edu.iastate.metnet.graphmodel
Class JMetaphorGraph

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              org.jgraph.JGraph
                  edu.iastate.metnet.graphmodel.JMetaphorGraph

All Implemented Interfaces:

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

public class JMetaphorGraph
extends org.jgraph.JGraph

extend the JGraph by applying the metaphor description based on the content of the pathway

Author:

Jie Li

See Also:

Serialized Form

Nested Class Summary

class

JMetaphorGraph.EditorGraphUI Definition of the custom GraphUI.

Nested classes/interfaces inherited from class org.jgraph.JGraph

org.jgraph.JGraph.EmptySelectionModel, org.jgraph.JGraph.GraphSelectionRedirector

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) boolean	aracycUpdate
(package private) static org.apache.log4j.Logger	logger log4j facility
(package private) int	multiNodeFlag

Fields inherited from class org.jgraph.JGraph

antiAliased, ANTIALIASED_PROPERTY, autoResizeGraph, bendable, cloneable, connectable, CROSS_GRID_MODE, disconnectable, disconnectOnMove, DOT_GRID_MODE, dragEnabled, dropEnabled, editable, EDITABLE_PROPERTY, editClickCount, enabled, GRAPH_LAYOUT_CACHE_PROPERTY, GRAPH_MODEL_PROPERTY, graphLayoutCache, graphModel, GRID_COLOR_PROPERTY, GRID_SIZE_PROPERTY, GRID_VISIBLE_PROPERTY, gridColor, gridEnabled, gridMode, gridSize, gridVisible, HANDLE_COLOR_PROPERTY, HANDLE_SIZE_PROPERTY, handleColor, handleSize, highlightColor, INVOKES_STOP_CELL_EDITING_PROPERTY, invokesStopCellEditing, isJumpToDefaultPort, isMoveIntoGroups, isMoveOutOfGroups, LINE_GRID_MODE, LOCKED_HANDLE_COLOR_PROPERTY, lockedHandleColor, marquee, MARQUEE_HANDLER_PROPERTY, marqueeColor, minimumMove, moveable, moveBelowZero, PORTS_SCALED_PROPERTY, PORTS_VISIBLE_PROPERTY, portsScaled, portsVisible, previewInvalidNullPorts, scale, SCALE_PROPERTY, SELECTION_MODEL_PROPERTY, selectionEnabled, SELECTIONENABLED_PROPERTY, selectionModel, selectionRedirector, sizeable, tolerance, VERSION

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

JMetaphorGraph()
default constructor

JMetaphorGraph(org.jgraph.graph.GraphModel model)
constructor

JMetaphorGraph(org.jgraph.graph.GraphModel model, org.jgraph.graph.BasicMarqueeHandler mh)
constructor

JMetaphorGraph(org.jgraph.graph.GraphModel model, boolean isAraCycUpdate)
constructor

JMetaphorGraph(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphLayoutCache view)
constructor

JMetaphorGraph(org.jgraph.graph.GraphModel model, org.jgraph.graph.GraphLayoutCache view, org.jgraph.graph.BasicMarqueeHandler mh)
constructor

Method Summary

void	applyMetaphore(IGraphMetaphor metaphor) apply the metaphor instance, similar to the layout
java.lang.Object[]	findGenes() find the gene object in the graph model
java.lang.Object[]	findOrphans(PathwayModel pathwayModel)
java.lang.Object[]	findRNAs() get RNA object in graph model
java.util.Set	getAllIbidSet() get all interaction blockid in the mapping view
int	getMultiNodeFlag()
java.lang.String	getToolTipText(java.awt.event.MouseEvent mouseEvent) get the tooltips
boolean	isAracycUpdate()
boolean	isCellEditable(java.lang.Object cell) override the parent method with our definition
void	setAracycUpdate(boolean isAraCycUpdate)
void	setMultiNodeFlag(int multiNodeFlag)
void	updateUI() Override parent method with custom GraphUI.

