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

A

absoulteURLPattern - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

AbstractMacroExpansionVisitor - Class in org.obolibrary.macro

Empty abstract visitor for macro expansion.

AbstractMacroExpansionVisitor(OWLOntology, Logger) - Constructor for class org.obolibrary.macro.AbstractMacroExpansionVisitor

add(OWLAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

add(Set<OWLAxiom>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

add(Frame) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

addClause(Clause) - Method in class org.obolibrary.oboformat.model.Frame

addDeclaredAnnotationProperties(Collection<OWLAnnotationProperty>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

addDefaultOntologyHeader(String) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the default ontology header.

addFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the frame.

addImportedOBODoc(OBODoc) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the imported obo doc.

addInstanceFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the instance frame.

addOntologyAnnotation(OWLAnnotationProperty, OWLAnnotationValue, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

addPropertyValueHeaders(Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

addQualifiers(Clause, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

addQualifierValue(QualifierValue) - Method in class org.obolibrary.oboformat.model.Clause

addTermFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the term frame.

addTypedefFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc

Adds the typedef frame.

addValue(Object) - Method in class org.obolibrary.oboformat.model.Clause

addXref(Xref) - Method in class org.obolibrary.oboformat.model.Clause

advance(int) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

advanceLine() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

AnnotationCardinalityException(String, Throwable) - Constructor for exception org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityException

Create a new Exception.

AnnotationCardinalityException(String) - Constructor for exception org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityException

Create a new Exception.

annotationFrames - Variable in class org.obolibrary.oboformat.model.OBODoc

The annotation frames.

annotationPropertyMap - Static variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

annotationPropertyMap - Static variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

annotation map

apply(OWLOntologyChange) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

apply(List<OWLOntologyChange>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

apToDeclare - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

apToDeclare - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

C

canStoreOntology(OWLOntologyFormat) - Method in class org.coode.owlapi.oboformat.OBOFormatStorer

canStoreOntology(OWLOntologyFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer

check() - Method in class org.obolibrary.oboformat.model.Frame

Check this frame for violations, i.e.

check() - Method in class org.obolibrary.oboformat.model.OBODoc

Check this document for violations, i.e.

checkAnnotationCardinality(OWLOntology, OboInOwlCardinalityTools.AnnotationCardinalityReporter, OboInOwlCardinalityTools.AnnotationCardinalityConfictHandler) - Static method in class org.obolibrary.obo2owl.OboInOwlCardinalityTools

Check the annotations for cardinality violations.

checkAnnotationCardinality(OWLOntology) - Static method in class org.obolibrary.obo2owl.OboInOwlCardinalityTools

Check the annotations for cardinality violations.

checkAnnotationCardinality(OWLOntology, OboInOwlCardinalityTools.AnnotationCardinalityReporter) - Static method in class org.obolibrary.obo2owl.OboInOwlCardinalityTools

Check the annotations for cardinality violations.

checkDanglingReferences(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Clause - Class in org.obolibrary.oboformat.model

Clause

Clause(OBOFormatConstants.OboFormatTag) - Constructor for class org.obolibrary.oboformat.model.Clause

Clause(String) - Constructor for class org.obolibrary.oboformat.model.Clause

Clause(String, String) - Constructor for class org.obolibrary.oboformat.model.Clause

Clause(OBOFormatConstants.OboFormatTag, String) - Constructor for class org.obolibrary.oboformat.model.Clause

Clause() - Constructor for class org.obolibrary.oboformat.model.Clause

Deprecated.

use Clause(String). Using this constructor makes the hashcode variable.

clauses - Variable in class org.obolibrary.oboformat.model.Frame

The clauses.

clsToDeclar - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

consume(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

convert(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

Creates an OBOFormatParser object to parse a file and then converts it using the convert method

convert(OBODoc) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

convert(OBODoc, OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

convert(OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

convertURL(String, String, OWLOntologyManager) - Static method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

Static convenience method which: (1) creates an Obo2Owl bridge object (2) parses an obo file from a URL (3) converts that to an OWL ontology (4) saves the OWL ontology as RDF/XML

convertURL(String, String, String, OWLOntologyManager) - Static method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

See OWLAPIObo2Owl.convertURL(String iri, String outFile, OWLOntologyManager manager)

createGCIOntology() - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor

createParser(OWLOntologyManager) - Method in class org.coode.owlapi.oboformat.OBOFormatParserFactory

createRelationshipClauseWithCardinality(OWLObjectCardinalityRestriction, String, Set<QualifierValue>, OWLSubClassOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

createRelationshipClauseWithRestrictions(OWLQuantifiedObjectRestriction, String, Set<QualifierValue>, OWLSubClassOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

D

DEFAULT_CHARACTER_ENCODING - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants

UTF-8 default encoding

DEFAULT_HANDLER - Static variable in class org.obolibrary.obo2owl.OboInOwlCardinalityTools

default handler

DEFAULT_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants

default iri

defaultIDSpace - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

Diff - Class in org.obolibrary.oboformat.diff

Diff

Diff(String, String, Frame, int) - Constructor for class org.obolibrary.oboformat.diff.Diff

Diff(String, String, Frame, Frame, Clause, int) - Constructor for class org.obolibrary.oboformat.diff.Diff

discardUntranslatable - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

dispose() - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor

Call this method to clear internal references.

dispose() - Method in class org.obolibrary.macro.MacroExpansionVisitor

Call this method to clear internal references.

dispose() - Method in class org.obolibrary.macro.ManchesterSyntaxTool

Call this method to dispose the internal data structures.

