org.coode.owlapi.obo12.parser

Enum OBOVocabulary

java.lang.Object

java.lang.Enum<OBOVocabulary>

org.coode.owlapi.obo12.parser.OBOVocabulary

All Implemented Interfaces:

Serializable, Comparable<OBOVocabulary>, HasIRI

public enum OBOVocabulary
extends Enum<OBOVocabulary>
implements HasIRI

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALT_ID
ALT_NAME
AUTO_GENERATED_BY
BROAD_SYNONYM
BUILTIN
CARDINALITY
COMMENT
CONSIDER
DATA_VERSION
DATE
DEF
DEFAULT_NAMESPACE
DEFAULT_RELATIONSHIP_ID_PREFIX
DISJOINT_FROM
DOMAIN
EXACT_SYNONYM
FORMAT_VERSION
HAS_SCOPE
ID
ID_MAPPING
ID_SPACE
IMPORT
INSTANCE
INSTANCE_OF
INTERSECTION_OF
INVERSE
IS_A
IS_ANONYMOUS
IS_ASYMMETRIC
IS_CYCLIC
IS_METADATA_TAG
IS_OBSOLETE
IS_REFLEXIVE
IS_SYMMETRIC
IS_TRANSITIVE
MAX_CARDINALITY
MIN_CARDINALITY
NAME
NAMESPACE
NARROW_SYNONYM
ONTOLOGY
PART_OF
PROPERTY_VALUE
RANGE
RELATED_SYNONYM
RELATIONSHIP
REMARK
REPLACED_BY
SAVED_BY
SHORT_HAND
SUBSET
SUBSETDEF
SYNONYM
SYNONYM_TYPE
SYNONYM_TYPE_DEF
TERM
TRANSITIVE_OVER
TYPEDEF
UNION_OF
USE_TERM
VERSION
XREF
XREF_ANALOGUE
XREF_UNKNOWN

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATION_URI_BASE Deprecated. Use OBO_IRI_BASE
static String	LEGACY_OBO_IRI_BASE
static Pattern	OBO_ID_PATTERN The pattern for OBO IDs.
static String	OBO_IRI_BASE
static Pattern	OBO_IRI_PATTERN
static String	ONTOLOGY_URI_BASE Deprecated. Use OBO_IRI_BASE

Method Summary

Modifier and Type	Method and Description
static List<OBOVocabulary>	getHeaderTags()
static List<OBOVocabulary>	getInstanceStanzaTags()
IRI	getIRI()
String	getName()
static List<OBOVocabulary>	getTermStanzaTags()
static List<OBOVocabulary>	getTypeDefStanzaTags()
static IRI	ID2IRI(String oboId) Converts OBO Ids to IRIs.
static IRI	ID2IRI(String oboId, org.coode.owlapi.obo12.parser.IDSpaceManager idSpaceManager) Converts OBO Ids to IRIs.
static String	IRI2ID(IRI oboIRI)
static boolean	isOBOIRI(IRI oboIRI)
String	toString()
static OBOVocabulary	valueOf(String name) Returns the enum constant of this type with the specified name.
static OBOVocabulary[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

