ubic.erminej.gui.geneset.table

Class GeneSetTablePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JScrollPane

ubic.erminej.gui.geneset.GeneSetPanel

ubic.erminej.gui.geneset.table.GeneSetTablePanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, ScrollPaneConstants

public class GeneSetTablePanel
extends GeneSetPanel

A table that lists the Gene Sets with their scores, and allows user interaction.

Version:

$Id: GeneSetTablePanel.java,v 1.32 2013/05/05 20:08:47 paul Exp $

Author:

Homin Lee, Paul Pavlidis

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JScrollPane

JScrollPane.AccessibleJScrollPane, JScrollPane.ScrollBar

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
static int	GENE_COUNT_COLUMN_INDEX
protected GeneSetTableModel	model
static int	MULTIFUNC_COLUMN_INDEX
protected List<String>	resultToolTips
protected JTable	table

Fields inherited from class ubic.erminej.gui.geneset.GeneSetPanel

callingFrame, DELETED, FDR_THRESHOLD_FOR_FILTER, geneData, hideEmpty, hideInsignificant, hideNonCustom, MAX_DEFINITION_LENGTH, messenger, NOACTION, RESOURCE_LOCATION, RESTORED, settings, USER_NODE_COLOR, USER_NODE_TEXT_COLOR

Fields inherited from class javax.swing.JScrollPane

columnHeader, horizontalScrollBar, horizontalScrollBarPolicy, lowerLeft, lowerRight, rowHeader, upperLeft, upperRight, verticalScrollBar, verticalScrollBarPolicy, viewport

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 javax.swing.ScrollPaneConstants

COLUMN_HEADER, HORIZONTAL_SCROLLBAR, HORIZONTAL_SCROLLBAR_ALWAYS, HORIZONTAL_SCROLLBAR_AS_NEEDED, HORIZONTAL_SCROLLBAR_NEVER, HORIZONTAL_SCROLLBAR_POLICY, LOWER_LEADING_CORNER, LOWER_LEFT_CORNER, LOWER_RIGHT_CORNER, LOWER_TRAILING_CORNER, ROW_HEADER, UPPER_LEADING_CORNER, UPPER_LEFT_CORNER, UPPER_RIGHT_CORNER, UPPER_TRAILING_CORNER, VERTICAL_SCROLLBAR, VERTICAL_SCROLLBAR_ALWAYS, VERTICAL_SCROLLBAR_AS_NEEDED, VERTICAL_SCROLLBAR_NEVER, VERTICAL_SCROLLBAR_POLICY, VIEWPORT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
GeneSetTablePanel(MainFrame callingFrame, Settings settings)

Method Summary

Methods

Modifier and Type	Method and Description
void	addedGeneSet(GeneSetTerm id)
void	addRun()
protected boolean	deleteUserGeneSet(GeneSetTerm classID)
void	filter(boolean propagate)
void	filter(Collection<GeneSetTerm> selectedTerms)
void	filterByUserGeneSets(boolean b)
protected void	generateResultColumnHeadingTooltip(int runIndex) Create the text shown when user hovers mouse over the heading of a result column
protected String	getHeaderToolTip(int index)
int	getRowCount()
protected String	getRunName(int runIndex)
void	initialize(GeneAnnotations initialGoData)
protected GeneSetTerm	popupRespondAndGetGeneSet(MouseEvent e)
void	refreshView() Revalidate, refilter and (resort? NO) the table.
protected void	removedGeneSet(GeneSetTerm addedTerm) Update the view to reflect changes
void	removeRun(GeneSetPvalRun runToRemove) Do any extra cleanup after a run has been deleted.
protected void	removeRunPopupMenu_actionPerformed(ActionEvent e)
protected void	renameRun(int runIndex, String newName)
void	resetView() Restore view
protected void	setUpHeaderPopupMenus() for the table heading
void	showPopupMenu(MouseEvent e)

Methods inherited from class ubic.erminej.gui.geneset.GeneSetPanel

addDependentPanel, configurePopup, configurePopupListener, findInTree, modMenuItem_actionPerformed, openUrlForGeneSet, setMessenger, showDetailsForGeneSet