DocumentStructureException - Exception in org.obolibrary.oboformat.model

The Class DocumentStructureException.

DocumentStructureException(String) - Constructor for exception org.obolibrary.oboformat.model.DocumentStructureException

Instantiates a new document structure exception.

E

eof() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

eol() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

equals(Object) - Method in class org.obolibrary.oboformat.model.Clause

equals(Object) - Method in class org.obolibrary.oboformat.model.QualifierValue

equals(Object) - Method in class org.obolibrary.oboformat.model.Xref

EquivalenceExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.EquivalenceExpansion

error(String, OWLAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

error(OWLAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

error(String) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.EquivalenceExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.HasSubClassExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.IsaExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion

expand(Frame, String, String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.Rule

expandAll() - Method in class org.obolibrary.macro.MacroExpansionVisitor

expandOWLObjHasVal(OWLObjectHasValue, OWLIndividual, OWLObjectPropertyExpression) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

expandOWLObjSomeVal(OWLClassExpression, OWLObjectPropertyExpression) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

expandPrefix(String) - Method in class org.obolibrary.obo2owl.IdTranslator

Expands an OBO prefix such as "GO" to "http://purl.obolibrary.org/obo/GO_".

expandXrefs() - Method in class org.obolibrary.oboformat.parser.XrefExpander

expand xrefs

F

fac - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

fac - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

forceEol() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

forceParseNlOrEof() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

format(Date) - Static method in class org.obolibrary.obo2owl.Obo2OWLConstants

Frame - Class in org.obolibrary.oboformat.model

The Class Frame.

Frame() - Constructor for class org.obolibrary.oboformat.model.Frame

Instantiates a new frame.

Frame(Frame.FrameType) - Constructor for class org.obolibrary.oboformat.model.Frame

Instantiates a new frame.

Frame.FrameType - Enum in org.obolibrary.oboformat.model

The Enum FrameType.

FrameMergeException - Exception in org.obolibrary.oboformat.model

The Class FrameMergeException.

FrameMergeException(String) - Constructor for exception org.obolibrary.oboformat.model.FrameMergeException

Instantiates a new frame merge exception.

FrameStructureException - Exception in org.obolibrary.oboformat.model

The Class FrameStructureException.

FrameStructureException(String) - Constructor for exception org.obolibrary.oboformat.model.FrameStructureException

Instantiates a new frame structure exception.

FrameStructureException(Frame, String) - Constructor for exception org.obolibrary.oboformat.model.FrameStructureException

Instantiates a new frame structure exception.

G

GenusDifferentiaExpansion(String, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion

getAnnotation() - Method in class org.obolibrary.oboformat.model.Xref

getClause(String) - Method in class org.obolibrary.oboformat.model.Frame

getClause(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame

getClause1() - Method in class org.obolibrary.oboformat.diff.Diff

getClause2() - Method in class org.obolibrary.oboformat.diff.Diff

getClauses() - Method in class org.obolibrary.oboformat.model.Frame

getClauses(String) - Method in class org.obolibrary.oboformat.model.Frame

getClauses(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame

getDataVersion(OWLOntology) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getDefaultIDSpace() - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getDefaultOboNamespace() - Method in interface org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider

Retrieve the default OBO namespace.

getDefaultOboNamespace() - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider

getDiffs(OBODoc, OBODoc) - Method in class org.obolibrary.oboformat.diff.OBODocDiffer

getFollowImports() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

getFrame1() - Method in class org.obolibrary.oboformat.diff.Diff

getFrame2() - Method in class org.obolibrary.oboformat.diff.Diff

getHeaderFrame() - Method in class org.obolibrary.oboformat.model.OBODoc

getId(IRI) - Method in class org.obolibrary.macro.ManchesterSyntaxTool

Translate the IRI into the short form as expected by the parser.

getId(OWLEntity) - Method in class org.obolibrary.macro.ManchesterSyntaxTool

Translate the OWLEntity identifier into the short form as expected by the parser.

getId() - Method in class org.obolibrary.oboformat.model.Frame

getIdentifier(OWLObject) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getIdentifier(IRI) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

See table 5.9.2.

getIdentifier(IRI, OWLOntology) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getIdentifierFromObject(OWLObject, OWLOntology, String) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

Retrieve the identifier for a given OWLObject.

getIdentifierFromObject(OWLObject, OWLOntology) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

Retrieve the identifier for a given OWLObject.

getIdentifierUsingBaseOntology(IRI) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getIdPrefix(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getIdref() - Method in class org.obolibrary.oboformat.model.Xref

getIDSpace(String) - Method in class org.obolibrary.oboformat.model.OBODoc

Looks up the ID prefix to IRI prefix mapping.

