org.obolibrary.obo2owl.test
Class OboFormatTestBasics

java.lang.Object
  extended by org.obolibrary.obo2owl.test.OboFormatTestBasics
Direct Known Subclasses:
BFOROXrefTest, CAROTest, CHEBITest, ChebiXRefTest, CLTest, DanglingOwl2OboTest, DanglingRestrictionOwl2OboTest, DanglingRoundTripTest, EmptyLinesTest, EquivalentToTest, ExpandExpressionGCITest, ExpandExpressionTest, ExpandSynapsedToTest, FlyXPTest, GCIQualifierTest, GOTest, HeaderLostBug, HomeomorphicRelationTest, ManchesterSyntaxToolTest, Obo2OwlOldMappingTest, Obo2OwlTest, OBODocDifferTest, OboEscapeCharsTest, ObsoleteTermTest, Owl2OboDefTest, Owl2OboTest, PropertyChainTest, PropertyValueTest, RelationShorthandTest, RoundTripTest, SBOTest, SimpleGOTest, SingleIntersectionOfTagTest, SubsetTest, SynonymTest, TagTest, UnionOfTest, UnmappableExpressionsTest, XPBridgeFileTest, XrefExpanderTest

public class OboFormatTestBasics
extends Object


Constructor Summary
OboFormatTestBasics()
           
 
Method Summary
protected  org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc)
           
protected  org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc, String filename)
           
protected  OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ontology)
           
protected  org.semanticweb.owlapi.model.IRI getIriByLabel(org.semanticweb.owlapi.model.OWLOntology ontology, String label)
           
protected  OBODoc parseOBOFile(File file)
           
protected  OBODoc parseOBOFile(String fn)
           
protected  OBODoc parseOBOFile(String fn, boolean allowEmptyFrames)
           
protected  OBODoc parseOBOURL(String fn)
           
protected  org.semanticweb.owlapi.model.OWLOntology parseOWLFile(String fn)
           
protected static void renderOBO(OBODoc oboDoc)
           
protected  File writeOBO(OBODoc obodoc, String fn)
           
protected  File writeOWL(org.semanticweb.owlapi.model.OWLOntology ontology, String filename)
           
protected  File writeOWL(org.semanticweb.owlapi.model.OWLOntology ontology, String filename, org.semanticweb.owlapi.model.OWLOntologyFormat format)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OboFormatTestBasics

public OboFormatTestBasics()
Method Detail

parseOBOURL

protected OBODoc parseOBOURL(String fn)
                      throws IOException
Throws:
IOException

parseOBOFile

protected OBODoc parseOBOFile(String fn)
                       throws IOException
Throws:
IOException

parseOBOFile

protected OBODoc parseOBOFile(String fn,
                              boolean allowEmptyFrames)
                       throws IOException
Throws:
IOException

parseOBOFile

protected OBODoc parseOBOFile(File file)
                       throws IOException
Throws:
IOException

parseOWLFile

protected org.semanticweb.owlapi.model.OWLOntology parseOWLFile(String fn)
                                                         throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

convert

protected org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc)
                                                    throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

convert

protected org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc,
                                                           String filename)
                                                    throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                           org.semanticweb.owlapi.model.OWLOntologyStorageException,
                                                           IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
IOException

convert

protected OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ontology)
                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

writeOBO

protected File writeOBO(OBODoc obodoc,
                        String fn)
                 throws IOException
Throws:
IOException

writeOWL

protected File writeOWL(org.semanticweb.owlapi.model.OWLOntology ontology,
                        String filename)
                 throws org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
org.semanticweb.owlapi.model.OWLOntologyStorageException

writeOWL

protected File writeOWL(org.semanticweb.owlapi.model.OWLOntology ontology,
                        String filename,
                        org.semanticweb.owlapi.model.OWLOntologyFormat format)
                 throws org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
org.semanticweb.owlapi.model.OWLOntologyStorageException

renderOBO

protected static void renderOBO(OBODoc oboDoc)
                         throws IOException
Throws:
IOException

getIriByLabel

protected org.semanticweb.owlapi.model.IRI getIriByLabel(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                         String label)


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