org.obolibrary.oboformat.model
Class OBODoc

java.lang.Object
  extended by org.obolibrary.oboformat.model.OBODoc

public class OBODoc
extends Object

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


Field Summary
protected  Collection<Frame> annotationFrames
           
protected  Frame headerFrame
           
protected  Collection<OBODoc> importedOBODocs
           
protected  Map<String,Frame> instanceFrameMap
           
protected  Map<String,Frame> termFrameMap
           
protected  Map<String,Frame> typedefFrameMap
           
 
Constructor Summary
OBODoc()
           
 
Method Summary
 void addDefaultOntologyHeader(String defaultOnt)
           
 void addFrame(Frame f)
           
 void addImportedOBODoc(OBODoc doc)
           
 void addInstanceFrame(Frame f)
           
 void addTermFrame(Frame f)
           
 void addTypedefFrame(Frame f)
           
 void check()
          Check this document for violations, i.e.
 Frame getHeaderFrame()
           
 String getIDSpace(String prefix)
          Looks up the ID prefix to IRI prefix mapping.
 Collection<OBODoc> getImportedOBODocs()
           
 Frame getInstanceFrame(String id)
           
 Collection<Frame> getInstanceFrames()
           
 Frame getTermFrame(String id)
           
 Frame getTermFrame(String id, boolean followImport)
           
 Collection<Frame> getTermFrames()
           
 Frame getTypedefFrame(String id)
           
 Frame getTypedefFrame(String id, boolean followImports)
           
 Collection<Frame> getTypedefFrames()
           
 boolean isTreatXrefsAsEquivalent(String prefix)
           
 void mergeContents(OBODoc extDoc)
           
 void setHeaderFrame(Frame headerFrame)
           
 void setImportedOBODocs(Collection<OBODoc> importedOBODocs)
           
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

headerFrame

protected Frame headerFrame

termFrameMap

protected Map<String,Frame> termFrameMap

typedefFrameMap

protected Map<String,Frame> typedefFrameMap

instanceFrameMap

protected Map<String,Frame> instanceFrameMap

annotationFrames

protected Collection<Frame> annotationFrames

importedOBODocs

protected Collection<OBODoc> importedOBODocs
Constructor Detail

OBODoc

public OBODoc()
Method Detail

getHeaderFrame

public Frame getHeaderFrame()

setHeaderFrame

public void setHeaderFrame(Frame headerFrame)

getTermFrames

public Collection<Frame> getTermFrames()

getTypedefFrames

public Collection<Frame> getTypedefFrames()

getInstanceFrames

public Collection<Frame> getInstanceFrames()

getTermFrame

public Frame getTermFrame(String id)

getTermFrame

public Frame getTermFrame(String id,
                          boolean followImport)

getTypedefFrame

public Frame getTypedefFrame(String id)

getTypedefFrame

public Frame getTypedefFrame(String id,
                             boolean followImports)

getInstanceFrame

public Frame getInstanceFrame(String id)

getImportedOBODocs

public Collection<OBODoc> getImportedOBODocs()

setImportedOBODocs

public void setImportedOBODocs(Collection<OBODoc> importedOBODocs)

addImportedOBODoc

public void addImportedOBODoc(OBODoc doc)

addFrame

public void addFrame(Frame f)
              throws FrameMergeException
Throws:
FrameMergeException

addTermFrame

public void addTermFrame(Frame f)
                  throws FrameMergeException
Throws:
FrameMergeException

addTypedefFrame

public void addTypedefFrame(Frame f)
                     throws FrameMergeException
Throws:
FrameMergeException

addInstanceFrame

public void addInstanceFrame(Frame f)
                      throws FrameMergeException
Throws:
FrameMergeException

getIDSpace

public String getIDSpace(String prefix)
Looks up the ID prefix to IRI prefix mapping. Header-Tag: idspace

Parameters:
prefix - prefix
Returns:
IRI prefix as string

isTreatXrefsAsEquivalent

public boolean isTreatXrefsAsEquivalent(String prefix)

mergeContents

public void mergeContents(OBODoc extDoc)
                   throws FrameMergeException
Throws:
FrameMergeException

addDefaultOntologyHeader

public void addDefaultOntologyHeader(String defaultOnt)

check

public void check()
           throws FrameStructureException
Check this document for violations, i.e. cardinality constraint violations.

Throws:
FrameStructureException
See Also:
for equivalent checks in OWL

toString

public String toString()
Overrides:
toString in class Object


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