getImportedOBODocs() - Method in class org.obolibrary.oboformat.model.OBODoc

getInstanceFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc

getInstanceFrames() - Method in class org.obolibrary.oboformat.model.OBODoc

getIRI() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

getLabel() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

getLine() - Method in exception org.obolibrary.oboformat.parser.OBOFormatParserException

Gets the line.

getLineNo() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

getLineNo() - Method in exception org.obolibrary.oboformat.parser.OBOFormatParserException

Gets the line no.

getManager() - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getManager() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getMappedTag() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

getMessage() - Method in exception org.obolibrary.oboformat.parser.OBOFormatParserException

getName(String) - Method in interface org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider

Try to retrieve the valid name for the given identifier.

getName(String) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider

getNamespace() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

getObodoc() - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getObodoc() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getOntologyId(OWLOntology) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

if does not match this pattern, then retain original IRI

getOntologyId(IRI) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getOwlOntology() - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getQualifier() - Method in class org.obolibrary.oboformat.model.QualifierValue

getQualifierValues() - Method in class org.obolibrary.oboformat.model.Clause

getQVBoolean(String, Collection<QualifierValue>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getQVInt(String, Collection<QualifierValue>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getQVString(String, Collection<QualifierValue>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getShortName() - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

getStrictConversion() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getTag() - Method in class org.obolibrary.oboformat.model.Clause

getTag(String) - Static method in class org.obolibrary.oboformat.parser.OBOFormatConstants

getTag() - Method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

getTag() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

getTags() - Method in class org.obolibrary.oboformat.model.Frame

getTagValue(String) - Method in class org.obolibrary.oboformat.model.Frame

getTagValue(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame

getTagValue(String, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame

getTagValue(OBOFormatConstants.OboFormatTag, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame

getTagValues(OBOFormatConstants.OboFormatTag) - Method in class org.obolibrary.oboformat.model.Frame

getTagValues(String) - Method in class org.obolibrary.oboformat.model.Frame

getTagValues(OBOFormatConstants.OboFormatTag, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame

getTagValues(String, Class<T>) - Method in class org.obolibrary.oboformat.model.Frame

getTagXrefs(String) - Method in class org.obolibrary.oboformat.model.Frame

getTargetDoc(String) - Method in class org.obolibrary.oboformat.parser.XrefExpander

getTargetFrame(String) - Method in class org.obolibrary.oboformat.parser.XrefExpander.Rule

getTermFrame(OWLClass) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getTermFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc

getTermFrame(String, boolean) - Method in class org.obolibrary.oboformat.model.OBODoc

getTermFrames() - Method in class org.obolibrary.oboformat.model.OBODoc

getType() - Method in class org.obolibrary.oboformat.diff.Diff

getType() - Method in class org.obolibrary.oboformat.model.Frame

getTypedefFrame(OWLEntity) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getTypedefFrame(String) - Method in class org.obolibrary.oboformat.model.OBODoc

getTypedefFrame(String, boolean) - Method in class org.obolibrary.oboformat.model.OBODoc

getTypedefFrames() - Method in class org.obolibrary.oboformat.model.OBODoc

getUntranslatableAxioms() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getURI(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

getValue(OWLAnnotationValue, String) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

getValue() - Method in class org.obolibrary.oboformat.model.Clause

getValue(Class<T>) - Method in class org.obolibrary.oboformat.model.Clause

getValue() - Method in class org.obolibrary.oboformat.model.QualifierValue

getValue2() - Method in class org.obolibrary.oboformat.model.Clause

getValue2(Class<T>) - Method in class org.obolibrary.oboformat.model.Clause

getValues() - Method in class org.obolibrary.oboformat.model.Clause

getVocabularyObj(String) - Static method in class org.obolibrary.obo2owl.Obo2OWLConstants

getXrefs() - Method in class org.obolibrary.oboformat.model.Clause

H

handleConflict(OWLEntity, OWLAnnotationProperty, Collection<OWLAnnotationAssertionAxiom>) - Method in interface org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityConfictHandler

Resolve a conflict for a given annotation property and axioms.

handleConflict(OWLAnnotationProperty, Collection<OWLAnnotation>) - Method in interface org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityConfictHandler

Resolve a conflict for a given annotation property and ontology annotations.

handleDuplicateClause(Frame, Clause) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

Handle a duplicate clause in a frame during translation.

handleSynonym(Set<OWLAnnotation>, String, Clause, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

hashCode() - Method in class org.obolibrary.oboformat.model.Clause

hashCode() - Method in class org.obolibrary.oboformat.model.QualifierValue

hashCode() - Method in class org.obolibrary.oboformat.model.Xref

HasSubClassExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.HasSubClassExpansion

headerDateFormat - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants

Date format for OboFormatTag.TAG_DATE Use Thread local to ensure thread safety, as SimpleDateFormat is not thread safe.

headerFrame - Variable in class org.obolibrary.oboformat.model.OBODoc

The header frame.

I

id - Variable in class org.obolibrary.oboformat.model.Frame

The id.

idSpace - Variable in class org.obolibrary.oboformat.parser.XrefExpander.Rule

id space

idSpaceMap - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

idSpaceMap - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

IdTranslator - Class in org.obolibrary.obo2owl

This class will eventually replace the id to uri translation in Owl2Obo and OboO2Owl
It is currently in-progress.

IdTranslator() - Constructor for class org.obolibrary.obo2owl.IdTranslator

importedOBODocs - Variable in class org.obolibrary.oboformat.model.OBODoc

The imported obo docs.

indexOf(char) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

init(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

init() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

init() - Method in class org.obolibrary.oboformat.model.Frame

Init clauses.

initAnnotationPropertyMap() - Static method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

Table 5.8 Translation of Annotation Vocabulary.

initAnnotationPropertyMap() - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

instanceFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc

The instance frame map.

InvalidXrefMapException - Exception in org.obolibrary.oboformat.parser

The Class InvalidXrefMapException.

InvalidXrefMapException() - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException

Instantiates a new invalid xref map exception.

InvalidXrefMapException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException

Instantiates a new invalid xref map exception.

InvalidXrefMapException(String) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException

Instantiates a new invalid xref map exception.

InvalidXrefMapException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException

Instantiates a new invalid xref map exception.

IRI_PROP_isReversiblePropertyChain - Static variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

reversible property chain iri

iriShortFormProvider - Variable in class org.obolibrary.macro.ManchesterSyntaxTool

IsaExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.IsaExpansion

isCheckStructure() - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Checks if is check structure.

isDiscardUntranslatable() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

isTreatXrefsAsEquivalent(String) - Method in class org.obolibrary.oboformat.model.OBODoc

isURI(String) - Method in class org.obolibrary.obo2owl.IdTranslator

True if id starts with a standard URI prefix (http, ftp, https) followed by a ":".

L

LabelFunctionalFormat - Class in org.obolibrary.owl

Format for serializing an OWL ontology in a functional syntax format and labels instead of identifiers.

LabelFunctionalFormat() - Constructor for class org.obolibrary.owl.LabelFunctionalFormat

LabelFunctionalSyntaxOntologyStorer - Class in org.obolibrary.owl

Implement the writer for LabelFunctionalFormat.

LabelFunctionalSyntaxOntologyStorer() - Constructor for class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer

log - Static variable in class org.obolibrary.macro.MacroExpansionGCIVisitor

log - Static variable in class org.obolibrary.macro.MacroExpansionVisitor

LOGGER - Static variable in class org.obolibrary.obo2owl.OboInOwlCardinalityTools

M

MacroExpansionGCIVisitor - Class in org.obolibrary.macro

macro expansion gci visitor

MacroExpansionGCIVisitor(OWLOntology, OWLOntologyManager) - Constructor for class org.obolibrary.macro.MacroExpansionGCIVisitor

MacroExpansionVisitor - Class in org.obolibrary.macro

MacroExpansionVisitor(OWLOntology) - Constructor for class org.obolibrary.macro.MacroExpansionVisitor

main(String[]) - Static method in class org.obolibrary.oboformat.diff.OBODocDiffer

manager - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

manager - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

manchesterSyntaxTool - Variable in class org.obolibrary.macro.MacroExpansionGCIVisitor

manchesterSyntaxTool - Variable in class org.obolibrary.macro.MacroExpansionVisitor

ManchesterSyntaxTool - Class in org.obolibrary.macro

wrapper for parsing Manchester Syntax.

ManchesterSyntaxTool(OWLOntology) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool

Create a new parser instance for the given ontology.

ManchesterSyntaxTool(OWLOntology, Collection<OWLOntology>) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool

Create a new parser instance for the given ontologies.

ManchesterSyntaxTool(OWLOntology, Collection<OWLOntology>, boolean) - Constructor for class org.obolibrary.macro.ManchesterSyntaxTool

Create a new parser instance for the given ontologies.

mapPropId(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

See section "header macros" and treat-xrefs-as-equivalent

merge(Frame) - Method in class org.obolibrary.oboformat.model.Frame

mergeContents(OBODoc) - Method in class org.obolibrary.oboformat.model.OBODoc

Merge contents.

MyStream() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

MyStream(BufferedReader) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

N

nextChar() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

normalizeRelationshipClauses(List<Clause>) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

Join clauses and its QualifierValue which have the same relationship type and target.

O

Obo2OWLConstants - Class in org.obolibrary.obo2owl

Obo2OWLConstants() - Constructor for class org.obolibrary.obo2owl.Obo2OWLConstants

Obo2OWLConstants.Obo2OWLVocabulary - Enum in org.obolibrary.obo2owl

obo to owl vocabulary

obodoc - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

obodoc - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

OBODoc - Class in org.obolibrary.oboformat.model

An OBODoc is a container for a header frame and zero or more entity frames.

OBODoc() - Constructor for class org.obolibrary.oboformat.model.OBODoc

default constructor.

OBODocDiffer - Class in org.obolibrary.oboformat.diff

Diffs two OBO Documents.

