A B C D E F G H I J K L M N O P Q R S T U V W X

A

AbstractTagValueHandler - Class in org.coode.owlapi.obo.parser

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

AbstractTagValueHandler(String, OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AbstractTagValueHandler

addAnnotation(String, String, OWLLiteral) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

addEscapes(String) - Static method in error org.coode.owlapi.obo.parser.TokenMgrError

Replaces unprintable characters by their escaped (or unicode escaped) equivalents in the given string

addException(OBOStorageException) - Method in interface org.coode.owlapi.obo.renderer.OBOExceptionHandler

addException(OBOStorageException) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer

addIntersectionOfOperand(OWLClassExpression) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

addModifier(String, String) - Method in class org.coode.owlapi.obo.parser.Modifiers

Adds a modifier

addPair(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

addPair(IRI, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

addSymbolicIdMapping(String, IRI) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

addUnionOfOperand(OWLClassExpression) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

adjustBeginLineColumn(int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Method to adjust line and column numbers for the start of a token.

AdjustBuffSize() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

AltIdTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 10/05/2012

AltIdTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AltIdTagValueHandler

ANNOTATION_URI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

Deprecated. Use OBOVocabulary.OBO_IRI_BASE

applyChange(OWLOntologyChange) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

AsymmetricHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

AsymmetricHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.AsymmetricHandler

B

backup(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Retreat.

beginColumn - Variable in class org.coode.owlapi.obo.parser.Token

The column number of the first character of this Token.

beginLine - Variable in class org.coode.owlapi.obo.parser.Token

The line number of the first character of this Token.

BeginToken() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

bufcolumn - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

buffer - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

bufline - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

bufpos - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

Position in buffer.

C

canStoreOntology(OWLOntologyFormat) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer

clear() - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

CLOSE_SQUARE_BRACKET - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

column - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

Comment() - Method in class org.coode.owlapi.obo.parser.OBOParser

COMMENT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

COMMENT_END - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

COMMENT_START - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

createParser(OWLOntologyManager) - Method in class org.coode.owlapi.obo.parser.OBOParserFactory

curChar - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

currentToken - Variable in exception org.coode.owlapi.obo.parser.ParseException

This is the last token that has been consumed successfully.

D

DataVersionTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

DataVersionTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DataVersionTagValueHandler

debugStream - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Debug output.

DEFAULT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

DefaultNamespaceTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Information Management Group
Date: 01-Sep-2008

OBO Namespaces are NOT like XML Namespaces.

DefaultNamespaceTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DefaultNamespaceTagValueHandler

DefTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

DefTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DefTagValueHandler

disable_tracing() - Method in class org.coode.owlapi.obo.parser.OBOParser

Disable tracing.

DisjointFromHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

DisjointFromHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DisjointFromHandler

DomainHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 20-May-2007

DomainHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.DomainHandler

Done() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Set buffers back to null when finished.

E

enable_tracing() - Method in class org.coode.owlapi.obo.parser.OBOParser

Enable tracing.

endColumn - Variable in class org.coode.owlapi.obo.parser.Token

The column number of the last character of this Token.

endFrame() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

endFrame() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler

endFrame() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

endFrame() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

endHeader() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

endHeader() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler

endHeader() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

endHeader() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

endLine - Variable in class org.coode.owlapi.obo.parser.Token

The line number of the last character of this Token.

EOF - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

End of File.

eol - Variable in exception org.coode.owlapi.obo.parser.ParseException

The end of line string for this machine.

ERROR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

ExpandBuff(boolean) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

expectedTokenSequences - Variable in exception org.coode.owlapi.obo.parser.ParseException

Each entry in this array is an array of integers.

F

FillBuff() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

G

generateParseException() - Method in class org.coode.owlapi.obo.parser.OBOParser

Generate ParseException.

getAnnotationForTagValuePair(String, String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

Gets an OWLAnnotation for a tag value pair.

getBeginColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

getBeginLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

getBooleanConstant(boolean) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship

getCauses() - Method in exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException

getClassFromId(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Deprecated.

getComment() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair

getConsumer() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getCurrentClass() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getCurrentClass() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getCurrentEntity() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getCurrentId() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getDataFactory() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getDefaultIRIPrefix() - Method in class org.coode.owlapi.obo.parser.IDSpaceManager

Gets the default IRI prefix (which is returned by the IDSpaceManager.getIRIPrefix(String) for unregistered id prefixes.

getDefaultNamespaceTagValue() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Gets the default-namespace tag value for the current ontology.

