:
the JScrollPane which holds the expression analysis - all time points chart panel

getScrollAnalyzingExpressionBiclusterPattern

public javax.swing.JScrollPane getScrollAnalyzingExpressionBiclusterPattern()
Returns the scroll pane which holds the expression analysis - bicluster pattern chart panel.

Returns:
the JScrollPane which holds the expression analysis - bicluster pattern chart panel

getScrollAnalyzingExpressionBiclusterTimePoints

public javax.swing.JScrollPane getScrollAnalyzingExpressionBiclusterTimePoints()
Returns the scroll pane which holds the expression analysis - bicluster time points chart panel.

Returns:
the JScrollPane which holds the expression analysis - bicluster time points chart panel

getScrollAnalyzingFunctionSignificanceGraph

public javax.swing.JScrollPane getScrollAnalyzingFunctionSignificanceGraph()
Returns the scroll pane which holds the function analysis - significance graph panel.

Returns:
the JScrollPane which holds the function analysis - significance graph panel

getScrollAnalyzingFunctionTable

public javax.swing.JScrollPane getScrollAnalyzingFunctionTable()
Returns the scroll pane which holds the function analysis - table of functions panel.

Returns:
the JScrollPane which holds the function analysis - table of functions panel

getScrollAnalyzingMatrixColors

public javax.swing.JScrollPane getScrollAnalyzingMatrixColors()
Returns the scroll pane which holds the matrix analysis by colors panel.

Returns:
the JScrollPane which holds the matrix analysis by colors panel

getScrollAnalyzingMatrixSymbols

public javax.swing.JScrollPane getScrollAnalyzingMatrixSymbols()
Returns the scroll pane which holds the matrix analysis by symbols panel.

Returns:
the JScrollPane which holds the matrix analysis by symbols panel

getScrollAnalyzingMatrixValues

public javax.swing.JScrollPane getScrollAnalyzingMatrixValues()
Returns the scroll pane which holds the matrix analysis by values panel.

Returns:
the JScrollPane which holds the matrix analysis by values panel

getScrollBiclustering

public javax.swing.JScrollPane getScrollBiclustering()
Returns the scroll pane which scrolls biclustering panel.

Returns:
the JScrollPane which scrolls biclustering panel

getScrollInfo

public javax.swing.JScrollPane getScrollInfo()
Returns the scroll pane which scrolls information text pane.

Returns:
the JScrollPane which scrolls information text pane

getScrollLoading

public javax.swing.JScrollPane getScrollLoading()
Returns the scroll pane which scrolls loading panel.

Returns:
the JScrollPane which scrolls loading panel

getScrollPreProcessing

public javax.swing.JScrollPane getScrollPreProcessing()
Returns the scroll pane which scrolls preprocessing panel.

Returns:
the JScrollPane which scrolls preprocessing panel

getScrollTree

public javax.swing.JScrollPane getScrollTree()
Returns the scroll pane which scrolls the dataset tree.

Returns:
the JScrollPane which scrolls the dataset tree

getSplitLeftRight

public javax.swing.JSplitPane getSplitLeftRight()
Returns the left-right split pane.

Returns:
the left-right JSplitPane

getSplitTopBottom

public javax.swing.JSplitPane getSplitTopBottom()
Returns the top-bottom split pane.

Returns:
the top-bottom JSplitPane

getTabbedPane

public javax.swing.JTabbedPane getTabbedPane()
Returns the main tabbed pane.

Returns:
the main JTabbedPane

getTabbedPaneAnalyzing

public javax.swing.JTabbedPane getTabbedPaneAnalyzing()
Returns the analysis tabbed pane.

Returns:
the analysis JTabbedPane

getTabbedPaneAnalyzingExpression

public javax.swing.JTabbedPane getTabbedPaneAnalyzingExpression()
Returns the expression analysis tabbed pane.

Returns:
the expression analysis JTabbedPane

getTabbedPaneAnalyzingFunction

public javax.swing.JTabbedPane getTabbedPaneAnalyzingFunction()
Returns the function analysis tabbed pane.

Returns:
the function analysis JTabbedPane

getTabbedPaneAnalyzingMatrix

public javax.swing.JTabbedPane getTabbedPaneAnalyzingMatrix()
Returns the matrix analysis tabbed pane.

Returns:
the matrix analysis JTabbedPane

setTree

public void setTree(DatasetTree t)
Sets a new dataset tree.

Parameters:
t - the new DatasetTree

setTabbedPaneEnabledTabs

public void setTabbedPaneEnabledTabs(boolean loading,
                                     boolean preprocessing,
                                     boolean biclustering,
                                     boolean analyzing,
                                     boolean postprocessing,
                                     boolean comparing)
Enables/disables tabs on the main tabbed pane.

Parameters:
loading - boolean indicating if tab loading is to be enabled (true) /disabled (false)
preprocessing - boolean indicating if tab preprocessing is to be enabled (true) /disabled (false)
biclustering - boolean indicating if tab biclustering is to be enabled (true) /disabled (false)
analyzing - boolean indicating if tab analyzing is to be enabled (true) /disabled (false)
postprocessing - boolean indicating if tab post-processing is to be enabled (true) /disabled (false)
comparing - boolean indicating if tab comparing is to be enabled (true) /disabled (false)

setTabbedPaneAnalyzingEnabledTabs

public void setTabbedPaneAnalyzingEnabledTabs(boolean matrix,
                                              boolean expression,
                                              boolean function)
Enables/disables tabs on the analyzing tabbed pane.

Parameters:
matrix - boolean indicating if tab matrix is to be enabled (true) /disabled (false)
expression - boolean indicating if tab expression is to be enabled (true) /disabled (false)
function - boolean indicating if tab function is to be enabled (true) /disabled (false)

setTabbedPaneAnalyzingMatrixEnabledTabs

public void setTabbedPaneAnalyzingMatrixEnabledTabs(boolean values,
                                                    boolean colors,
                                                    boolean symbols,
                                                    boolean dendrogram)
Enables/disables tabs on the matrix analysis tabbed pane.

Parameters:
values - boolean indicating if tab values is to be enabled (true) /disabled (false)
colors - boolean indicating if tab colors is to be enabled (true) /disabled (false)
symbols - boolean indicating if tab symbols is to be enabled (true) /disabled (false)
dendrogram - boolean indicating if tab dendrogram is to be enabled (true) /disabled (false)

clearAllPanels

public void clearAllPanels()
Clears all application's panels, so that they contain no information.


tree_valueChanged

public void tree_valueChanged(javax.swing.event.TreeSelectionEvent e)
Handles a change in dataset tree's selection.

Parameters:
e - TreeSelectionEvent

closeOperation

public void closeOperation(boolean saveWithCancelOption)
Close operation. Exits the application. Asks the user if he/she wants to save current session.

Parameters:
saveWithCancelOption - boolean true if save dialog should have a cancel option, false if only yes and no options should be displayed
Throws:
java.lang.Exception

saveCurrentSession

public boolean saveCurrentSession(boolean cancelOption)
                           throws java.lang.Exception
Saves current session to a zip archive file.

Parameters:
cancelOption - boolean
Returns:
boolean true if operation succeeded, false if operation did not succeed or if user canceled
Throws:
java.lang.Exception

this_windowClosing

public void this_windowClosing(java.awt.event.WindowEvent e)
Handles the event fired when the main window of the application is closing.

Parameters:
e - WindowEvent

sessionLoadDataset_actionPerformed

public void sessionLoadDataset_actionPerformed(java.awt.event.ActionEvent actionEvent)
Handles the event fired when the user clicks the menu item Session -> Load Dataset. Enables Loading tab.

Parameters:
actionEvent - ActionEvent

sessionLoadSession_actionPerformed

public void sessionLoadSession_actionPerformed(java.awt.event.ActionEvent actionEvent)
Handles the event fired when the user clicks the menu item Session -> Load Session. Allows the user to load a session. Displays a load session dialog.

Parameters:
actionEvent - ActionEvent

sessionSaveSession_actionPerformed

public void sessionSaveSession_actionPerformed(java.awt.event.ActionEvent actionEvent)
Handles the event fired when the user clicks the menu item Session -> Save Session. Allows the user to save current session. Displays a save session dialog.

Parameters:
actionEvent - ActionEvent

sessionExit_actionPerformed

public void sessionExit_actionPerformed(java.awt.event.ActionEvent actionEvent)
Handles the event fired when the user clicks Session -> Exit item menu. Exits the application. First asks the user if he/she wants to save current session.

Parameters:
actionEvent - ActionEvent

helpAbout_actionPerformed

public void helpAbout_actionPerformed(java.awt.event.ActionEvent actionEvent)
Handles the event fired when the user clicks Help -> About item menu. Shows about dialog box.

Parameters:
actionEvent - ActionEvent

colorsRedGreen_actionPerformed

public void colorsRedGreen_actionPerformed(java.awt.event.ActionEvent actionEvent)

colorsYellowBlue_actionPerformed

public void colorsYellowBlue_actionPerformed(java.awt.event.ActionEvent actionEvent)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent actionEvent)
Specified by:
actionPerformed in interface java.awt.event.ActionListener

this_windowStateChanged

public void this_windowStateChanged(java.awt.event.WindowEvent e)
Handles the event fired when the state of the main window changes.

Parameters:
e - WindowEvent

this_componentResized

public void this_componentResized(java.awt.event.ComponentEvent e)
Handles the event fired when the user resizes the main window.

Parameters:
e - ComponentEvent

startTaskInLabelContext

protected void startTaskInLabelContext(java.lang.String message)

finishTaskInLabelContext

protected void finishTaskInLabelContext(java.lang.String message)