OBODocDiffer() - Constructor for class org.obolibrary.oboformat.diff.OBODocDiffer

OBODocNameProvider(OBODoc) - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider

Instantiates a new OBO doc name provider.

OBOFormatConstants - Class in org.obolibrary.oboformat.parser

oboformat constants

OBOFormatConstants() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatConstants

OBOFormatConstants.OboFormatTag - Enum in org.obolibrary.oboformat.parser

oboformat tags

OBOFormatDanglingReferenceException - Exception in org.obolibrary.oboformat.parser

The Class OBOFormatDanglingReferenceException.

OBOFormatDanglingReferenceException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException

Instantiates a new oBO format dangling reference exception.

OBOFormatDanglingReferenceException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException

Instantiates a new oBO format dangling reference exception.

OBOFormatDanglingReferenceException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException

Instantiates a new oBO format dangling reference exception.

OBOFormatDanglingReferenceException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException

Instantiates a new oBO format dangling reference exception.

OBOFormatException - Exception in org.obolibrary.oboformat.parser

The Class OBOFormatException.

OBOFormatException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException

Instantiates a new oBO format exception.

OBOFormatException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException

Instantiates a new oBO format exception.

OBOFormatException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException

Instantiates a new oBO format exception.

OBOFormatException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException

Instantiates a new oBO format exception.

OBOFormatOWLAPIParser - Class in org.coode.owlapi.oboformat

oboformat parser

OBOFormatOWLAPIParser(OWLOntologyManager) - Constructor for class org.coode.owlapi.oboformat.OBOFormatOWLAPIParser

OBOFormatParser - Class in org.obolibrary.oboformat.parser

implements the OBO Format 1.4 specification.

OBOFormatParser() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser

OBOFormatParser(OBOFormatParser.MyStream) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser

OBOFormatParser.MyStream - Class in org.obolibrary.oboformat.parser

OBOFormatParserException - Exception in org.obolibrary.oboformat.parser

The Class OBOFormatParserException.

OBOFormatParserException(String, Throwable, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException

Instantiates a new oBO format parser exception.

OBOFormatParserException(String, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException

Instantiates a new oBO format parser exception.

OBOFormatParserException(Throwable, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException

Instantiates a new oBO format parser exception.

OBOFormatParserFactory - Class in org.coode.owlapi.oboformat

OBOFormatParserFactory() - Constructor for class org.coode.owlapi.oboformat.OBOFormatParserFactory

OBOFormatRenderer - Class in org.coode.owlapi.oboformat

renderer for obo

OBOFormatRenderer() - Constructor for class org.coode.owlapi.oboformat.OBOFormatRenderer

OBOFormatStorer - Class in org.coode.owlapi.oboformat

OBOFormatStorer() - Constructor for class org.coode.owlapi.oboformat.OBOFormatStorer

OBOFormatWriter - Class in org.obolibrary.oboformat.writer

The Class OBOFormatWriter.

OBOFormatWriter() - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter

OBOFormatWriter.NameProvider - Interface in org.obolibrary.oboformat.writer

Provide names for given OBO identifiers.

OBOFormatWriter.OBODocNameProvider - Class in org.obolibrary.oboformat.writer

Default implementation of a OBOFormatWriter.NameProvider using an underlying.

oboIdToIRI(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

OboInOwlCardinalityTools - Class in org.obolibrary.obo2owl

Tools for checking and fixing cardinality constrains for OBO ontologies in OWL.

OboInOwlCardinalityTools() - Constructor for class org.obolibrary.obo2owl.OboInOwlCardinalityTools

OboInOwlCardinalityTools.AnnotationCardinalityConfictHandler - Interface in org.obolibrary.obo2owl

Functor for resolving conflicts for an annotation property and its cardinality constraint.

OboInOwlCardinalityTools.AnnotationCardinalityException - Exception in org.obolibrary.obo2owl

Exception indication a non-resolvable conflict for an annotation property and its cardinality constraint.

OboInOwlCardinalityTools.AnnotationCardinalityReporter - Interface in org.obolibrary.obo2owl

Functor for reporting conflicts for an annotation property and its cardinality constraint.

OIOVOCAB_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants

OIO vocabulary prefix

ontologyId - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

org.coode.owlapi.oboformat - package org.coode.owlapi.oboformat

org.obolibrary.macro - package org.obolibrary.macro

org.obolibrary.obo2owl - package org.obolibrary.obo2owl

org.obolibrary.oboformat.diff - package org.obolibrary.oboformat.diff

org.obolibrary.oboformat.model - package org.obolibrary.oboformat.model

org.obolibrary.oboformat.parser - package org.obolibrary.oboformat.parser

org.obolibrary.oboformat.writer - package org.obolibrary.oboformat.writer

org.obolibrary.owl - package org.obolibrary.owl

output(OWLAxiom) - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor

OWLAPIObo2Owl - Class in org.obolibrary.obo2owl

OWLAPI version of Obo2Owl

OWLAPIObo2Owl(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.OWLAPIObo2Owl

OWLAPIOwl2Obo - Class in org.obolibrary.obo2owl

owlapi version of Owl2Obo

OWLAPIOwl2Obo(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.OWLAPIOwl2Obo

OWLAPIOwl2Obo.UntranslatableAxiomException - Exception in org.obolibrary.obo2owl

untranslatable axiom exception

owlObjectToTag(OWLObject) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

owlOntology - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

owlOntology - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

OwlStringException(Throwable) - Constructor for exception org.obolibrary.obo2owl.OwlStringTools.OwlStringException

OwlStringTools - Class in org.obolibrary.obo2owl

Tools to read and write a set of owl axioms to/from a string.