getEndColumn() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Get end column.

getEndLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Get end line.

getExceptions() - Method in interface org.coode.owlapi.obo.renderer.OBOExceptionHandler

getExceptions() - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer

getFiller() - Method in class org.coode.owlapi.obo.renderer.OBORelationship

getFrameType() - Method in class org.coode.owlapi.obo.parser.OBOFrame

getHeaderFrame() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

getHeaderTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getIdSpaceManager() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Gets a COPY of the IDSpaceManager held by this OBOConsumer.

getIdSpaceManager() - Method in class org.coode.owlapi.obo.parser.OBOOntologyFormat

Gets the OBO id-space manager.

getIdType(String) - Static method in enum org.coode.owlapi.obo.parser.OBOIdType

Gets the OBOIdType for a given OBO ID.

GetImage() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

getInstanceStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getIRI() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Gets an IRI from an OBO ID.

getIRIFromOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOIdTranslator

getIRIFromOBOId(OWLOntologyID, IDSpaceManager, String) - Method in enum org.coode.owlapi.obo.parser.OBOIdType

getIRIFromTagName(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Gets an IRI from a tag name.

getIRIPrefix(String) - Method in class org.coode.owlapi.obo.parser.IDSpaceManager

Gets an IRI prefix from an id prefix.

getLine() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Deprecated.

getMaxCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship

getMessage() - Method in error org.coode.owlapi.obo.parser.TokenMgrError

You can also modify the body of this method to customize your error messages.

getMessage() - Method in exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException

getMinCardinality() - Method in class org.coode.owlapi.obo.renderer.OBORelationship

getModifierNames() - Method in class org.coode.owlapi.obo.parser.Modifiers

Returns the names of modifiers stored in this modifier object

getModifierValues(String) - Method in class org.coode.owlapi.obo.parser.Modifiers

getName() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getNextToken() - Method in class org.coode.owlapi.obo.parser.OBOParser

Get the next Token.

getNextToken() - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Get the next Token.

getNonTypeDefFrames() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

getOBOIdFromIRI() - Method in class org.coode.owlapi.obo.parser.OBOIdTranslator

getOBORelationships() - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

getOntology() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getOntology() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getOWLClass(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getOWLClassOrRestriction(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getOWLObjectProperty(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getOWLOntologyManager() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getOWLOntologyManager() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getPattern() - Method in enum org.coode.owlapi.obo.parser.OBOIdType

getPrefix() - Method in enum org.coode.owlapi.obo.parser.OBOPrefix

getProperty() - Method in class org.coode.owlapi.obo.renderer.OBORelationship

getQualifier() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair

getRelationIRIFromSymbolicIdOrOBOId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

getStanzaType() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

GetSuffix(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

getTabSize(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

getTagIRI(OBOVocabulary) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getTagIRI(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

Gets an IRI for a tag name.

getTagName() - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getTagName() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair

getTagName() - Method in interface org.coode.owlapi.obo.parser.TagValueHandler

Gets the name of the tag handled by this tag value handler

getTagValuePairs() - Method in class org.coode.owlapi.obo.parser.OBOFrame

getTermStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getToken(int) - Method in class org.coode.owlapi.obo.parser.OBOParser

Get the specific Token.

getTypeDefFrames() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

getTypeDefStanzaTags() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

getUnquotedString(String) - Method in class org.coode.owlapi.obo.parser.AbstractTagValueHandler

getValue() - Method in class org.coode.owlapi.obo.parser.OBOTagValuePair

getValue() - Method in class org.coode.owlapi.obo.parser.Token

An optional attribute value of the Token.

getValues(OBOVocabulary) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

H

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.AltIdTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.AsymmetricHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DataVersionTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DefaultNamespaceTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DefTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DisjointFromHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.DomainHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IDSpaceTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IDTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IntersectionOfHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.InverseHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IsATagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.IsObsoleteTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.NameTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OntologyTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.PartOfTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.ReflexiveHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.RelationshipTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SymmetricTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SynonymTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler

handle(String, String, String, String) - Method in interface org.coode.owlapi.obo.parser.TagValueHandler

Handles a tag.

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.TransitiveOverHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.TransitiveTagValueHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.UnionOfHandler

handle(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.XRefTagHandler

handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

handleTagValue(String, String, String, String) - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler

handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

handleTagValue(String, String, String, String) - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

Header() - Method in class org.coode.owlapi.obo.parser.OBOParser

I

IDSpaceManager - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

IDSpaceManager() - Constructor for class org.coode.owlapi.obo.parser.IDSpaceManager

IDSpaceManager(IDSpaceManager) - Constructor for class org.coode.owlapi.obo.parser.IDSpaceManager

Creates an IDSpaceManager and copying the id prefix to IRI prefix mappings contained in some other IDSpaceManager.

IDSpaceTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

IDSpaceTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IDSpaceTagValueHandler

IDTagValueHandler - Class in org.coode.owlapi.obo.parser

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

IDTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IDTagValueHandler

image - Variable in class org.coode.owlapi.obo.parser.Token

The string image of the token.

IN_COMMENT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

IN_QUOTED_STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

IN_STANZA_HEADER - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

IN_TAG_VALUE - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

IN_TAG_VALUE_PAIR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Lexical state.

inBuf - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

input_stream - Variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

inputStream - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

IntersectionOfHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

IntersectionOfHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IntersectionOfHandler

InverseHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

InverseHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.InverseHandler

IsATagValueHandler - Class in org.coode.owlapi.obo.parser

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

IsATagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IsATagValueHandler

isHeaderFrame() - Method in class org.coode.owlapi.obo.parser.OBOFrame

isInstanceType() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

isOBOIRI(IRI) - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

IsObsoleteTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

IsObsoleteTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.IsObsoleteTagValueHandler

isTerm() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

isTypedef() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

isTypeDefFrame() - Method in class org.coode.owlapi.obo.parser.OBOFrame

J

JavaCharStream - Class in org.coode.owlapi.obo.parser

An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (with java-like unicode escape processing).

JavaCharStream(Reader, int, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream

Constructor.

JavaCharStream(Reader, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream

Constructor.

JavaCharStream(InputStream, String, int, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream

Constructor.

JavaCharStream(InputStream, String, int, int) - Constructor for class org.coode.owlapi.obo.parser.JavaCharStream

Constructor.

jj_nt - Variable in class org.coode.owlapi.obo.parser.OBOParser

Next token.

jjFillToken() - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

jjnewLexState - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Lex State array.

jjstrLiteralImages - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Token literal values.

K

kind - Variable in class org.coode.owlapi.obo.parser.Token

An integer that describes the kind of this token.

L

LEGACY_OBO_IRI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

LexicalError(boolean, int, int, int, String, char) - Static method in error org.coode.owlapi.obo.parser.TokenMgrError

Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.

lexStateNames - Static variable in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Lexer state names.

line - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

LINE_COMMENTED_OUT - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

M

maxNextCharInd - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

Modifiers - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011

Modifiers() - Constructor for class org.coode.owlapi.obo.parser.Modifiers

N

NameTagValueHandler - Class in org.coode.owlapi.obo.parser

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

NameTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.NameTagValueHandler

newToken(int, String) - Static method in class org.coode.owlapi.obo.parser.Token

Returns a new Token object, by default.

newToken(int) - Static method in class org.coode.owlapi.obo.parser.Token

next - Variable in class org.coode.owlapi.obo.parser.Token

A reference to the next regular (non-special) token from the input stream.

nextCharBuf - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

nextCharInd - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

O

OBO_ID_PATTERN - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

The pattern for OBO IDs.

OBO_IRI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

OBO_IRI_PATTERN - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

OBOConsumer - Class in org.coode.owlapi.obo.parser

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

OBOConsumer(OWLOntology, OWLOntologyLoaderConfiguration, IRI) - Constructor for class org.coode.owlapi.obo.parser.OBOConsumer

OBOConsumer(OWLOntologyManager, OWLOntology, OWLOntologyLoaderConfiguration, IRI) - Constructor for class org.coode.owlapi.obo.parser.OBOConsumer

OBOExceptionHandler - Interface in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

OBOFlatFileOntologyStorer - Class in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 17, 2008

OBOFlatFileOntologyStorer() - Constructor for class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer

OBOFlatFileRenderer - Class in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 17, 2008

Renders OBO 1.2 flat file format.

OBOFlatFileRenderer(OWLOntologyManager) - Constructor for class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer

OBOFrame - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

OBOFrame(List<OBOTagValuePair>) - Constructor for class org.coode.owlapi.obo.parser.OBOFrame

OBOFrame(String, List<OBOTagValuePair>) - Constructor for class org.coode.owlapi.obo.parser.OBOFrame

OBOIdTranslator - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

OBOIdTranslator() - Constructor for class org.coode.owlapi.obo.parser.OBOIdTranslator

OBOIdType - Enum in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

OBOOntologyFormat - Class in org.coode.owlapi.obo.parser

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

OBOOntologyFormat() - Constructor for class org.coode.owlapi.obo.parser.OBOOntologyFormat

OBOOntologyFormat(IDSpaceManager) - Constructor for class org.coode.owlapi.obo.parser.OBOOntologyFormat

Constructs an OBOOntologyFormat object.

