ubic.erminej.gui.geneset.tree

Class GeneSetTreePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JScrollPane

ubic.erminej.gui.geneset.GeneSetPanel

ubic.erminej.gui.geneset.tree.GeneSetTreePanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, ScrollPaneConstants

public class GeneSetTreePanel
extends GeneSetPanel

A Tree display that shows Gene Sets and their scores, and allows uer interaction.

Version:

$Id: GeneSetTreePanel.java,v 1.32 2013/05/02 23:33:20 paul Exp $

Author:

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
protected GeneSetTerm	currentlySelectedGeneSet

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
GeneSetTreePanel(MainFrame callingFrame, Settings settings)

Method Summary

Methods

Modifier and Type	Method and Description
void	addedGeneSet(GeneSetTerm id)
void	addRun()
protected boolean	deleteUserGeneSet(GeneSetTerm classID)
protected void	expandAll(boolean expand)
protected void	expandNode(TreePath parent, boolean expand) Fully expand or collapse a node.
boolean	expandToGeneSet(GeneSetTerm classID)
void	filter(boolean propagate)
void	filter(Collection<GeneSetTerm> selectedTerms)
TreePath	find(GeneSetTerm id)
void	fireResultsChanged()
GeneSetTerm	getCurrentlySelectedGeneSet()
Collection<GeneSetTreeNode>	getLeaves()
void	initialize(GeneAnnotations gd) Called after data files are read in.
void	mouseReleased(MouseEvent e)
protected GeneSetTerm	popupRespondAndGetGeneSet(MouseEvent e)
void	refreshView() Force to repaint, reapply filters.
protected void	removedGeneSet(GeneSetTerm id) Update the view to reflect changes
void	removeRun(GeneSetPvalRun runToRemove) Do any extra cleanup after a run has been deleted.
void	resetView() Restore view
void	setHideInsignificant(boolean b) Has no effect unless you call filter() afterwards
protected 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

currentlySelectedGeneSet

protected GeneSetTerm currentlySelectedGeneSet

Constructor Detail

GeneSetTreePanel

public GeneSetTreePanel(MainFrame callingFrame,
                Settings settings)

Method Detail

addedGeneSet

public void addedGeneSet(GeneSetTerm id)

Specified by:

addedGeneSet in class GeneSetPanel

addRun

public void addRun()

Specified by:

addRun in class GeneSetPanel

expandToGeneSet

public boolean expandToGeneSet(GeneSetTerm classID)

Parameters:

classID - a node somewhere in the tree; we expand the path

filter

public void filter(boolean propagate)

Specified by:

filter in class GeneSetPanel

filter

public void filter(Collection<GeneSetTerm> selectedTerms)

Parameters:

selectedTerms -

find

public TreePath find(GeneSetTerm id)

Parameters:

tree -

names -

Returns:

fireResultsChanged

public void fireResultsChanged()

getCurrentlySelectedGeneSet

public GeneSetTerm getCurrentlySelectedGeneSet()

Returns:

Returns the currentlySelectedGeneSet.

getLeaves

public Collection<GeneSetTreeNode> getLeaves()

Returns:

initialize

public void initialize(GeneAnnotations gd)

Called after data files are read in.

Parameters:

goData -

geneData -

mouseReleased

public void mouseReleased(MouseEvent e)

Parameters:

e -

refreshView

public void refreshView()

Force to repaint, reapply filters.

Specified by:

refreshView 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

resetView

public void resetView()

Description copied from class: GeneSetPanel

Restore view

Specified by:

resetView in class GeneSetPanel

setHideInsignificant

public void setHideInsignificant(boolean b)

Has no effect unless you call filter() afterwards

Parameters:

b -

deleteUserGeneSet

protected boolean deleteUserGeneSet(GeneSetTerm classID)

Overrides:

deleteUserGeneSet in class GeneSetPanel

Returns:

expandAll

protected void expandAll(boolean expand)

Parameters:

expand - If false, collapses all nodes. If true, expands them all.

expandNode

protected void expandNode(TreePath parent,
              boolean expand)

Fully expand or collapse a node.

Parameters:

parent -

expand -

popupRespondAndGetGeneSet

protected GeneSetTerm popupRespondAndGetGeneSet(MouseEvent e)

Specified by:

popupRespondAndGetGeneSet in class GeneSetPanel

Parameters:

e -

Returns:

removedGeneSet

protected void removedGeneSet(GeneSetTerm id)

Description copied from class: GeneSetPanel

Update the view to reflect changes

Specified by:

removedGeneSet in class GeneSetPanel

showPopupMenu

protected void showPopupMenu(MouseEvent e)

Specified by:

showPopupMenu in class GeneSetPanel