DATA_VERSION

public static final OBOVocabulary DATA_VERSION

VERSION

public static final OBOVocabulary VERSION

DATE

public static final OBOVocabulary DATE

SAVED_BY

public static final OBOVocabulary SAVED_BY

AUTO_GENERATED_BY

public static final OBOVocabulary AUTO_GENERATED_BY

ONTOLOGY

public static final OBOVocabulary ONTOLOGY

SUBSETDEF

public static final OBOVocabulary SUBSETDEF

IMPORT

public static final OBOVocabulary IMPORT

SYNONYM_TYPE_DEF

public static final OBOVocabulary SYNONYM_TYPE_DEF

SYNONYM_TYPE

public static final OBOVocabulary SYNONYM_TYPE

ID_SPACE

public static final OBOVocabulary ID_SPACE

DEFAULT_RELATIONSHIP_ID_PREFIX

public static final OBOVocabulary DEFAULT_RELATIONSHIP_ID_PREFIX

ID_MAPPING

public static final OBOVocabulary ID_MAPPING

REMARK

public static final OBOVocabulary REMARK

ID

public static final OBOVocabulary ID

NAME

public static final OBOVocabulary NAME

FORMAT_VERSION

public static final OBOVocabulary FORMAT_VERSION

TYPEDEF

public static final OBOVocabulary TYPEDEF

ALT_ID

public static final OBOVocabulary ALT_ID

SHORT_HAND

public static final OBOVocabulary SHORT_HAND

ALT_NAME

public static final OBOVocabulary ALT_NAME

NAMESPACE

public static final OBOVocabulary NAMESPACE

DEFAULT_NAMESPACE

public static final OBOVocabulary DEFAULT_NAMESPACE

DEF

public static final OBOVocabulary DEF

COMMENT

public static final OBOVocabulary COMMENT

SUBSET

public static final OBOVocabulary SUBSET

SYNONYM

public static final OBOVocabulary SYNONYM

HAS_SCOPE

public static final OBOVocabulary HAS_SCOPE

RELATED_SYNONYM

public static final OBOVocabulary RELATED_SYNONYM

EXACT_SYNONYM

public static final OBOVocabulary EXACT_SYNONYM

BROAD_SYNONYM

public static final OBOVocabulary BROAD_SYNONYM

NARROW_SYNONYM

public static final OBOVocabulary NARROW_SYNONYM

XREF

public static final OBOVocabulary XREF

XREF_ANALOGUE

public static final OBOVocabulary XREF_ANALOGUE

XREF_UNKNOWN

public static final OBOVocabulary XREF_UNKNOWN

IS_A

public static final OBOVocabulary IS_A

IS_OBSOLETE

public static final OBOVocabulary IS_OBSOLETE

PART_OF

public static final OBOVocabulary PART_OF

RELATIONSHIP

public static final OBOVocabulary RELATIONSHIP

REPLACED_BY

public static final OBOVocabulary REPLACED_BY

CONSIDER

public static final OBOVocabulary CONSIDER

USE_TERM

public static final OBOVocabulary USE_TERM

DOMAIN

public static final OBOVocabulary DOMAIN

RANGE

public static final OBOVocabulary RANGE

IS_CYCLIC

public static final OBOVocabulary IS_CYCLIC

IS_TRANSITIVE

public static final OBOVocabulary IS_TRANSITIVE

IS_SYMMETRIC

public static final OBOVocabulary IS_SYMMETRIC

IS_ASYMMETRIC

public static final OBOVocabulary IS_ASYMMETRIC

IS_REFLEXIVE

public static final OBOVocabulary IS_REFLEXIVE

INVERSE

public static final OBOVocabulary INVERSE

TRANSITIVE_OVER

public static final OBOVocabulary TRANSITIVE_OVER

INTERSECTION_OF

public static final OBOVocabulary INTERSECTION_OF

UNION_OF

public static final OBOVocabulary UNION_OF

DISJOINT_FROM

public static final OBOVocabulary DISJOINT_FROM

TERM

public static final OBOVocabulary TERM

BUILTIN

public static final OBOVocabulary BUILTIN

IS_METADATA_TAG

public static final OBOVocabulary IS_METADATA_TAG

CARDINALITY

public static final OBOVocabulary CARDINALITY

MAX_CARDINALITY

public static final OBOVocabulary MAX_CARDINALITY

MIN_CARDINALITY

public static final OBOVocabulary MIN_CARDINALITY

INSTANCE

public static final OBOVocabulary INSTANCE

INSTANCE_OF

public static final OBOVocabulary INSTANCE_OF

PROPERTY_VALUE

public static final OBOVocabulary PROPERTY_VALUE

IS_ANONYMOUS

public static final OBOVocabulary IS_ANONYMOUS

Field Detail

ONTOLOGY_URI_BASE

@Deprecated
public static final String ONTOLOGY_URI_BASE

Deprecated. Use OBO_IRI_BASE

See Also:

Constant Field Values

ANNOTATION_URI_BASE

@Deprecated
public static final String ANNOTATION_URI_BASE

Deprecated. Use OBO_IRI_BASE

OBO_IRI_BASE

public static final String OBO_IRI_BASE

LEGACY_OBO_IRI_BASE

public static final String LEGACY_OBO_IRI_BASE

See Also:

Constant Field Values

OBO_ID_PATTERN

public static final Pattern OBO_ID_PATTERN

The pattern for OBO IDs. Specified at http://www.obofoundry.org/id-policy.shtml

OBO_IRI_PATTERN

public static final Pattern OBO_IRI_PATTERN

Method Detail

values

public static OBOVocabulary[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (OBOVocabulary c : OBOVocabulary.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static OBOVocabulary valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

ID2IRI

public static IRI ID2IRI(String oboId)

Converts OBO Ids to IRIs. The conversion is defined at http://www.obofoundry.org/id-policy.shtml

Parameters:

oboId - The Id to convert

Returns:

The IRI of the converted Id

ID2IRI

public static IRI ID2IRI(String oboId,
                         org.coode.owlapi.obo12.parser.IDSpaceManager idSpaceManager)

Converts OBO Ids to IRIs. The conversion is defined at http://www.obofoundry.org/id-policy.shtml.

Parameters:

oboId - The OBO Id to convert.

idSpaceManager - An IDSpaceManager which can be used to customise the IRI prefixes used in the conversion.

Returns:

The IRI of the converted Id.

IRI2ID

public static String IRI2ID(IRI oboIRI)

isOBOIRI

public static boolean isOBOIRI(IRI oboIRI)

getName

public String getName()

getIRI

public IRI getIRI()

Specified by:

getIRI in interface HasIRI

toString

public String toString()

Overrides:

toString in class Enum<OBOVocabulary>

getHeaderTags

public static List<OBOVocabulary> getHeaderTags()

getTermStanzaTags

public static List<OBOVocabulary> getTermStanzaTags()

getTypeDefStanzaTags

public static List<OBOVocabulary> getTypeDefStanzaTags()

getInstanceStanzaTags

public static List<OBOVocabulary> getInstanceStanzaTags()