Methods inherited from class org.jgraph.JGraph

addGraphSelectionListener, addSampleData, addSelectionCell, addSelectionCells, cancelEditing, clearSelection, cloneCells, convertValueToString, createBounds, fireValueChanged, fromScreen, fromScreen, getAttributes, getCellBounds, getCellBounds, getDefaultPortForCell, getDescendants, getEditClickCount, getEditingCell, getFirstCellForLocation, getGraphLayoutCache, getGridColor, getGridMode, getGridSize, getHandleColor, getHandleSize, getHighlightColor, getImage, getInvokesStopCellEditing, getLeafViewAt, getLockedHandleColor, getMarqueeColor, getMarqueeHandler, getMinimumMove, getModel, getNextCellForLocation, getNextSelectableViewAt, getNextViewAt, getNextViewAt, getNextViewAt, getNextViewAt, getPortForLocation, getPortViewAt, getPortViewAt, getPreferredScrollableViewportSize, getRoots, getRoots, getScale, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSelectionCell, getSelectionCellAt, getSelectionCells, getSelectionCells, getSelectionCount, getSelectionModel, getTolerance, getTopmostViewAt, getUI, getUIClassID, graphDidChange, isAntiAliased, isAutoResizeGraph, isBendable, isCellSelected, isCloneable, isConnectable, isDisconnectable, isDisconnectOnMove, isDragEnabled, isDropEnabled, isEditable, isEditing, isGridEnabled, isGridVisible, isJumpToDefaultPort, isMoveable, isMoveBelowZero, isMoveIntoGroups, isMoveOutOfGroups, isPortsScaled, isPortsVisible, isPreviewInvalidNullPorts, isSelectionEmpty, isSelectionEnabled, isSizeable, main, order, paramString, removeGraphSelectionListener, removeSelectionCell, scrollCellToVisible, scrollPointToVisible, setAntiAliased, setAutoResizeGraph, setBendable, setCloneable, setConnectable, setDisconnectable, setDisconnectOnMove, setDragEnabled, setDropEnabled, setEditable, setEditClickCount, setGraphLayoutCache, setGridColor, setGridEnabled, setGridMode, setGridSize, setGridVisible, setHandleColor, setHandleSize, setHighlightColor, setInvokesStopCellEditing, setJumpToDefaultPort, setLockedHandleColor, setMarqueeColor, setMarqueeHandler, setMinimumMove, setModel, setMoveable, setMoveBelowZero, setMoveIntoGroups, setMoveOutOfGroups, setPortsScaled, setPortsVisible, setPreviewInvalidNullPorts, setScale, setSelectionCell, setSelectionCells, setSelectionEnabled, setSelectionModel, setSizeable, setTolerance, setUI, snap, snap, snap, startEditingAtCell, stopEditing, toScreen, toScreen, updateAutoSize

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, 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, 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

Methods inherited from interface javax.accessibility.Accessible

getAccessibleContext

Field Detail

logger

static org.apache.log4j.Logger logger

log4j facility

multiNodeFlag

int multiNodeFlag

aracycUpdate

boolean aracycUpdate

Constructor Detail

JMetaphorGraph

public JMetaphorGraph()

default constructor

JMetaphorGraph

public JMetaphorGraph(org.jgraph.graph.GraphModel model)

constructor

Parameters:

model - graph model

JMetaphorGraph

public JMetaphorGraph(org.jgraph.graph.GraphModel model,
                      boolean isAraCycUpdate)

constructor

Parameters:

model - graph model

JMetaphorGraph

public JMetaphorGraph(org.jgraph.graph.GraphModel model,
                      org.jgraph.graph.BasicMarqueeHandler mh)

constructor

Parameters:

model - graph model

mh - nothing

JMetaphorGraph

public JMetaphorGraph(org.jgraph.graph.GraphModel model,
                      org.jgraph.graph.GraphLayoutCache view)

constructor

Parameters:

model - graph model

view - nothing

JMetaphorGraph

public JMetaphorGraph(org.jgraph.graph.GraphModel model,
                      org.jgraph.graph.GraphLayoutCache view,
                      org.jgraph.graph.BasicMarqueeHandler mh)

constructor

Parameters:

model - graph model

view - nothing

mh - nothing

Method Detail

updateUI

public void updateUI()

Override parent method with custom GraphUI.

Overrides:

updateUI in class org.jgraph.JGraph

isCellEditable

public boolean isCellEditable(java.lang.Object cell)

override the parent method with our definition

Overrides:

isCellEditable in class org.jgraph.JGraph

applyMetaphore

public void applyMetaphore(IGraphMetaphor metaphor)

apply the metaphor instance, similar to the layout

Parameters:

metaphor - the metaphor to be applied

findOrphans

public java.lang.Object[] findOrphans(PathwayModel pathwayModel)

getAllIbidSet

public java.util.Set getAllIbidSet()

get all interaction blockid in the mapping view

Returns:

allinteraction in the view.

findGenes

public java.lang.Object[] findGenes()

find the gene object in the graph model

Returns:

gene object list

findRNAs

public java.lang.Object[] findRNAs()

get RNA object in graph model

Returns:

rna object list

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent mouseEvent)

get the tooltips

Overrides:

getToolTipText in class org.jgraph.JGraph

getMultiNodeFlag

public int getMultiNodeFlag()

Returns:

Returns the multiNodeFlag.

setMultiNodeFlag

public void setMultiNodeFlag(int multiNodeFlag)

Parameters:

multiNodeFlag - The multiNodeFlag to set. 2 or more for multi-pathway, 1 or less for normal pathway

isAracycUpdate

public boolean isAracycUpdate()

Returns:

the isAraCycUpdate

setAracycUpdate

public void setAracycUpdate(boolean isAraCycUpdate)

Parameters:

isAraCycUpdate - the isAraCycUpdate to set