OwlStringTools() - Constructor for class org.obolibrary.obo2owl.OwlStringTools

OwlStringTools.OwlStringException - Exception in org.obolibrary.obo2owl

Exception indicating an un-recoverable error during the handling of axiom strings.

P

parse(IRI, OWLOntology) - Method in class org.coode.owlapi.oboformat.OBOFormatOWLAPIParser

parse(OWLOntologyDocumentSource, OWLOntology) - Method in class org.coode.owlapi.oboformat.OBOFormatOWLAPIParser

parse(OWLOntologyDocumentSource, OWLOntology, OWLOntologyLoaderConfiguration) - Method in class org.coode.owlapi.oboformat.OBOFormatOWLAPIParser

parse(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Parses a local file or URL to an OBODoc.

parse(File) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Parses a local file to an OBODoc.

parse(URL) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Parses a remote URL to an OBODoc.

parse(BufferedReader) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseEntityFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseEOL(Clause) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseHeaderClause(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseHeaderClauseNl(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

header-clause ::= format-version-TVP | ...

parseHeaderFrame(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseIdLine(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseManchesterExpression(String) - Method in class org.obolibrary.macro.ManchesterSyntaxTool

Parse a class expression in Manchester syntax.

parseManchesterExpressionFrames(String) - Method in class org.obolibrary.macro.ManchesterSyntaxTool

Parse frame expressions in Manchester syntax.

parseOBODoc(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseOneOrMoreWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseTermFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }.

parseTermFrameClause() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseTermFrameClauseEOL(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseTypedefFrame(OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }.

parseTypedefFrameClause() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseTypedefFrameClauseEOL(Frame) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseUnquotedString(Clause) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseURL(String) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

Parses a remote URL to an OBODoc.

parseWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseZeroOrMoreWs() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

parseZeroOrMoreWsOptCmtNl() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

peekChar() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

peekCharIs(char) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

postProcess(OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

perform any necessary post-processing.

prepare() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

preProcess() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

Q

qualifier - Variable in class org.obolibrary.oboformat.model.QualifierValue

QualifierValue - Class in org.obolibrary.oboformat.model

qualifier value

QualifierValue(String, String) - Constructor for class org.obolibrary.oboformat.model.QualifierValue

qualifierValues - Variable in class org.obolibrary.oboformat.model.Clause

R

rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion

rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion

rel - Variable in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion

RelationshipExpansion(String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.RelationshipExpansion

render(OWLOntology, OutputStream) - Method in class org.coode.owlapi.oboformat.OBOFormatRenderer

render(OWLOntology, Writer) - Method in class org.coode.owlapi.oboformat.OBOFormatRenderer

reportConflict(OWLEntity, OWLAnnotationProperty, Collection<OWLAnnotationAssertionAxiom>) - Method in interface org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityReporter

Report a conflict for a given annotation property and axioms.

reportConflict(OWLAnnotationProperty, Collection<OWLAnnotation>) - Method in interface org.obolibrary.obo2owl.OboInOwlCardinalityTools.AnnotationCardinalityReporter

Report a conflict for a given annotation property and ontology annotations.

rest() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

ReverseGenusDifferentiaExpansion(String, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion

Rule() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.Rule

S

sameIRI(OWLEntity) - Method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

setAnnotation(String) - Method in class org.obolibrary.oboformat.model.Xref

setCheckStructure(boolean) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Sets the check structure.

setClause1(Clause) - Method in class org.obolibrary.oboformat.diff.Diff

setClause2(Clause) - Method in class org.obolibrary.oboformat.diff.Diff

setClauses(Collection<Clause>) - Method in class org.obolibrary.oboformat.model.Frame

setDiscardUntranslatable(boolean) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

setFollowImports(boolean) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

setFrame1(Frame) - Method in class org.obolibrary.oboformat.diff.Diff

setFrame2(Frame) - Method in class org.obolibrary.oboformat.diff.Diff

setHeaderFrame(Frame) - Method in class org.obolibrary.oboformat.model.OBODoc

setId(String) - Method in class org.obolibrary.oboformat.model.Frame

setIdref(String) - Method in class org.obolibrary.oboformat.model.Xref

setImportedOBODocs(Collection<OBODoc>) - Method in class org.obolibrary.oboformat.model.OBODoc

setManager(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

setManager(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

setObodoc(OBODoc) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

setObodoc(OBODoc) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

setOwlOntology(OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

setOWLOntologyManager(OWLOntologyManager) - Method in class org.coode.owlapi.oboformat.OBOFormatOWLAPIParser

setOWLOntologyManager(OWLOntologyManager) - Method in class org.coode.owlapi.oboformat.OBOFormatRenderer

setQualifier(String) - Method in class org.obolibrary.oboformat.model.QualifierValue

setQualifierValues(Collection<QualifierValue>) - Method in class org.obolibrary.oboformat.model.Clause

setReader(BufferedReader) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

setStrictConversion(boolean) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

setTag(String) - Method in class org.obolibrary.oboformat.model.Clause

Deprecated.

