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 java.lang.Object
implements OboFileEventListener

A file handler for .obo files

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	ALT_ID
static java.lang.String	BROAD_SYNONYM
static java.lang.String	COMMENT
static java.lang.String	DEF
static java.lang.String	DISJOINT_FROM
static java.lang.String	EXACT_SYNONYM
static java.lang.String	ID_KEY
static java.lang.String	INTERSECTION_OF
static java.lang.String	IS_A
static java.lang.String	IS_OBSOLETE
static java.lang.String	NAME
static java.lang.String	NAMESPACE
static java.lang.String	NARROW_SYNONYM
static java.lang.String	ONTOLOGY
static java.lang.String	REL_SYNONYM
static java.lang.String	RELATIONSHIP
static java.lang.String	REPLACED_BY
static java.lang.String	SUBSET
static java.lang.String	SYNONYM
static java.lang.String	TERM
static java.lang.String	TYPEDEF
static java.lang.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(java.lang.String key, java.lang.String value)	found a new key in the file
void	newOboFileHeader()	parsed a new OBO file header
void	newStanza(java.lang.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 Detail

TERM

public static final java.lang.String TERM

See Also:

Constant Field Values

TYPEDEF

public static final java.lang.String TYPEDEF

See Also:

Constant Field Values

ONTOLOGY

public static final java.lang.String ONTOLOGY

See Also:

Constant Field Values

ID_KEY

public static final java.lang.String ID_KEY

See Also:

Constant Field Values

SYNONYM

public static final java.lang.String SYNONYM

See Also:

Constant Field Values

EXACT_SYNONYM

public static final java.lang.String EXACT_SYNONYM

See Also:

Constant Field Values

BROAD_SYNONYM

public static final java.lang.String BROAD_SYNONYM

See Also:

Constant Field Values

NARROW_SYNONYM

public static final java.lang.String NARROW_SYNONYM

See Also:

Constant Field Values

REL_SYNONYM

public static final java.lang.String REL_SYNONYM

See Also:

Constant Field Values

NAME

public static final java.lang.String NAME

See Also:

Constant Field Values

DEF

public static final java.lang.String DEF

See Also:

Constant Field Values

XREF_ANALOG

public static final java.lang.String XREF_ANALOG

See Also:

Constant Field Values

COMMENT

public static final java.lang.String COMMENT

See Also:

Constant Field Values

IS_A

public static final java.lang.String IS_A

See Also:

Constant Field Values

IS_OBSOLETE

public static final java.lang.String IS_OBSOLETE

See Also:

Constant Field Values

RELATIONSHIP

public static final java.lang.String RELATIONSHIP

See Also:

Constant Field Values

DISJOINT_FROM

public static final java.lang.String DISJOINT_FROM

See Also:

Constant Field Values

SUBSET

public static final java.lang.String SUBSET

See Also:

Constant Field Values

INTERSECTION_OF

public static final java.lang.String INTERSECTION_OF

See Also:

Constant Field Values

NAMESPACE

public static final java.lang.String NAMESPACE

See Also:

Constant Field Values

REPLACED_BY

public static final java.lang.String REPLACED_BY

See Also:

Constant Field Values

ALT_ID

public static final java.lang.String ALT_ID

See Also:

Constant Field Values

Constructor Detail

OboFileHandler

public OboFileHandler(Ontology ontology)

Method Detail

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(java.lang.String stanza)

Description copied from interface: OboFileEventListener

parsed a new stanza in the file

Specified by:

newStanza in interface OboFileEventListener

newKey

public void newKey(java.lang.String key,
                   java.lang.String value)

Description copied from interface: OboFileEventListener

found a new key in the file

Specified by:

newKey in interface OboFileEventListener

newSynonym

public void newSynonym(Synonym synonym)

Description copied from interface: OboFileEventListener

a new synonym has been found

Specified by:

newSynonym in interface OboFileEventListener