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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
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