edu.iastate.metnet.birdseyeview.pathwayview
Class Pathway

java.lang.Object
  edu.iastate.metnet.birdseyeview.pathwayview.Pathway

public class Pathway
extends java.lang.Object

The Pathway Class encapsulates the functionality of one pathway component in the pathway view. It holds a panel that displays the pathway's name and gene products.

Author:

Matt Studham Created Jan 25, 2005

Constructor Summary

Pathway(java.lang.String i, java.util.ArrayList d, java.lang.String c, boolean flag, BirdsEyeView bev)
Constructor.

Method Summary

void	addGene(Annotation a) This method adds a gene panel to represent the given gene product annotation to the gene panel list.
java.lang.String	getCompartment() This method returns the name of the cellular compartment (location) for this pathway.
java.awt.Component	getComponent() This method causes the genes to be packaged and displayed, and then returns the finished image panel.
java.util.ArrayList	getDbNames() This method returns the list of database names for this pathway.
int	getNumGenes() This method returns the number of genes displayed in this pathway.
boolean	isActive() This method returns the active flag.
static void	main(java.lang.String[] args, java.lang.String algorithm) This method tests the Pathway class.
void	removeAllGenes() This method removes all the gene data by clearing out the gene container.
void	setGenes(int genesize) This method adds the gene panels to the panel.
int	setPanel(java.awt.Rectangle r) This method sets the dimensions of the panel and sets up the gene panel.

Methods inherited from class java.lang.Object

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

Constructor Detail

Pathway

public Pathway(java.lang.String i,
               java.util.ArrayList d,
               java.lang.String c,
               boolean flag,
               BirdsEyeView bev)

Constructor.

Parameters:

i - Name of pathway in display

d - Names of pathway in database

c - Cellular compartment (location)

flag - Flag indicating that this pathway is in the database

bev -

Method Detail

addGene

public void addGene(Annotation a)

This method adds a gene panel to represent the given gene product annotation to the gene panel list.

Parameters:

a -

getComponent

public java.awt.Component getComponent()

This method causes the genes to be packaged and displayed, and then returns the finished image panel.

Returns:

Component

removeAllGenes

public void removeAllGenes()

This method removes all the gene data by clearing out the gene container.

getDbNames

public java.util.ArrayList getDbNames()

This method returns the list of database names for this pathway.

Returns:

ArrayList List of Database names for this pathway

getCompartment

public java.lang.String getCompartment()

This method returns the name of the cellular compartment (location) for this pathway.

Returns:

String Name of cellular compartment (location)

isActive

public boolean isActive()

This method returns the active flag.

Returns:

boolean

getNumGenes

public int getNumGenes()

This method returns the number of genes displayed in this pathway.

Returns:

int

setGenes

public void setGenes(int genesize)

This method adds the gene panels to the panel.

setPanel

public int setPanel(java.awt.Rectangle r)

This method sets the dimensions of the panel and sets up the gene panel.

Parameters:

r - Rectangle defining size and location of the panel

main

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

This method tests the Pathway class.

Parameters:

args -