org.obolibrary.oboformat.model
Class OBODoc
java.lang.Object
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
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
OBODoc
public OBODoc()
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
- Throws:
FrameStructureException
toString
public String toString()
- Overrides:
toString
in class Object
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