org.compbio.bioverse.viewer
Class ViewerPanel

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjava.awt.Panel
              extended byorg.compbio.bioverse.viewer.ViewerPanel
All Implemented Interfaces:
javax.accessibility.Accessible, java.util.EventListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.lang.Runnable, java.io.Serializable

public class ViewerPanel
extends java.awt.Panel
implements java.lang.Runnable, java.awt.event.MouseListener, java.awt.event.MouseMotionListener

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class java.awt.Panel
java.awt.Panel.AccessibleAWTPanel
 
Nested classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
 GoInfo[] GOcats
           
 Interaction[] Interactions
           
 int neighbours_level_actual
           
 int nGOcats
           
 int nInteractions
           
 Node[] Nodes
           
 
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
ViewerPanel(ViewerApplet graph)
          CONSTRUCTOR
 
Method Summary
 void addGoCat(java.lang.String bvRecord, java.lang.String goCategory)
          add a go cat to gocat array (up to MAXGOCATS)
 void addGoFlagToNode(java.lang.String nodeName, java.lang.String bvRecord)
          mini func name that gets displayed next to a member node if so desire - defunct in AC's version
 int addGoInfoToArray(java.lang.String bioverseId)
          create a new GoInfo object, store bioverseId, and and store object into array
 void addInteraction(java.lang.String from, java.lang.String to, int length, double strength)
          INTERACTION HANDLING METHODS
 int addNode(java.lang.String label)
          add node
 int findGoInfoIndex(java.lang.String bioverseId)
          FUNCTION LABEL METHODS*****************************
 int findMember(java.lang.String label)
          MEMBER HANDLING METHODS*************************************
 java.lang.String[] getGOcats(java.lang.String nodeLabel)
          get a node's list of a GO cats
 Interaction[] getInteractions()
          get interactions
 int getNodeCount()
           
 Node[] getNodes()
          get nodes
 void mouseClicked(java.awt.event.MouseEvent e)
           
 void mouseDragged(java.awt.event.MouseEvent e)
           
 void mouseEntered(java.awt.event.MouseEvent e)
           
 void mouseExited(java.awt.event.MouseEvent e)
           
 void mouseMoved(java.awt.event.MouseEvent e)
           
 void mousePressed(java.awt.event.MouseEvent e)
           
 void mouseReleased(java.awt.event.MouseEvent e)
           
 void paintMember(java.awt.Graphics g, Node n, java.awt.FontMetrics fm)
          method that determines node display
 void relax()
          relaxation algorithm : determines the "springyness" of edge connections
 void run()
           
 void setInteractions(Interaction[] newInteractions)
           
 void setNodes(Node[] newNodes)
          Member and Interaction setting/getting - for external class access from TableApplet
 void start()
           
 void stop()
           
 void update(java.awt.Graphics g)
          freshing the panel graphics
 
Methods inherited from class java.awt.Panel
addNotify, getAccessibleContext
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, paramString, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, removeNotify, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isOpaque, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, 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

GOcats

public GoInfo[] GOcats

Interactions

public Interaction[] Interactions

Nodes

public Node[] Nodes

neighbours_level_actual

public int neighbours_level_actual

nGOcats

public int nGOcats

nInteractions

public int nInteractions
Constructor Detail

ViewerPanel

public ViewerPanel(ViewerApplet graph)
CONSTRUCTOR

Parameters:
graph -
Method Detail

getNodeCount

public int getNodeCount()
Returns:

addGoInfoToArray

public int addGoInfoToArray(java.lang.String bioverseId)
create a new GoInfo object, store bioverseId, and and store object into array

Parameters:
bioverseId -
Returns:

addGoCat

public void addGoCat(java.lang.String bvRecord,
                     java.lang.String goCategory)
add a go cat to gocat array (up to MAXGOCATS)

Parameters:
bvRecord -
goCategory -

addGoFlagToNode

public void addGoFlagToNode(java.lang.String nodeName,
                            java.lang.String bvRecord)
mini func name that gets displayed next to a member node if so desire - defunct in AC's version

Parameters:
nodeName -
bvRecord -

addInteraction

public void addInteraction(java.lang.String from,
                           java.lang.String to,
                           int length,
                           double strength)
INTERACTION HANDLING METHODS

Parameters:
from -
to -
length -
strength -

addNode

public int addNode(java.lang.String label)
add node

Parameters:
label -
Returns:

findGoInfoIndex

public int findGoInfoIndex(java.lang.String bioverseId)
FUNCTION LABEL METHODS*****************************

Parameters:
bioverseId -
Returns:

findMember

public int findMember(java.lang.String label)
MEMBER HANDLING METHODS*************************************

Parameters:
label -
Returns:

getGOcats

public java.lang.String[] getGOcats(java.lang.String nodeLabel)
get a node's list of a GO cats

Parameters:
nodeLabel -
Returns:

getInteractions

public Interaction[] getInteractions()
get interactions

Returns:

getNodes

public Node[] getNodes()
get nodes

Returns:

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)
Specified by:
mouseClicked in interface java.awt.event.MouseListener

mouseDragged

public void mouseDragged(java.awt.event.MouseEvent e)
Specified by:
mouseDragged in interface java.awt.event.MouseMotionListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)
Specified by:
mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)
Specified by:
mouseExited in interface java.awt.event.MouseListener

mouseMoved

public void mouseMoved(java.awt.event.MouseEvent e)
Specified by:
mouseMoved in interface java.awt.event.MouseMotionListener

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)
Specified by:
mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)
Specified by:
mouseReleased in interface java.awt.event.MouseListener

paintMember

public void paintMember(java.awt.Graphics g,
                        Node n,
                        java.awt.FontMetrics fm)
method that determines node display

Parameters:
g -
n -
fm -

relax

public void relax()
relaxation algorithm : determines the "springyness" of edge connections


run

public void run()
Specified by:
run in interface java.lang.Runnable

setInteractions

public void setInteractions(Interaction[] newInteractions)
Parameters:
newInteractions -

setNodes

public void setNodes(Node[] newNodes)
Member and Interaction setting/getting - for external class access from TableApplet

Parameters:
newNodes -

start

public void start()

stop

public void stop()

update

public void update(java.awt.Graphics g)
freshing the panel graphics