Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.data.ontology.readers
Class OBOFlatFileReader

java.lang.Object
  extended by 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
           
 
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
equals, 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
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!

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