OBOParser - Class in org.coode.owlapi.obo.parser

OBOParser(InputStream) - Constructor for class org.coode.owlapi.obo.parser.OBOParser

Constructor with InputStream.

OBOParser(InputStream, String) - Constructor for class org.coode.owlapi.obo.parser.OBOParser

Constructor with InputStream and supplied encoding

OBOParser(Reader) - Constructor for class org.coode.owlapi.obo.parser.OBOParser

Constructor.

OBOParser(OBOParserTokenManager) - Constructor for class org.coode.owlapi.obo.parser.OBOParser

Constructor with generated Token Manager.

OBOParserConstants - Interface in org.coode.owlapi.obo.parser

Token literal values and constants.

OBOParserException - Exception in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 13-Apr-2007

OBOParserException(String) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException

OBOParserException(String, Throwable) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException

OBOParserException(Throwable) - Constructor for exception org.coode.owlapi.obo.parser.OBOParserException

OBOParserFactory - Class in org.coode.owlapi.obo.parser

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

OBOParserFactory() - Constructor for class org.coode.owlapi.obo.parser.OBOParserFactory

OBOParserHandler - Interface in org.coode.owlapi.obo.parser

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

OBOParserHandlerAdapter - Class in org.coode.owlapi.obo.parser

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

OBOParserHandlerAdapter() - Constructor for class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

OBOParserTokenManager - Class in org.coode.owlapi.obo.parser

Token Manager.

OBOParserTokenManager(JavaCharStream) - Constructor for class org.coode.owlapi.obo.parser.OBOParserTokenManager

Constructor.

OBOParserTokenManager(JavaCharStream, int) - Constructor for class org.coode.owlapi.obo.parser.OBOParserTokenManager

Constructor.

OBOPrefix - Enum in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

OBORelationship - Class in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 18, 2008

OBORelationship(OWLObjectProperty, OWLNamedIndividual) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationship

OBORelationship(OWLObjectProperty, OWLClass) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationship

OBORelationshipGenerator - Class in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 18, 2008

OBORelationshipGenerator(OBOExceptionHandler) - Constructor for class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

OBOStorageException - Exception in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

OBOStorageException(OWLObject, OWLObject, String) - Constructor for exception org.coode.owlapi.obo.renderer.OBOStorageException

OBOStorageIncompleteException - Exception in org.coode.owlapi.obo.renderer

Author: drummond
http://www.cs.man.ac.uk/~drummond/

The University Of Manchester
Bio Health Informatics Group
Date: Apr 9, 2009

OBOStorageIncompleteException(List<OBOStorageException>) - Constructor for exception org.coode.owlapi.obo.renderer.OBOStorageIncompleteException

OBOTagValuePair - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

OBOTagValuePair(String, String, String, String) - Constructor for class org.coode.owlapi.obo.parser.OBOTagValuePair

OBOTagValuePairList - Class in org.coode.owlapi.obo.renderer

Author: Nick Drummond
The University Of Manchester
Bio Health Informatics Group
Date: Dec 19, 2008

An ordered rendering of the Tag Value Pairs that also supports: - default values - unknown tags (which are rendered at the end of the known tags) - extraction of TVPs from annotations

OBOTagValuePairList(List<OBOVocabulary>) - Constructor for class org.coode.owlapi.obo.renderer.OBOTagValuePairList

OBOVocabulary - Enum in org.coode.owlapi.obo.parser

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

ONTOLOGY_URI_BASE - Static variable in enum org.coode.owlapi.obo.parser.OBOVocabulary

Deprecated. Use OBOVocabulary.OBO_IRI_BASE

OntologyTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011

OntologyTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.OntologyTagValueHandler

OPEN_SQUARE_BRACKET - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

org.coode.owlapi.obo.parser - package org.coode.owlapi.obo.parser

org.coode.owlapi.obo.renderer - package org.coode.owlapi.obo.renderer

OWLOBOParser - Class in org.coode.owlapi.obo.parser

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

OWLOBOParser() - Constructor for class org.coode.owlapi.obo.parser.OWLOBOParser

P

parse() - Method in class org.coode.owlapi.obo.parser.OBOParser

parse(OWLOntologyDocumentSource, OWLOntology) - Method in class org.coode.owlapi.obo.parser.OWLOBOParser

parse(OWLOntologyDocumentSource, OWLOntology, OWLOntologyLoaderConfiguration) - Method in class org.coode.owlapi.obo.parser.OWLOBOParser

ParseException - Exception in org.coode.owlapi.obo.parser

This exception is thrown when parse errors are encountered.

ParseException(Token, int[][], String[]) - Constructor for exception org.coode.owlapi.obo.parser.ParseException

This constructor is used by the method "generateParseException" in the generated parser.

ParseException() - Constructor for exception org.coode.owlapi.obo.parser.ParseException

The following constructors are for use by you for whatever purpose you can think of.

ParseException(String) - Constructor for exception org.coode.owlapi.obo.parser.ParseException

Constructor with message.

parseModifiers(String) - Static method in class org.coode.owlapi.obo.parser.Modifiers

Parses a list of modifiers.

parseXRef(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

PartOfTagValueHandler - Class in org.coode.owlapi.obo.parser

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

PartOfTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.PartOfTagValueHandler

PATTERN - Static variable in class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler

prevCharIsCR - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

prevCharIsLF - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

Q

QUOTED_STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

QUOTED_STRING_DBL_QUOTE_TERMINATOR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

QUOTED_STRING_NEW_LINE_TERMINATOR - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

QUOTED_STRING_START - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

R

RawFrameHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 19/04/2012

RawFrameHandler() - Constructor for class org.coode.owlapi.obo.parser.RawFrameHandler

ReadByte() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

readChar() - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Read a character.

ReflexiveHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

ReflexiveHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.ReflexiveHandler

registerIdSpace(String, String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

ReInit(Reader, int, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Reinitialise.

ReInit(Reader, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Reinitialise.

ReInit(InputStream, String, int, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Reinitialise.

ReInit(InputStream, String, int, int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

Reinitialise.

ReInit(InputStream) - Method in class org.coode.owlapi.obo.parser.OBOParser

Reinitialise.

ReInit(InputStream, String) - Method in class org.coode.owlapi.obo.parser.OBOParser

Reinitialise.

ReInit(Reader) - Method in class org.coode.owlapi.obo.parser.OBOParser

Reinitialise.

ReInit(OBOParserTokenManager) - Method in class org.coode.owlapi.obo.parser.OBOParser

Reinitialise.

ReInit(JavaCharStream) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Reinitialise parser.

ReInit(JavaCharStream, int) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Reinitialise parser.

RelationshipTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

RelationshipTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.RelationshipTagValueHandler

render(OWLOntology, Writer) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileRenderer

S

setCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship

setClass(OWLClass) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

setCurrentId(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

setDataVersionTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Sets the value of the data-version tag for the current ontology that is being parsed.

setDebugStream(PrintStream) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Set debug output.

setDefault(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

setDefault(IRI, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

setDefaultNamespaceTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Sets the value of the default-namespace tag for the current ontology being parsed.

setHandler(OBOParserHandler) - Method in class org.coode.owlapi.obo.parser.OBOParser

setIRIPrefix(String, String) - Method in class org.coode.owlapi.obo.parser.IDSpaceManager

Sets the IRI prefix for a given id prefix.

setMaxCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship

setMinCardinality(int) - Method in class org.coode.owlapi.obo.renderer.OBORelationship

setOntologyTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

Sets the value of the ontology tag for the current ontology that is being parsed.

setPair(OBOVocabulary, String) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

setTabSize(int) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

specialToken - Variable in class org.coode.owlapi.obo.parser.Token

This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.

Stanza() - Method in class org.coode.owlapi.obo.parser.OBOParser

STANZA_TYPE - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

startFrame(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

startFrame(String) - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler

startFrame(String) - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

startFrame(String) - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

startHeader() - Method in class org.coode.owlapi.obo.parser.OBOConsumer

startHeader() - Method in interface org.coode.owlapi.obo.parser.OBOParserHandler

startHeader() - Method in class org.coode.owlapi.obo.parser.OBOParserHandlerAdapter

startHeader() - Method in class org.coode.owlapi.obo.parser.RawFrameHandler

staticFlag - Static variable in class org.coode.owlapi.obo.parser.JavaCharStream

Whether parser is static.

storeOntology(OWLOntologyManager, OWLOntology, Writer, OWLOntologyFormat) - Method in class org.coode.owlapi.obo.renderer.OBOFlatFileOntologyStorer

STRING - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

SwitchTo(int) - Method in class org.coode.owlapi.obo.parser.OBOParserTokenManager

Switch to specified lex state.