Methods inherited from class javax.swing.JScrollPane

createHorizontalScrollBar, createVerticalScrollBar, createViewport, getAccessibleContext, getColumnHeader, getCorner, getHorizontalScrollBar, getHorizontalScrollBarPolicy, getRowHeader, getUI, getUIClassID, getVerticalScrollBar, getVerticalScrollBarPolicy, getViewport, getViewportBorder, getViewportBorderBounds, isValidateRoot, isWheelScrollingEnabled, paramString, setColumnHeader, setColumnHeaderView, setComponentOrientation, setCorner, setHorizontalScrollBar, setHorizontalScrollBarPolicy, setLayout, setRowHeader, setRowHeaderView, setUI, setVerticalScrollBar, setVerticalScrollBarPolicy, setViewport, setViewportBorder, setViewportView, setWheelScrollingEnabled, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, 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, 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, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

GENE_COUNT_COLUMN_INDEX

public static final int GENE_COUNT_COLUMN_INDEX

See Also:

Constant Field Values

MULTIFUNC_COLUMN_INDEX

public static final int MULTIFUNC_COLUMN_INDEX

See Also:

Constant Field Values

model

protected GeneSetTableModel model

resultToolTips

protected List<String> resultToolTips

table

protected JTable table

Constructor Detail

GeneSetTablePanel

public GeneSetTablePanel(MainFrame callingFrame,
                 Settings settings)

Method Detail

getRowCount

public int getRowCount()

setUpHeaderPopupMenus

protected void setUpHeaderPopupMenus()

for the table heading

getRunName

protected String getRunName(int runIndex)

Parameters:

runIndex -

Returns:

renameRun

protected void renameRun(int runIndex,
             String newName)

Parameters:

runIndex -

newName -

addedGeneSet

public void addedGeneSet(GeneSetTerm id)

Specified by:

addedGeneSet in class GeneSetPanel

refreshView

public void refreshView()

Revalidate, refilter and (resort? NO) the table.

Specified by:

refreshView in class GeneSetPanel

removedGeneSet

protected void removedGeneSet(GeneSetTerm addedTerm)

Description copied from class: GeneSetPanel

Update the view to reflect changes

Specified by:

removedGeneSet in class GeneSetPanel

initialize

public void initialize(GeneAnnotations initialGoData)

addRun

public void addRun()

Specified by:

addRun in class GeneSetPanel

resetView

public void resetView()

Description copied from class: GeneSetPanel

Restore view

Specified by:

resetView in class GeneSetPanel

deleteUserGeneSet

protected boolean deleteUserGeneSet(GeneSetTerm classID)

Overrides:

deleteUserGeneSet in class GeneSetPanel

Returns:

popupRespondAndGetGeneSet

protected GeneSetTerm popupRespondAndGetGeneSet(MouseEvent e)

Specified by:

popupRespondAndGetGeneSet in class GeneSetPanel

Parameters:

e -

Returns:

generateResultColumnHeadingTooltip

protected void generateResultColumnHeadingTooltip(int runIndex)

Create the text shown when user hovers mouse over the heading of a result column

Parameters:

runIndex -

getHeaderToolTip

protected String getHeaderToolTip(int index)

Parameters:

index -

Returns:

removeRunPopupMenu_actionPerformed

protected void removeRunPopupMenu_actionPerformed(ActionEvent e)

showPopupMenu

public void showPopupMenu(MouseEvent e)

Specified by:

showPopupMenu in class GeneSetPanel

filterByUserGeneSets

public void filterByUserGeneSets(boolean b)

filter

public void filter(Collection<GeneSetTerm> selectedTerms)

filter

public void filter(boolean propagate)

Specified by:

filter in class GeneSetPanel

removeRun

public void removeRun(GeneSetPvalRun runToRemove)

Description copied from class: GeneSetPanel

Do any extra cleanup after a run has been deleted.

Specified by:

removeRun in class GeneSetPanel