baseCode.bio.geneset
Class GONames

java.lang.Object
  baseCode.bio.geneset.GONames

public class GONames

extends java.lang.Object

Rea data from GO XML file, store in easy-to-use data structure.

Copyright (c) 2004 Columbia University

Version:

$Id: GONames.java,v 1.3 2004/12/28 22:07:27 pavlidis Exp $

Author:

Paul Pavlidis, Homin Lee

Constructor Summary

GONames(java.io.InputStream inputStream)

GONames(java.lang.String filename)

Method Summary

void	addClass(java.lang.String id, java.lang.String name)
java.lang.String	getAspectForId(java.lang.String go_ID) Get the aspect (molecular_function etc) for an id.
java.util.Set	getChildren(java.lang.String id)
DirectedGraph	getGraph() Get the graph representation of the GO hierarchy.
java.util.Map	getMap() Get the Map representation of the GO id - name associations.
java.lang.String	getNameForId(java.lang.String go_ID)
java.util.Set	getNewGeneSets() Return the Set of all new gene sets (ones which were added after loading the file)
java.util.Set	getParents(java.lang.String id)
void	modifyClass(java.lang.String id, java.lang.String name)
boolean	newSet(java.lang.String id) Check if a gene set is already defined.

Methods inherited from class java.lang.Object

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

Constructor Detail

GONames

public GONames(java.lang.String filename)
        throws org.xml.sax.SAXException,
               java.io.IOException

Parameters:

filename - String The XML file containing class to name mappings. First column is the class id, second is a description that will be used int program output.

Throws:

java.io.IOException

org.xml.sax.SAXException

GONames

public GONames(java.io.InputStream inputStream)
        throws java.io.IOException,
               org.xml.sax.SAXException

Parameters:

inputStream -

Throws:

java.io.IOException

org.xml.sax.SAXException

Method Detail

getGraph

public DirectedGraph getGraph()

Get the graph representation of the GO hierarchy. This can be used to support JTree representations.

Returns:

getChildren

public java.util.Set getChildren(java.lang.String id)

Parameters:

id -

Returns:

a Set containing the ids of geneSets which are immediately below the selected one in the hierarchy.

getParents

public java.util.Set getParents(java.lang.String id)

Parameters:

id -

Returns:

a Set containing the ids of geneSets which are immediately above the selected one in the hierarchy.

getMap

public java.util.Map getMap()

Get the Map representation of the GO id - name associations.

Returns:

Map

getNameForId

public java.lang.String getNameForId(java.lang.String go_ID)

Parameters:

go_ID - String

Returns:

String

getAspectForId

public java.lang.String getAspectForId(java.lang.String go_ID)

Get the aspect (molecular_function etc) for an id.

Parameters:

go_ID -

Returns:

addClass

public void addClass(java.lang.String id,
                     java.lang.String name)

Parameters:

id - String

name - String

modifyClass

public void modifyClass(java.lang.String id,
                        java.lang.String name)

Parameters:

id - String

name - String

newSet

public boolean newSet(java.lang.String id)

Check if a gene set is already defined.

Parameters:

id -

Returns:

getNewGeneSets

public java.util.Set getNewGeneSets()

Return the Set of all new gene sets (ones which were added after loading the file)

Returns: