cytoscape.data.ontology.readers
Class OBOFlatFileReader

java.lang.Object
  cytoscape.data.ontology.readers.OBOFlatFileReader

All Implemented Interfaces:

OntologyReader

public class OBOFlatFileReader
extends Object
implements OntologyReader

OBO file reader.

This is a general OBO (Open Biomedical Ontologies: http://obo.sourceforge.net/) flatfile reader.
In Cytoscape, This will be used mainly for reading gene ontology. However, it is compatible with all files written in OBO format.

OBO files are available at:
http://obo.sourceforge.net/cgi-bin/table.cgi

Since:

Cytoscape 2.4

Version:

0.7

Author:

Keiichiro Ono

Field Summary

static String	OBO_PREFIX
static String	ONTOLOGY_DAG_ROOT
protected static String	TERM_TAG

Constructor Summary

OBOFlatFileReader(InputStream oboStream, String name)

OBOFlatFileReader(String fileName, String name)

OBOFlatFileReader(URL dataSource, String name)

Method Summary

CyNetwork	getDag() DOCUMENT ME!
Map<String,String>	getHeader() DOCUMENT ME!
CyAttributes	getTermsAttributes() DOCUMENT ME!
void	readOntology() DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Field Detail

ONTOLOGY_DAG_ROOT

public static final String ONTOLOGY_DAG_ROOT

See Also:

Constant Field Values

OBO_PREFIX

public static final String OBO_PREFIX

See Also:

Constant Field Values

TERM_TAG

protected static final String TERM_TAG

See Also:

Constant Field Values

Constructor Detail

OBOFlatFileReader

public OBOFlatFileReader(String fileName,
                         String name)
                  throws FileNotFoundException

Parameters:

fileName -

Throws:

FileNotFoundException

OBOFlatFileReader

public OBOFlatFileReader(URL dataSource,
                         String name)
                  throws IOException

Parameters:

dataSource -

Throws:

IOException

OBOFlatFileReader

public OBOFlatFileReader(InputStream oboStream,
                         String name)

Parameters:

oboStream -

name -

Method Detail

readOntology

public void readOntology()
                  throws IOException

Description copied from interface: OntologyReader

DOCUMENT ME!

Specified by:

readOntology in interface OntologyReader

Throws:

IOException

getHeader

public Map<String,String> getHeader()

DOCUMENT ME!

Specified by:

getHeader in interface OntologyReader

Returns:

DOCUMENT ME!

getTermsAttributes

public CyAttributes getTermsAttributes()

DOCUMENT ME!

Returns:

DOCUMENT ME!

getDag

public CyNetwork getDag()

DOCUMENT ME!

Specified by:

getDag in interface OntologyReader

Returns:

DOCUMENT ME!