baseCode.xml
Class GOParser

java.lang.Object
  baseCode.xml.GOParser

public class GOParser

extends java.lang.Object

Read in the GO XML file provided by the Gene Ontology Consortium.

Copyright (c) Columbia University

Version:

$Id: GOParser.java,v 1.14 2004/08/04 09:47:44 pavlidis Exp $

Author:

Paul Pavlidis

Constructor Summary

GOParser(java.io.InputStream i)

Method Summary

java.util.Map	getGONameMap() Get a simple Map that contains keys that are the GO ids, values are the names.
DirectedGraph	getGraph() Get the graph that was created.

Methods inherited from class java.lang.Object

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

Constructor Detail

GOParser

public GOParser(java.io.InputStream i)
         throws java.io.IOException,
                org.xml.sax.SAXException

Method Detail

getGraph

public DirectedGraph getGraph()

Get the graph that was created.

Returns:

a DirectedGraph. Nodes contain OntologyEntry instances.

getGONameMap

public java.util.Map getGONameMap()

Get a simple Map that contains keys that are the GO ids, values are the names. This can replace the functionality of the GONameReader in classScore.

Returns:

Map