edu.iastate.metnet.birdseyeview.goview
Class GoBioProcessView

java.lang.Object
  edu.iastate.metnet.birdseyeview.AbstractView
      edu.iastate.metnet.birdseyeview.goview.GoView
          edu.iastate.metnet.birdseyeview.goview.GoBioProcessView

public class GoBioProcessView
extends GoView

The GoBioProcessView Class displays the Bird's Eye View of the gene products' location in the Gene Ontology biological process directed acyclic graph. In this display genes may be duplicated in order to create a hierarchy of GO biological processes.

Author:

Matt Studham Created Jan 25, 2005

Field Summary

int

capacity

Fields inherited from class edu.iastate.metnet.birdseyeview.goview.GoView

bottomLevel, currentLevel, goLevelColors, goLevels, MaxLevel, rootNode

Fields inherited from class edu.iastate.metnet.birdseyeview.AbstractView

algorithm, annotations, birdsEyeView, size, viewInfo

Constructor Summary

GoBioProcessView(ViewInfo vi, BirdsEyeView bev, java.util.ArrayList anns, java.awt.Dimension s, java.lang.String alg)
Constructor.

Method Summary

void	addGenesToNodes(java.util.ArrayList nodes) Subclasses must provide a way to match nodes and annotations (genes).
java.util.ArrayList	getLevelColors() Subclasses must provide the different level colors.
static void	main(java.lang.String[] args) This method tests the GoBioProcessView class.
void	redisplayGenesToNodes(java.util.ArrayList nodes)

Methods inherited from class edu.iastate.metnet.birdseyeview.goview.GoView

createLevelColors, displayChildren, getBackground, getComponent, getCurrentGoLevel, getLayout, goDown, goUp, loadConfiguration, reloadData, replayChildren, setlevelCapacity

Methods inherited from class edu.iastate.metnet.birdseyeview.AbstractView

getViewInfo, loadData, toggleMapLabels

Methods inherited from class java.lang.Object

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

Field Detail

capacity

public int capacity

Constructor Detail

GoBioProcessView

public GoBioProcessView(ViewInfo vi,
                        BirdsEyeView bev,
                        java.util.ArrayList anns,
                        java.awt.Dimension s,
                        java.lang.String alg)

Constructor.

Parameters:

vi -

bev -

anns - List of Annotation objects

s - Size of the view

alg - Selected treemap algorithm = null

Method Detail

getLevelColors

public java.util.ArrayList getLevelColors()

Description copied from class: GoView

Subclasses must provide the different level colors.

Specified by:

getLevelColors in class GoView

Returns:

ArrayList

addGenesToNodes

public void addGenesToNodes(java.util.ArrayList nodes)

Description copied from class: GoView

Subclasses must provide a way to match nodes and annotations (genes).

Specified by:

addGenesToNodes in class GoView

Parameters:

nodes - Array List of GoNode objects

redisplayGenesToNodes

public void redisplayGenesToNodes(java.util.ArrayList nodes)

Specified by:

redisplayGenesToNodes in class GoView

main

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

This method tests the GoBioProcessView class.

Parameters:

args -