ontologizer.io.obo

Class OBOParser

java.lang.Object

ontologizer.io.obo.OBOParser

public class OBOParser
extends Object

OBOParser parses the Gene Ontology OBO term definition file. Please see www.geneontology.org for background on this file format.

Author:

Peter N. Robinson, Sebastian Bauer, Sebastian Koehler

Field Summary

Fields

Modifier and Type	Field and Description
static int	IGNORE_SYNONYMS Ignore synonyms
static int	PARSE_DEFINITIONS Flag to keep the definitions
static int	PARSE_INTERSECTIONS Flag to keep the intersections
static int	PARSE_XREFS Flag to keep the xrefs
static int	SETNAMEEQUALTOID Takes the id as name, if the name is not present

Constructor Summary

Constructors

Constructor and Description
OBOParser(IParserInput input) Construct an obo parser.
OBOParser(IParserInput input, int options) Constructs an obo parser for a particular input.

Method Summary

Modifier and Type	Method and Description
String	doParse() The main parsing routine for the gene_ontology.obo file
String	doParse(IOBOParserProgress progress) The main parsing routine for the gene_ontology.obo file
ByteString	getDataVersion()
ByteString	getDate()
ByteString	getFormatVersion()
Set<Term>	getTermMap()

Methods inherited from class java.lang.Object

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

Field Detail

PARSE_DEFINITIONS

public static final int PARSE_DEFINITIONS

Flag to keep the definitions

See Also:

Constant Field Values

PARSE_XREFS

public static final int PARSE_XREFS

Flag to keep the xrefs

See Also:

Constant Field Values

PARSE_INTERSECTIONS

public static final int PARSE_INTERSECTIONS

Flag to keep the intersections

See Also:

Constant Field Values

SETNAMEEQUALTOID

public static final int SETNAMEEQUALTOID

Takes the id as name, if the name is not present

See Also:

Constant Field Values

IGNORE_SYNONYMS

public static final int IGNORE_SYNONYMS

Ignore synonyms

See Also:

Constant Field Values

Constructor Detail

OBOParser

public OBOParser(IParserInput input)

Construct an obo parser.

Parameters:

input - defines the input wrapping the stanza file

OBOParser

public OBOParser(IParserInput input,
                 int options)

Constructs an obo parser for a particular input. Options can be combined via logical or. Valid options are:

• PARSE_DEFINITIONS - to gather the textual definition entry.

Parameters:

input - defines the input wrapping the stanza files

options - defines some options.

Method Detail

getTermMap

public Set<Term> getTermMap()

doParse

public String doParse()
               throws IOException,
                      OBOParserException

The main parsing routine for the gene_ontology.obo file

Returns:

A string giving details about the parsed obo file

Throws:

OBOParserException

IOException

doParse

public String doParse(IOBOParserProgress progress)
               throws IOException,
                      OBOParserException

The main parsing routine for the gene_ontology.obo file

Parameters:

progress -

Returns:

A string giving details about the parsed obo file

Throws:

OBOParserException

IOException

getFormatVersion

public ByteString getFormatVersion()

getDate

public ByteString getDate()

getDataVersion

public ByteString getDataVersion()

Returns:

the version number of the data of described by obo file.