Package org.biojava.nbio.ontology.obo

Class OboFileHandler

java.lang.Object

org.biojava.nbio.ontology.obo.OboFileHandler

All Implemented Interfaces:

OboFileEventListener

public class OboFileHandler
extends Object
implements OboFileEventListener

A file handler for .obo files

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ALT_ID
static final String	BROAD_SYNONYM
static final String	COMMENT
static final String	DEF
static final String	DISJOINT_FROM
static final String	EXACT_SYNONYM
static final String	ID_KEY
static final String	INTERSECTION_OF
static final String	IS_A
static final String	IS_OBSOLETE
static final String	NAME
static final String	NAMESPACE
static final String	NARROW_SYNONYM
static final String	ONTOLOGY
static final String	REL_SYNONYM
static final String	RELATIONSHIP
static final String	REPLACED_BY
static final String	SUBSET
static final String	SYNONYM
static final String	TERM
static final String	TYPEDEF
static final String	XREF_ANALOG

Constructor Summary

Constructors

Constructor	Description
OboFileHandler(Ontology ontology)

Method Summary

Modifier and Type	Method	Description
void	documentEnd()	end of parsing a new OBO file
void	documentStart()	starting to parse a new OBO file
void	newKey(String key, String value)	found a new key in the file
void	newOboFileHeader()	parsed a new OBO file header
void	newStanza(String stanza)	parsed a new stanza in the file
void	newSynonym(Synonym synonym)	a new synonym has been found

Methods inherited from class java.lang.Object

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

Field Details

TERM

public static final String TERM

See Also:

• Constant Field Values

TYPEDEF

public static final String TYPEDEF

See Also:

• Constant Field Values

ONTOLOGY

public static final String ONTOLOGY

See Also:

• Constant Field Values

ID_KEY

public static final String ID_KEY

See Also:

• Constant Field Values

SYNONYM

public static final String SYNONYM

See Also:

• Constant Field Values

EXACT_SYNONYM

public static final String EXACT_SYNONYM

See Also:

• Constant Field Values

BROAD_SYNONYM

public static final String BROAD_SYNONYM

See Also:

• Constant Field Values

NARROW_SYNONYM

public static final String NARROW_SYNONYM

See Also:

• Constant Field Values

REL_SYNONYM

public static final String REL_SYNONYM

See Also:

• Constant Field Values

NAME

public static final String NAME

See Also:

• Constant Field Values

DEF

public static final String DEF

See Also:

• Constant Field Values

XREF_ANALOG

public static final String XREF_ANALOG

See Also:

• Constant Field Values

COMMENT

public static final String COMMENT

See Also:

• Constant Field Values

IS_A

public static final String IS_A

See Also:

• Constant Field Values

IS_OBSOLETE

public static final String IS_OBSOLETE

See Also:

• Constant Field Values

RELATIONSHIP

public static final String RELATIONSHIP

See Also:

• Constant Field Values

DISJOINT_FROM

public static final String DISJOINT_FROM

See Also:

• Constant Field Values

SUBSET

public static final String SUBSET

See Also:

• Constant Field Values

INTERSECTION_OF

public static final String INTERSECTION_OF

See Also:

• Constant Field Values

NAMESPACE

public static final String NAMESPACE

See Also:

• Constant Field Values

REPLACED_BY

public static final String REPLACED_BY

See Also:

• Constant Field Values

ALT_ID

public static final String ALT_ID

See Also:

• Constant Field Values

Constructor Details

OboFileHandler

public OboFileHandler(Ontology ontology)

Method Details

documentEnd

public void documentEnd()

Description copied from interface: OboFileEventListener

end of parsing a new OBO file

Specified by:

documentEnd in interface OboFileEventListener

documentStart

public void documentStart()

Description copied from interface: OboFileEventListener

starting to parse a new OBO file

Specified by:

documentStart in interface OboFileEventListener

newOboFileHeader

public void newOboFileHeader()

Description copied from interface: OboFileEventListener

parsed a new OBO file header

Specified by:

newOboFileHeader in interface OboFileEventListener

newStanza

public void newStanza(String stanza)

Description copied from interface: OboFileEventListener

parsed a new stanza in the file

Specified by:

newStanza in interface OboFileEventListener

Parameters:

stanza -

newKey

public void newKey(String key,
 String value)

Description copied from interface: OboFileEventListener

found a new key in the file

Specified by:

newKey in interface OboFileEventListener

Parameters:

key -

value -

newSynonym

public void newSynonym(Synonym synonym)

Description copied from interface: OboFileEventListener

a new synonym has been found

Specified by:

newSynonym in interface OboFileEventListener

Parameters:

synonym -