Using this method makes the hashcode variable.

setType(String) - Method in class org.obolibrary.oboformat.diff.Diff

setType(Frame.FrameType) - Method in class org.obolibrary.oboformat.model.Frame

setUp() - Method in class org.obolibrary.oboformat.parser.XrefExpander

setValue(Object) - Method in class org.obolibrary.oboformat.model.Clause

setValue(Object) - Method in class org.obolibrary.oboformat.model.QualifierValue

setValues(Collection<Object>) - Method in class org.obolibrary.oboformat.model.Clause

setXrefs(Collection<Xref>) - Method in class org.obolibrary.oboformat.model.Clause

sortTermClauses(List<Clause>) - Static method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Sort a list of term frame clauses according to in the OBO format specified tag and value order.

storeOntology(OWLOntologyManager, OWLOntology, Writer, OWLOntologyFormat) - Method in class org.coode.owlapi.oboformat.OBOFormatStorer

storeOntology(OWLOntology, Writer, OWLOntologyFormat) - Method in class org.coode.owlapi.oboformat.OBOFormatStorer

storeOntology(OWLOntologyManager, OWLOntology, Writer, OWLOntologyFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer

storeOntology(OWLOntology, Writer, OWLOntologyFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxOntologyStorer

stream - Variable in class org.obolibrary.oboformat.parser.OBOFormatParser

strictConversion - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

T

tag - Variable in class org.obolibrary.oboformat.model.Clause

TAGS - Static variable in class org.obolibrary.oboformat.parser.OBOFormatConstants

tags

termFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc

The term frame map.

tgt - Variable in class org.obolibrary.oboformat.parser.XrefExpander.GenusDifferentiaExpansion

tgt - Variable in class org.obolibrary.oboformat.parser.XrefExpander.ReverseGenusDifferentiaExpansion

toString() - Method in class org.obolibrary.oboformat.diff.Diff

toString() - Method in class org.obolibrary.oboformat.model.Clause

toString() - Method in class org.obolibrary.oboformat.model.Frame

toString() - Method in class org.obolibrary.oboformat.model.OBODoc

toString() - Method in class org.obolibrary.oboformat.model.QualifierValue

toString() - Method in class org.obolibrary.oboformat.model.Xref

toString() - Method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

toString() - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream

toString() - Method in exception org.obolibrary.oboformat.parser.OBOFormatParserException

tr(OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

tr() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLSubPropertyChainOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLEquivalentObjectPropertiesAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLTransitiveObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLDisjointObjectPropertiesAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLReflexiveObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLInverseFunctionalObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLInverseObjectPropertiesAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLObjectPropertyDomainAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLAsymmetricObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLSymmetricObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLFunctionalObjectPropertyAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLObjectPropertyRangeAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLSubObjectPropertyOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLSubAnnotationPropertyOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLAnnotationAssertionAxiom, Frame) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLAnnotationProperty, OWLAnnotationValue, Set<OWLAnnotation>, Frame) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLOntology) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLEquivalentClassesAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLDisjointClassesAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLDeclarationAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLClassAssertionAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

tr(OWLSubClassOfAxiom) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

trAnnotationProp(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trAnnotations(Clause) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trAnnotations(Clause, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trAnnotations(Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

translate(Set<OWLAxiom>, OWLOntologyManager) - Static method in class org.obolibrary.obo2owl.OwlStringTools

Create a string for the given set of axioms.

translate(String, OWLOntologyManager) - Static method in class org.obolibrary.obo2owl.OwlStringTools

Parse the axioms from the given axiom string.

translateIdToIRIString(String) - Method in class org.obolibrary.obo2owl.IdTranslator

translateIRI(IRI) - Method in class org.obolibrary.obo2owl.IdTranslator

translateShorthandIdToExpandedId(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trClass(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trClass(Object) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trGenericClause(OWLNamedObject, String, Clause) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trGenericClause(OWLAnnotationSubject, String, Clause) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trGenericPropertyValue(OWLAnnotationProperty, OWLAnnotationValue, Set<OWLAnnotation>, Frame) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

trHeaderFrame(Frame) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trIndividual(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trIntersectionOf(OWLClass, Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trLiteral(Object) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trNaryPropertyAxiom(OWLNaryPropertyAxiom<OWLObjectPropertyExpression>, String) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

trObjectProp(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trObjectProp(Object) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trObjectProperty(OWLObjectProperty, String, String, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

trObjectProperty(OWLObjectProperty, String, Boolean, Set<OWLAnnotation>) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

trRel(String, String, Collection<QualifierValue>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trRelationIntersectionOf(String, OWLProperty<?, ?>, Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trRelationUnionOf(String, OWLProperty<?, ?>, Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trSynonymType(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTagToAnnotationProp(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTagToIRI(String) - Static method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTermClause(OWLClass, String, Clause) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

