ubic.erminej.data

Class GOParser

java.lang.Object

ubic.erminej.data.GOParser

public class GOParser
extends Object

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

Version:

$Id: GOParser.java,v 1.10 2012/04/26 20:43:17 paul Exp $

Author:

Paul Pavlidis

Constructor Summary

Constructors

Constructor and Description
GOParser(InputStream i)
GOParser(InputStream i, boolean oldFormat)

Method Summary

Methods

Modifier and Type	Method and Description
Map<String,GeneSetTerm>	getGONameMap() Get a simple Map that contains keys that are the GO ids, values are the names.
DirectedGraph<String,GeneSetTerm>	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(InputStream i)
         throws IOException,
                SAXException

Throws:

IOException

SAXException

GOParser

public GOParser(InputStream i,
        boolean oldFormat)
         throws IOException,
                SAXException

Parameters:

i -

oldFormat - if true, use the old-fashioned scheme

Throws:

IOException

SAXException

Method Detail

getGONameMap

public Map<String,GeneSetTerm> 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

getGraph

public DirectedGraph<String,GeneSetTerm> getGraph()

Get the graph that was created.

Returns:

a DirectedGraph. Nodes contain OntologyEntry instances.