edu.iastate.metnet.birdseyeview.goview
Class GoNode

java.lang.Object
  edu.iastate.metnet.birdseyeview.goview.GoNode

public class GoNode
extends java.lang.Object

The GoNode Class represents a node in the Directed Acyclic Graph of the GO biological processes or molecular functions.

Author:

Matt Studham Created Jan 25, 2005

Constructor Summary

GoNode(BirdsEyeView bev, GoView gv, GoTerm gt, java.awt.Color c, int l)
Constructor.

Method Summary

void	addGene(Annotation gene) This method adds the given gene to the gene list.
void	displayChildren(java.util.ArrayList childNodes) This method sets the panel to show the child panels.
void	displayGenes() This method sets the panel to show the gene panels.
void	finalizeGeneList() This method finalizes the gene list by creating the gene container panel based on the list.
java.util.ArrayList	getChildNodeIDs() This method returns the IDs of the child nodes
java.awt.Component	getComponent() This method returns the panel.
java.util.ArrayList	getGenes() This method returns the list of genes.
java.lang.Integer	getGoID() This method returns the GO term ID.
int	getLevel() This method returns the hierarchy level.
static void	main(java.lang.String[] args, java.lang.String algorithm) This method tests the GoNode class.
int	pointNumber() This method return the number of points in genepanel
void	removeAllGenes() This method clears out the gene list.
void	setMaximumsize(int w, int h) This method transfer the size information to node
void	setPreferredSize(java.awt.Dimension size) This method sets the panel's preferred size to the given size.

Methods inherited from class java.lang.Object

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

Constructor Detail

GoNode

public GoNode(BirdsEyeView bev,
              GoView gv,
              GoTerm gt,
              java.awt.Color c,
              int l)

Constructor. If there are any genes in this node then addGene() must be called. The finalizeGeneList() method must be called before displaying this node.

Parameters:

bev - BirdsEyeView controller object

gv - GoView controller object

gt - GO term object

c - Color object - background

l - GO hierarchy level

Method Detail

finalizeGeneList

public void finalizeGeneList()

This method finalizes the gene list by creating the gene container panel based on the list. This method should be called before displaying a GoNode with genes.

getChildNodeIDs

public java.util.ArrayList getChildNodeIDs()

This method returns the IDs of the child nodes

Returns:

ArrayList (Integer objects)

getLevel

public int getLevel()

This method returns the hierarchy level. The root=0, and the levels go up according to their distance from the root.

Returns:

int

displayGenes

public void displayGenes()

This method sets the panel to show the gene panels.

displayChildren

public void displayChildren(java.util.ArrayList childNodes)

This method sets the panel to show the child panels.

Parameters:

chillins - ArrayList of GoNode objects

setPreferredSize

public void setPreferredSize(java.awt.Dimension size)

This method sets the panel's preferred size to the given size. This is only necessary for the root GoNode.

Parameters:

size -

addGene

public void addGene(Annotation gene)

This method adds the given gene to the gene list.

Parameters:

gene - Annotation object

removeAllGenes

public void removeAllGenes()

This method clears out the gene list.

getGoID

public java.lang.Integer getGoID()

This method returns the GO term ID.

Returns:

Integer

getComponent

public java.awt.Component getComponent()

This method returns the panel.

Returns:

Component

getGenes

public java.util.ArrayList getGenes()

This method returns the list of genes.

Returns:

ArrayList of Annotation objects

pointNumber

public int pointNumber()

This method return the number of points in genepanel

setMaximumsize

public void setMaximumsize(int w,
                           int h)

This method transfer the size information to node

Parameters:

width, - height

main

public static void main(java.lang.String[] args,
                        java.lang.String algorithm)

This method tests the GoNode class.

Parameters:

args -