#5.2

trTermFrame(Frame) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTermFrameClauses(OWLClass, Collection<Clause>, String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTypedefClause(OWLObjectProperty, String, Clause) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTypedefFrame(Frame) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trTypedefToAnnotationProperty(Frame) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

trUnionOf(OWLClass, Collection<Clause>) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

type - Variable in class org.obolibrary.oboformat.model.Frame

The type.

typedefFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc

The typedef frame map.

typedefToAnnotationProperty - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl

U

UntranslatableAxiomException(String, Throwable) - Constructor for exception org.obolibrary.obo2owl.OWLAPIOwl2Obo.UntranslatableAxiomException

UntranslatableAxiomException(String) - Constructor for exception org.obolibrary.obo2owl.OWLAPIOwl2Obo.UntranslatableAxiomException

untranslatableAxioms - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

V

value - Variable in class org.obolibrary.oboformat.model.QualifierValue

valueOf(String) - Static method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

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

valueOf(String) - Static method in enum org.obolibrary.oboformat.model.Frame.FrameType

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

valueOf(String) - Static method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

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

values() - Static method in enum org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary

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

values - Variable in class org.obolibrary.oboformat.model.Clause

values() - Static method in enum org.obolibrary.oboformat.model.Frame.FrameType

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

values() - Static method in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

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

visit(OWLObjectIntersectionOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectUnionOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectComplementOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectSomeValuesFrom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectHasValue) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectAllValuesFrom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectMinCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectExactCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectMaxCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataSomeValuesFrom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataAllValuesFrom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataHasValue) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataExactCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataMaxCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataMinCardinality) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataOneOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataIntersectionOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataUnionOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSubClassOfAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDisjointClassesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataPropertyDomainAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectPropertyDomainAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectPropertyRangeAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDisjointUnionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataPropertyRangeAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLClassAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLEquivalentClassesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLClass) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectHasSelf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectOneOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDatatype) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataComplementOf) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLHasKeyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDatatypeRestriction) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLFacetRestriction) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLNegativeObjectPropertyAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLAsymmetricObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLReflexiveObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLEquivalentObjectPropertiesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLNegativeDataPropertyAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDifferentIndividualsAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDisjointDataPropertiesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDisjointObjectPropertiesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLObjectPropertyAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLFunctionalObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSubObjectPropertyOfAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDeclarationAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLAnnotationAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSymmetricObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLFunctionalDataPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLEquivalentDataPropertiesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDataPropertyAssertionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLTransitiveObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLIrreflexiveObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSubDataPropertyOfAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLInverseFunctionalObjectPropertyAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSameIndividualAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSubPropertyChainOfAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLInverseObjectPropertiesAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(SWRLRule) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLAnnotationPropertyDomainAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLAnnotationPropertyRangeAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLSubAnnotationPropertyOfAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLDatatypeDefinitionAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

visit(OWLLiteral) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

W

write(String, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write.

write(URL, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write.

write(BufferedReader, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

write(OBODoc, String) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

write(OBODoc, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

write(OBODoc, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

write(Frame, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

write(Clause, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write.

writeDef(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write def.

writeHeader(Frame, BufferedWriter, OBOFormatWriter.NameProvider) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write header.

writePropertyValue(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write property value.

writeSynonym(Clause, BufferedWriter) - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write synonym.

X

Xref - Class in org.obolibrary.oboformat.model

Xref

Xref(String) - Constructor for class org.obolibrary.oboformat.model.Xref

xref - Variable in class org.obolibrary.oboformat.parser.XrefExpander.Rule

XrefExpander - Class in org.obolibrary.oboformat.parser

xref expander

XrefExpander(OBODoc) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander

XrefExpander(OBODoc, String) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander

XrefExpander(OBODoc, OBODoc) - Constructor for class org.obolibrary.oboformat.parser.XrefExpander

XrefExpander.EquivalenceExpansion - Class in org.obolibrary.oboformat.parser

equivalence expansion

XrefExpander.GenusDifferentiaExpansion - Class in org.obolibrary.oboformat.parser

genus diff expansion

XrefExpander.HasSubClassExpansion - Class in org.obolibrary.oboformat.parser

subclass expansion

XrefExpander.IsaExpansion - Class in org.obolibrary.oboformat.parser

is a expansion

XrefExpander.RelationshipExpansion - Class in org.obolibrary.oboformat.parser

relationship expansion

XrefExpander.ReverseGenusDifferentiaExpansion - Class in org.obolibrary.oboformat.parser

reverse genus differentia expansion

XrefExpander.Rule - Class in org.obolibrary.oboformat.parser

rule

xrefs - Variable in class org.obolibrary.oboformat.model.Clause

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