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

Constructor Summary

Constructors

Constructor and Description
OboFileHandler(Ontology ontology)

Method Summary

Methods

Modifier and Type	Method and 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 Detail

TERM

public static final String TERM

See Also:

Constant Field Values

TYPEDEF

public static final String TYPEDEF

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Constant Field Values

ONTOLOGY

public static final String ONTOLOGY

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Constant Field Values

ID_KEY

public static final String ID_KEY

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Constant Field Values

SYNONYM

public static final String SYNONYM

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Constant Field Values

EXACT_SYNONYM

public static final String EXACT_SYNONYM

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Constant Field Values

BROAD_SYNONYM

public static final String BROAD_SYNONYM

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Constant Field Values

NARROW_SYNONYM

public static final String NARROW_SYNONYM

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Constant Field Values

REL_SYNONYM

public static final String REL_SYNONYM

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Constant Field Values

NAME

public static final String NAME

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Constant Field Values

DEF

public static final String DEF

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Constant Field Values

XREF_ANALOG

public static final String XREF_ANALOG

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Constant Field Values

COMMENT

public static final String COMMENT

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Constant Field Values

IS_A

public static final String IS_A

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Constant Field Values

IS_OBSOLETE

public static final String IS_OBSOLETE

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Constant Field Values

RELATIONSHIP

public static final String RELATIONSHIP

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Constant Field Values

DISJOINT_FROM

public static final String DISJOINT_FROM

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Constant Field Values

SUBSET

public static final String SUBSET

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Constant Field Values

INTERSECTION_OF

public static final String INTERSECTION_OF

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Constant Field Values

ALT_ID

public static final String ALT_ID

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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(String stanza)

Description copied from interface: OboFileEventListener

parsed a new stanza in the file

Specified by:

newStanza in interface OboFileEventListener

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

newSynonym

public void newSynonym(Synonym synonym)

Description copied from interface: OboFileEventListener

a new synonym has been found

Specified by:

newSynonym in interface OboFileEventListener