edu.iastate.metnet.ui
Class PathwayEditor

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  edu.iastate.metnet.ui.AbstractMetnetWindow
                      edu.iastate.metnet.ui.PathwayEditor

All Implemented Interfaces:

IMetnetWindow, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class PathwayEditor
extends AbstractMetnetWindow

main window for pathway preview

Author:

Jie Li

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JPanel.AccessibleJPanel

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

javax.swing.JComponent.AccessibleJComponent

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

(package private) int	alignmentIndex indicate current index of alignment result
(package private) java.util.List	esAlignmentList contain the esAlignmentList
(package private) static org.apache.log4j.Logger	logger log4j facility
(package private) static int	MENU_AA_GRAPH_QUERY after choose approximately amorphous graph query
(package private) static int	MENU_ALIGN_ARACYC after choose compare pathway 2, aracyc update
(package private) static int	MENU_ALL_COMPARE choose any type of pathway comparison
(package private) static int	MENU_ALL_GRAPH_QUERY choose any type of graph query
(package private) static int	MENU_EA_GRAPH_QUERY after choose exactly amorphous graph query
(package private) static int	MENU_ES_GRAPH_QUERY after choose exactly structural graph query
(package private) static int	MENU_HIGHLIGHT_DELTA after choose compare pathway 1, incremental change
(package private) static int	MENU_ZERO_DEGREE menu status

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 java.awt.image.ImageObserver

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

Constructor Summary

PathwayEditor()
default constructor

Method Summary

void	aaQuery(java.util.Collection blockList, java.util.Collection pathwayList, java.util.Collection trivialList) run approximately amorphous graph query and visualize it
void	eaQuery(java.util.Collection blockList, java.util.Collection pathwayList, java.util.Collection trivialList) run exactly amorphous graph query and visualize it
void	esQuery(org._3pq.jgrapht.DirectedGraph model) run exactly structural query
void	esQuery2(java.util.List alignmentList) sort list only
int	getAlignmentIndex()
java.util.List	getEsAlignmentList()
JMetaphorGraph	getJgraph()
protected javax.swing.JMenuItem	getMenuAlignAracyc() create menu for aligning pathway
protected javax.swing.JMenuItem	getMenuHighlightDelta() menu for comparing pathways
protected void	graphSelectionValueChanged(org.jgraph.event.GraphSelectionEvent e) pick the selection
void	highlightPathway(java.util.Collection pbidList) highlight the selected pathway
protected void	postInitData() initialize data after ui initialization
protected void	preInitData() initialize data before ui initialization
void	receivePathway(java.util.HashMap pathwayMap) accept the pathway and visualize it
void	searchInteractionType(java.lang.String type) search interaction type
void	searchNodeName(java.lang.String name) search node name in the graph
void	setAlignmentIndex(int alignmentIndex)
void	setEsAlignmentList(java.util.List esAlignmentList)
void	updateBirdEye()
void	visualizeEsAlignment() visualize the esQuery alignment result

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, 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, 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

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

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

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

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

MENU_ZERO_DEGREE

static final int MENU_ZERO_DEGREE

menu status

See Also:

Constant Field Values

MENU_HIGHLIGHT_DELTA

static final int MENU_HIGHLIGHT_DELTA

after choose compare pathway 1, incremental change

See Also:

Constant Field Values

MENU_ALIGN_ARACYC

static final int MENU_ALIGN_ARACYC

after choose compare pathway 2, aracyc update

See Also:

Constant Field Values

MENU_EA_GRAPH_QUERY

static final int MENU_EA_GRAPH_QUERY

after choose exactly amorphous graph query

See Also:

Constant Field Values

MENU_AA_GRAPH_QUERY

static final int MENU_AA_GRAPH_QUERY

after choose approximately amorphous graph query

See Also:

Constant Field Values

MENU_ES_GRAPH_QUERY

static final int MENU_ES_GRAPH_QUERY

after choose exactly structural graph query

See Also:

Constant Field Values

MENU_ALL_GRAPH_QUERY

static final int MENU_ALL_GRAPH_QUERY

choose any type of graph query

See Also:

Constant Field Values

MENU_ALL_COMPARE

static final int MENU_ALL_COMPARE

choose any type of pathway comparison

See Also:

Constant Field Values

alignmentIndex

int alignmentIndex

indicate current index of alignment result

esAlignmentList

java.util.List esAlignmentList

contain the esAlignmentList

Constructor Detail

PathwayEditor

public PathwayEditor()

default constructor

Method Detail

preInitData

protected void preInitData()

initialize data before ui initialization

postInitData

protected void postInitData()

initialize data after ui initialization

receivePathway

public void receivePathway(java.util.HashMap pathwayMap)

accept the pathway and visualize it

Specified by:

receivePathway in interface IMetnetWindow

Overrides:

receivePathway in class AbstractMetnetWindow

eaQuery

public void eaQuery(java.util.Collection blockList,
                    java.util.Collection pathwayList,
                    java.util.Collection trivialList)

run exactly amorphous graph query and visualize it

Parameters:

blockList - the system node

pathwayList - the pathway graph

trivialList - the trivial entity list

aaQuery

public void aaQuery(java.util.Collection blockList,
                    java.util.Collection pathwayList,
                    java.util.Collection trivialList)

run approximately amorphous graph query and visualize it

Parameters:

blockList - the system node

pathwayList - the pathway graphs

trivialList - the trivial nodes

esQuery

public void esQuery(org._3pq.jgrapht.DirectedGraph model)

run exactly structural query

Parameters:

collection - any parameters

esQuery2

public void esQuery2(java.util.List alignmentList)

sort list only

Parameters:

alignmentList -

visualizeEsAlignment

public void visualizeEsAlignment()

visualize the esQuery alignment result

Parameters:

index - the index of align result

graphSelectionValueChanged

protected void graphSelectionValueChanged(org.jgraph.event.GraphSelectionEvent e)

pick the selection

Parameters:

e - na

updateBirdEye

public void updateBirdEye()

searchNodeName

public void searchNodeName(java.lang.String name)

search node name in the graph

Parameters:

name - the node name

searchInteractionType

public void searchInteractionType(java.lang.String type)

search interaction type

Parameters:

type - the interaction type

highlightPathway

public void highlightPathway(java.util.Collection pbidList)

highlight the selected pathway

Parameters:

pbidList - the blockid of the pathway

getMenuAlignAracyc

protected javax.swing.JMenuItem getMenuAlignAracyc()

create menu for aligning pathway

Returns:

the menu item

getMenuHighlightDelta

protected javax.swing.JMenuItem getMenuHighlightDelta()

menu for comparing pathways

Returns:

the menu

getJgraph

public JMetaphorGraph getJgraph()

Returns:

Returns the jgraph.

getAlignmentIndex

public int getAlignmentIndex()

Returns:

the alignmentIndex

setAlignmentIndex

public void setAlignmentIndex(int alignmentIndex)

Parameters:

alignmentIndex - the alignmentIndex to set

getEsAlignmentList

public java.util.List getEsAlignmentList()

Returns:

the esAlignmentList

setEsAlignmentList

public void setEsAlignmentList(java.util.List esAlignmentList)

Parameters:

esAlignmentList - the esAlignmentList to set