A C D F G H I K L M N O P R S U V X Y

A

actionPerformed(ActionEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
ActionListener implementation method
addGoCat(String, String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
add a go cat to gocat array (up to MAXGOCATS)
addGoFlagToNode(String, String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
mini func name that gets displayed next to a member node if so desire - defunct in AC's version
addGoInfoToArray(String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
create a new GoInfo object, store bioverseId, and and store object into array
addInteraction(String, String, int, double) - Method in class org.compbio.bioverse.viewer.ViewerPanel
INTERACTION HANDLING METHODS
addNode(String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
add node
addSortedGoCatsToMenu() - Method in class org.compbio.bioverse.viewer.ViewerApplet
add sorted GO cats to menu bar

C

clearScreen() - Method in class org.compbio.bioverse.viewer.ViewerApplet
clear screen method

D

destroy() - Method in class org.compbio.bioverse.viewer.ViewerApplet
destroy panel
dx - Variable in class org.compbio.bioverse.viewer.Node
 
dy - Variable in class org.compbio.bioverse.viewer.Node
 

F

findGoInfoIndex(String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
FUNCTION LABEL METHODS*****************************
findMember(String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
MEMBER HANDLING METHODS*************************************
fixed - Variable in class org.compbio.bioverse.viewer.Node
 
fu_lbl - Variable in class org.compbio.bioverse.viewer.Node
 
funkflag - Variable in class org.compbio.bioverse.viewer.Node
 

G

GOcats - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
GoInfo - class org.compbio.bioverse.viewer.GoInfo.
 
GoInfo() - Constructor for class org.compbio.bioverse.viewer.GoInfo
 
getFunctionKeysFromHtml() - Method in class org.compbio.bioverse.viewer.ViewerApplet
data read in at init()
getFunctionListFromHtml() - Method in class org.compbio.bioverse.viewer.ViewerApplet
data read in at init()
getGOcats(String) - Method in class org.compbio.bioverse.viewer.ViewerPanel
get a node's list of a GO cats
getGenome() - Static method in class org.compbio.bioverse.viewer.Interaction
 
getInteractions() - Method in class org.compbio.bioverse.viewer.ViewerPanel
get interactions
getInteractionsFromHtml() - Method in class org.compbio.bioverse.viewer.ViewerApplet
for init() data read in
getNodeCount() - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
getNodes() - Method in class org.compbio.bioverse.viewer.ViewerPanel
get nodes
getStrength() - Method in class org.compbio.bioverse.viewer.Interaction
 

H

hide_relax - Variable in class org.compbio.bioverse.viewer.ViewerApplet
 

I

Interaction - class org.compbio.bioverse.viewer.Interaction.
 
Interaction() - Constructor for class org.compbio.bioverse.viewer.Interaction
 
Interactions - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
init() - Method in class org.compbio.bioverse.viewer.ViewerApplet
init() method
itemStateChanged(ItemEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
itemListener implementation

K

keyPressed(KeyEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
KeyListener implementation - for search field
keyReleased(KeyEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
keyListener implement
keyTyped(KeyEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
keyListener

L

lbl - Variable in class org.compbio.bioverse.viewer.Node
 

M

mouseClicked(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
handle right button mouse events separates for getting more detail on the protein node
mouseClicked(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mouseDragged(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mouseEntered(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
 
mouseEntered(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mouseExited(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
 
mouseExited(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mouseMoved(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mousePressed(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
 
mousePressed(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
mouseReleased(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerApplet
 
mouseReleased(MouseEvent) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 

N

Node - class org.compbio.bioverse.viewer.Node.
 
Node() - Constructor for class org.compbio.bioverse.viewer.Node
 
Nodes - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
nGOcats - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
nInteractions - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
neighbours_level - Variable in class org.compbio.bioverse.viewer.Node
 
neighbours_level_actual - Variable in class org.compbio.bioverse.viewer.ViewerPanel
 
nextneighbour - Variable in class org.compbio.bioverse.viewer.Node
 

O

on - Variable in class org.compbio.bioverse.viewer.Node
 
org.compbio.bioverse.viewer - package org.compbio.bioverse.viewer
 

P

paintMember(Graphics, Node, FontMetrics) - Method in class org.compbio.bioverse.viewer.ViewerPanel
method that determines node display
popPartitionIt(int, int, int) - Method in class org.compbio.bioverse.viewer.ViewerApplet
for quicksorting
popQuickSort(int, int) - Method in class org.compbio.bioverse.viewer.ViewerApplet
for quicksorting

R

relax() - Method in class org.compbio.bioverse.viewer.ViewerPanel
relaxation algorithm : determines the "springyness" of edge connections
run() - Method in class org.compbio.bioverse.viewer.ViewerPanel
 

S

selected - Variable in class org.compbio.bioverse.viewer.Node
 
selfRef - Static variable in class org.compbio.bioverse.viewer.ViewerApplet
 
setGenome(String) - Static method in class org.compbio.bioverse.viewer.Interaction
 
setInteractions(Interaction[]) - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
setNodes(Node[]) - Method in class org.compbio.bioverse.viewer.ViewerPanel
Member and Interaction setting/getting - for external class access from TableApplet
setTableSelectedNodes(ArrayList) - Method in class org.compbio.bioverse.viewer.ViewerApplet
for external calling from tableapplet - turn on table selected members on viewer
showSelectedNodes(String) - Method in class org.compbio.bioverse.viewer.ViewerApplet
MENU FUNCTIONALITY - get members of a given GO class
start() - Method in class org.compbio.bioverse.viewer.ViewerApplet
applet
start() - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
stop() - Method in class org.compbio.bioverse.viewer.ViewerApplet
applet
stop() - Method in class org.compbio.bioverse.viewer.ViewerPanel
 
swap(int, int) - Method in class org.compbio.bioverse.viewer.ViewerApplet
for quicksorting

U

update(Graphics) - Method in class org.compbio.bioverse.viewer.ViewerPanel
freshing the panel graphics

V

ViewerApplet - class org.compbio.bioverse.viewer.ViewerApplet.
 
ViewerApplet() - Constructor for class org.compbio.bioverse.viewer.ViewerApplet
CONSTRUCTOR
ViewerApplet(ArrayList) - Constructor for class org.compbio.bioverse.viewer.ViewerApplet
overload contructor to allow data to be PUSHED into the viewer from Action class
ViewerPanel - class org.compbio.bioverse.viewer.ViewerPanel.
 
ViewerPanel(ViewerApplet) - Constructor for class org.compbio.bioverse.viewer.ViewerPanel
CONSTRUCTOR

X

x - Variable in class org.compbio.bioverse.viewer.Node
 

Y

y - Variable in class org.compbio.bioverse.viewer.Node
 

A C D F G H I K L M N O P R S U V X Y