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

A

AbstractMacroExpansionVisitor - Class in org.obolibrary.macro

Empty abstract visitor for macro expansion.

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

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.

addImport(String, OBODoc) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser

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.

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

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.

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

The annotation property map.

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

The annotation property map.

C

canStoreOntology(OWLDocumentFormat) - Method in class org.obolibrary.owl.LabelFunctionalSyntaxStorer

canStoreOntology(OWLDocumentFormat) - Method in class org.semanticweb.owlapi.oboformat.OBOFormatStorer

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.

clear() - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

containsPrefixMapping(String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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.

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

Convert.

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

Convert.

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.

copyPrefixesFrom(PrefixManager) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

copyPrefixesFrom(Map<String, String>) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

createParser() - Method in class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory

createStorer() - Method in class org.semanticweb.owlapi.oboformat.OBOFormatStorerFactory

D

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

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

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

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

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

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 xref values.

F

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.

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

freezing a frame signals that a frame has become quiescent, and that data structures can be adjusted to increase performance or reduce memory consumption.

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

Freezing an OBODoc signals that the document has become quiescent, and that the system may optimize data structures for performance or space.

G

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

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

getAnnotationsWithOptionalExpansionMarker(OWLAxiom) - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

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

Gets the data version.

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

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

getDefaultPrefix() - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

getExpansionMarkerAnnotation() - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

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

Gets the identifier.

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

See table 5.9.2.

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

See table 5.9.2.

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.

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

Retrieve the identifier for a given OWLObject.

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

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

Looks up the ID prefix to IRI prefix mapping.

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

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

getIRI(String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

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

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

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

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

Gets the manager.

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

Gets the manager.

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

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

getName() - Method in class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser

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

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

Gets the obodoc.

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

Gets the obodoc.

getOIO_ISEXPANSION() - Method in class org.obolibrary.macro.AbstractMacroExpansionVisitor

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

E.g.

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

Gets the ontology id.

getPrefix(String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

getPrefixComparator() - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

getPrefixIRI(IRI) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

getPrefixIRIIgnoreQName(IRI) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

getPrefixName2PrefixMap() - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

getPrefixNames() - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

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

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

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

Gets the strict conversion.

getSupportedFormat() - Method in class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser

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

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

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(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

Gets the untranslatable axioms.

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.

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

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

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

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

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

header priority comparator

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

I

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

id space

IdTranslator - Class in org.obolibrary.obo2owl

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

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

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_IAO_0000227 - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants

IRI for the 'terms merged' individual

IRI_IAO_0000231 - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants

IRI for the 'has obsolescence reason' annotation property

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

The Constant IRI_PROP_isReversiblePropertyChain.

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

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

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

Checks if is discard untranslatable.

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

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

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

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

L

LabelFunctionalSyntaxStorer - Class in org.obolibrary.owl

Implement the writer for LabelFunctionalDocumentFormat.

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

M

MacroExpansionGCIVisitor - Class in org.obolibrary.macro

macro expansion gci visitor

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

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

MacroExpansionVisitor - Class in org.obolibrary.macro

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

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

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

MacroExpansionVisitor(OWLOntology, Set<OWLAnnotation>, boolean, boolean) - Constructor for 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.

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

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

Merge contents.

N

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 - 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.semanticweb.owlapi.oboformat

oboformat parser

OBOFormatOWLAPIParser() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser

OBOFormatOWLAPIParserFactory - Class in org.semanticweb.owlapi.oboformat

OBOFormatOWLAPIParserFactory() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory

default constructor

OBOFormatParser - Class in org.obolibrary.oboformat.parser

Implements the OBO Format 1.4 specification.

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

Default constructor.

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

OBOFormatParser(Map<String, OBODoc>) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser

OBOFormatParserException - Exception in org.obolibrary.oboformat.parser

The Class OBOFormatParserException.

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

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

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

OBOFormatPrefixManager - Class in org.obolibrary.obo2owl

OBOFormatPrefixManager(PrefixManager) - Constructor for class org.obolibrary.obo2owl.OBOFormatPrefixManager

OBOFormatRenderer - Class in org.semanticweb.owlapi.oboformat

renderer for obo

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

OBOFormatStorer - Class in org.semanticweb.owlapi.oboformat

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

OBOFormatStorerFactory - Class in org.semanticweb.owlapi.oboformat

OBOFormatStorerFactory() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatStorerFactory

default constructor

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.

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

Alternative implementation to lookup labels in an OWLOntology.

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

Obo id to iri.

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

oboIdToIRI_load(String, boolean) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl

Obo id to iri.

OboInOwlCardinalityTools - Class in org.obolibrary.obo2owl

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

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

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

org.semanticweb.owlapi.oboformat - package org.semanticweb.owlapi.oboformat

OWLAPIObo2Owl - Class in org.obolibrary.obo2owl

The Class OWLAPIObo2Owl.

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

OWLAPIOwl2Obo - Class in org.obolibrary.obo2owl

The Class OWLAPIOwl2Obo.

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

Instantiates a new OWLAPI owl2 obo.

OWLAPIOwl2Obo.UntranslatableAxiomException - Exception in org.obolibrary.obo2owl

The Class UntranslatableAxiomException.

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

Owl object to tag.

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

Owl object to tag.

OWLOntologyNameProvider(OWLOntology, String, OBODoc) - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter.OWLOntologyNameProvider

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(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

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

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

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

parseHeaderFrame(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

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

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

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

Parses a remote URL to an OBODoc.

Q

QualifierValue - Class in org.obolibrary.oboformat.model

qualifier value

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

R

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

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

render(OWLOntology, Writer, OWLDocumentFormat) - Static method in class org.semanticweb.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.

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

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

setDefaultPrefix(String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

Sets the discard untranslatable.

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

Sets the manager.

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

Sets the manager.

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

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

Sets the obodoc.

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

Sets the obodoc.

setPrefix(String, String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

setPrefixComparator(StringComparator) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

setPrefixManager(PrefixManager) - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo

setPreserveAnnotationsWhenExpanding(boolean) - Method in class org.obolibrary.macro.MacroExpansionGCIVisitor

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

setShouldTransferAnnotations(boolean) - Method in class org.obolibrary.macro.MacroExpansionVisitor

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

Sets the strict conversion.

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

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(String) - 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

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

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

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.

T

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

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

tag priority comparator

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

tags

TERM_FRAMES - Static variable in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

Term frames.

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 exception org.obolibrary.oboformat.parser.OBOFormatParserException

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) - Static method in class org.obolibrary.obo2owl.IdTranslator

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

Translate header frame.

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

Translate rel.

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

Translate tag to iri.

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

Translate term frame.

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

Translate term frame clauses.

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

Translate typedef frame.

TYPEDEF_FRAMES - Static variable in enum org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag

Typedef frames.

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

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

typedef priority comparator

U

unregisterNamespace(String) - Method in class org.obolibrary.obo2owl.OBOFormatPrefixManager

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

Instantiates a new untranslatable axiom exception.

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

Instantiates a new untranslatable axiom exception.

V

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() - 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(OWLDisjointUnionAxiom) - 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(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(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

W

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

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, File) - 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) - Static method in class org.obolibrary.oboformat.writer.OBOFormatWriter

Write.

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

Write property value.

writeSynonym(Clause, BufferedWriter) - Static 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

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

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