owltools.io
Class ParserWrapper

java.lang.Object
  extended by owltools.io.ParserWrapper

public class ParserWrapper
extends Object

Convenience class wrapping org.oboformat that abstracts away underlying details of ontology format or location

Author:
cjm

Constructor Summary
ParserWrapper()
           
 
Method Summary
 org.semanticweb.owlapi.model.OWLOntologyManager getManager()
           
 org.obolibrary.oboformat.model.OBODoc getOBOdoc()
           
 org.semanticweb.owlapi.model.OWLOntology parse(String iriString)
           
 org.semanticweb.owlapi.model.OWLOntology parseOBO(String iri)
           
 org.semanticweb.owlapi.model.OWLOntology parseOBOFiles(List<String> files)
           
 org.semanticweb.owlapi.model.OWLOntology parseOWL(org.semanticweb.owlapi.model.IRI iri)
           
 org.semanticweb.owlapi.model.OWLOntology parseOWL(String iriString)
           
 OWLGraphWrapper parseToOWLGraph(String iriString)
           
 OWLGraphWrapper parseToOWLGraph(String iriString, boolean isMergeImportClosure)
           
 void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont, org.semanticweb.owlapi.model.OWLOntologyFormat owlFormat, OutputStream outputStream)
           
 void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont, org.semanticweb.owlapi.model.OWLOntologyFormat owlFormat, String file)
           
 void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont, String file)
           
 void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ParserWrapper

public ParserWrapper()
Method Detail

getManager

public org.semanticweb.owlapi.model.OWLOntologyManager getManager()

setManager

public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)

parseToOWLGraph

public OWLGraphWrapper parseToOWLGraph(String iriString)
                                throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                       IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException

parseToOWLGraph

public OWLGraphWrapper parseToOWLGraph(String iriString,
                                       boolean isMergeImportClosure)
                                throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                       IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException

parse

public org.semanticweb.owlapi.model.OWLOntology parse(String iriString)
                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                      IOException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException

parseOBO

public org.semanticweb.owlapi.model.OWLOntology parseOBO(String iri)
                                                  throws IOException,
                                                         org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException

parseOBOFiles

public org.semanticweb.owlapi.model.OWLOntology parseOBOFiles(List<String> files)
                                                       throws IOException,
                                                              org.semanticweb.owlapi.model.OWLOntologyCreationException,
                                                              org.obolibrary.oboformat.model.FrameMergeException
Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.obolibrary.oboformat.model.FrameMergeException

parseOWL

public org.semanticweb.owlapi.model.OWLOntology parseOWL(String iriString)
                                                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

parseOWL

public org.semanticweb.owlapi.model.OWLOntology parseOWL(org.semanticweb.owlapi.model.IRI iri)
                                                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

saveOWL

public void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont,
                    String file)
             throws org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
org.semanticweb.owlapi.model.OWLOntologyStorageException

saveOWL

public void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont,
                    org.semanticweb.owlapi.model.OWLOntologyFormat owlFormat,
                    String file)
             throws org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
org.semanticweb.owlapi.model.OWLOntologyStorageException

saveOWL

public void saveOWL(org.semanticweb.owlapi.model.OWLOntology ont,
                    org.semanticweb.owlapi.model.OWLOntologyFormat owlFormat,
                    OutputStream outputStream)
             throws org.semanticweb.owlapi.model.OWLOntologyStorageException
Throws:
org.semanticweb.owlapi.model.OWLOntologyStorageException

getOBOdoc

public org.obolibrary.oboformat.model.OBODoc getOBOdoc()


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