SymmetricTagValueHandler - Class in org.coode.owlapi.obo.parser

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

SymmetricTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SymmetricTagValueHandler

SYNONYM_TYPE_IRI - Static variable in class org.coode.owlapi.obo.parser.SynonymTagValueHandler

SynonymScope - Enum in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

SynonymTagValueHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011

SynonymTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SynonymTagValueHandler

SynonymTypeDefTagHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012

SynonymTypeDefTagHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.SynonymTypeDefTagHandler

T

tabSize - Variable in class org.coode.owlapi.obo.parser.JavaCharStream

TAG_COLON - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

TAG_END - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

TAG_NAME - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

TAG_VALUE_WS - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

RegularExpression Id.

TagValueHandler - Interface in org.coode.owlapi.obo.parser

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

Concrete implementations of this interface allow specific behaviour for processing specific tag value pairs in an OBO file to be specified.

TagValuePair() - Method in class org.coode.owlapi.obo.parser.OBOParser

token - Variable in class org.coode.owlapi.obo.parser.OBOParser

Current token.

Token - Class in org.coode.owlapi.obo.parser

Describes the input token stream.

Token() - Constructor for class org.coode.owlapi.obo.parser.Token

No-argument constructor

Token(int) - Constructor for class org.coode.owlapi.obo.parser.Token

Constructs a new token for the specified Image.

Token(int, String) - Constructor for class org.coode.owlapi.obo.parser.Token

Constructs a new token for the specified Image and Kind.

token_source - Variable in class org.coode.owlapi.obo.parser.OBOParser

Generated Token Manager.

tokenImage - Static variable in interface org.coode.owlapi.obo.parser.OBOParserConstants

Literal token values.

tokenImage - Variable in exception org.coode.owlapi.obo.parser.ParseException

This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.

TokenMgrError - Error in org.coode.owlapi.obo.parser

Token Manager Error.

TokenMgrError() - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError

No arg constructor.

TokenMgrError(String, int) - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError

Constructor with message and reason.

TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error org.coode.owlapi.obo.parser.TokenMgrError

Full Constructor.

toString() - Method in class org.coode.owlapi.obo.parser.OBOOntologyFormat

Returns a string representation of the object.

toString() - Method in enum org.coode.owlapi.obo.parser.OBOVocabulary

toString() - Method in class org.coode.owlapi.obo.parser.Token

Returns the image.

TransitiveOverHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

TransitiveOverHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.TransitiveOverHandler

TransitiveTagValueHandler - Class in org.coode.owlapi.obo.parser

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

TransitiveTagValueHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.TransitiveTagValueHandler

U

unescapeTagValue(String) - Method in class org.coode.owlapi.obo.parser.OBOConsumer

UnionOfHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 06-Mar-2007

UnionOfHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.UnionOfHandler

UpdateLineColumn(char) - Method in class org.coode.owlapi.obo.parser.JavaCharStream

V

valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOIdType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOPrefix

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.coode.owlapi.obo.parser.SynonymScope

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.coode.owlapi.obo.parser.OBOIdType

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

values() - Static method in enum org.coode.owlapi.obo.parser.OBOPrefix

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

values() - Static method in enum org.coode.owlapi.obo.parser.OBOVocabulary

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

values() - Static method in enum org.coode.owlapi.obo.parser.SynonymScope

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

visit(OWLObjectSomeValuesFrom) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

visit(OWLObjectMinCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

visit(OWLObjectExactCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

visit(OWLObjectMaxCardinality) - Method in class org.coode.owlapi.obo.renderer.OBORelationshipGenerator

visit(OWLAnnotation) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

W

write(Writer) - Method in class org.coode.owlapi.obo.renderer.OBOTagValuePairList

X

XREF_IRI - Static variable in class org.coode.owlapi.obo.parser.SynonymTagValueHandler

XRefTagHandler - Class in org.coode.owlapi.obo.parser

Author: Matthew Horridge
The University of Manchester
Bio-Health Informatics Group
Date: 03/02/2011

XRefTagHandler(OBOConsumer) - Constructor for class org.coode.owlapi.obo.parser.XRefTagHandler

A B C D E F G H I J K L M N O P Q R S T U V W X