edu.iastate.metnet.birdseyeview.goview
Class GoFunctionView

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

public class GoFunctionView
extends GoView

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

Author:

Matt Studham Created Mar 13, 2005

Field Summary

int	capacity
static int	RootID

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

GoFunctionView(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, java.lang.String algorithm) This method tests the GoFunctionView 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

RootID

public static final int RootID

See Also:

Constant Field Values

capacity

public int capacity

Constructor Detail

GoFunctionView

public GoFunctionView(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,
                        java.lang.String algorithm)

This method tests the GoFunctionView class.

Parameters:

args -