Uses of Class
org.obolibrary.oboformat.model.OBODoc

Packages that use OBODoc

Package	Description
org.obolibrary.obo2owl	OBO to OWL.
org.obolibrary.oboformat.diff	Diff package.
org.obolibrary.oboformat.model	OBO Model.
org.obolibrary.oboformat.parser	OBO parser.
org.obolibrary.oboformat.writer

Uses of OBODoc in org.obolibrary.obo2owl

Methods in org.obolibrary.obo2owl that return OBODoc

Modifier and Type	Method and Description
OBODoc	OWLAPIOwl2Obo.convert(OWLOntology ont) Convert.
OBODoc	OWLAPIOwl2Obo.getObodoc() Gets the obodoc.
OBODoc	OWLAPIObo2Owl.getObodoc() Gets the obodoc.

Methods in org.obolibrary.obo2owl with parameters of type OBODoc

Modifier and Type	Method and Description
OWLOntology	OWLAPIObo2Owl.convert(OBODoc doc) Convert.
OWLOntology	OWLAPIObo2Owl.convert(OBODoc doc, OWLOntology in) Convert.
void	OWLAPIOwl2Obo.setObodoc(OBODoc obodoc) Sets the obodoc.
void	OWLAPIObo2Owl.setObodoc(OBODoc obodoc) Sets the obodoc.

Uses of OBODoc in org.obolibrary.oboformat.diff

Methods in org.obolibrary.oboformat.diff with parameters of type OBODoc

Modifier and Type	Method and Description
static List<Diff>	OBODocDiffer.getDiffs(OBODoc doc1, OBODoc doc2)

Uses of OBODoc in org.obolibrary.oboformat.model

Methods in org.obolibrary.oboformat.model that return types with arguments of type OBODoc

Modifier and Type	Method and Description
Collection<OBODoc>	OBODoc.getImportedOBODocs()

Methods in org.obolibrary.oboformat.model with parameters of type OBODoc

Modifier and Type	Method and Description
void	OBODoc.addImportedOBODoc(OBODoc doc) Adds the imported obo doc.
void	OBODoc.mergeContents(OBODoc extDoc) Merge contents.

Method parameters in org.obolibrary.oboformat.model with type arguments of type OBODoc

Modifier and Type	Method and Description
void	OBODoc.setImportedOBODocs(Collection<OBODoc> importedOBODocs)

Uses of OBODoc in org.obolibrary.oboformat.parser

Methods in org.obolibrary.oboformat.parser that return OBODoc

Modifier and Type	Method and Description
OBODoc	XrefExpander.getTargetDoc(String idSpace)
OBODoc	OBOFormatParser.parse(File file) Parses a local file to an OBODoc.
OBODoc	OBOFormatParser.parse(Reader reader)
OBODoc	OBOFormatParser.parse(String fn) Parses a local file or URL to an OBODoc.
OBODoc	OBOFormatParser.parse(URL url) Parses a remote URL to an OBODoc.
OBODoc	OBOFormatParser.parseURL(String urlstr) Parses a remote URL to an OBODoc.

Methods in org.obolibrary.oboformat.parser with parameters of type OBODoc

Modifier and Type	Method and Description
boolean	OBOFormatParser.addImport(String key, OBODoc doc)
List<String>	OBOFormatParser.checkDanglingReferences(OBODoc doc)
void	OBOFormatParser.parseEntityFrame(OBODoc obodoc)
void	OBOFormatParser.parseOBODoc(OBODoc obodoc)
void	OBOFormatParser.parseTermFrame(OBODoc obodoc) term-frame ::= nl* '[Term]' nl id-Tag Class-ID EOL { term-frame-clause EOL }.
void	OBOFormatParser.parseTypedefFrame(OBODoc obodoc) Typedef-frame ::= nl* '[Typedef]' nl id-Tag Class-ID EOL { Typedef-frame-clause EOL }.

Constructors in org.obolibrary.oboformat.parser with parameters of type OBODoc

Constructor and Description
XrefExpander(OBODoc src)
XrefExpander(OBODoc src, OBODoc tgt)
XrefExpander(OBODoc src, String targetBase)

Constructor parameters in org.obolibrary.oboformat.parser with type arguments of type OBODoc

Constructor and Description
OBOFormatParser(Map<String,OBODoc> importsMap)

Uses of OBODoc in org.obolibrary.oboformat.writer

Methods in org.obolibrary.oboformat.writer with parameters of type OBODoc

Modifier and Type	Method and Description
void	OBOFormatWriter.write(OBODoc doc, File outFile)
void	OBOFormatWriter.write(OBODoc doc, String outFilename)
void	OBOFormatWriter.write(OBODoc doc, Writer writer)
void	OBOFormatWriter.write(OBODoc doc, Writer writer, OBOFormatWriter.NameProvider nameProvider)

Constructors in org.obolibrary.oboformat.writer with parameters of type OBODoc

Constructor and Description
OBODocNameProvider(OBODoc oboDoc) Instantiates a new OBO doc name provider.
OWLOntologyNameProvider(OWLOntology ont, String defaultOboNamespace, OBODoc result)