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.

Field Summary

Fields

Modifier and Type	Field and Description
protected Collection<Frame>	annotationFrames The annotation frames.
protected Frame	headerFrame The header frame.
protected Collection<OBODoc>	importedOBODocs The imported obo docs.
protected Map<String,Frame>	instanceFrameMap The instance frame map.
protected Map<String,Frame>	termFrameMap The term frame map.
protected Map<String,Frame>	typedefFrameMap The typedef frame map.

Constructor Summary

Constructors

Constructor and Description
OBODoc() default constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addDefaultOntologyHeader(String defaultOnt) Adds the default ontology header.
void	addFrame(Frame f) Adds the frame.
void	addImportedOBODoc(OBODoc doc) Adds the imported obo doc.
void	addInstanceFrame(Frame f) Adds the instance frame.
void	addTermFrame(Frame f) Adds the term frame.
void	addTypedefFrame(Frame f) Adds the typedef frame.
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) Merge contents.
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

The header frame.

termFrameMap

protected Map<String,Frame> termFrameMap

The term frame map.

typedefFrameMap

protected Map<String,Frame> typedefFrameMap

The typedef frame map.

instanceFrameMap

protected Map<String,Frame> instanceFrameMap

The instance frame map.

annotationFrames

protected Collection<Frame> annotationFrames

The annotation frames.

importedOBODocs

protected Collection<OBODoc> importedOBODocs

The imported obo docs.

Constructor Detail

OBODoc

public OBODoc()

default constructor.

Method Detail

getHeaderFrame

public Frame getHeaderFrame()

Returns:

the header frame

setHeaderFrame

public void setHeaderFrame(Frame headerFrame)

Parameters:

headerFrame - the new header frame

getTermFrames

public Collection<Frame> getTermFrames()

Returns:

the term frames

getTypedefFrames

public Collection<Frame> getTypedefFrames()

Returns:

the typedef frames

getInstanceFrames

public Collection<Frame> getInstanceFrames()

Returns:

the instance frames

getTermFrame

public Frame getTermFrame(String id)

Parameters:

id - the id

Returns:

the term frame

getTermFrame

public Frame getTermFrame(String id,
                 boolean followImport)

Parameters:

id - the id

followImport - the follow import

Returns:

the term frame

getTypedefFrame

public Frame getTypedefFrame(String id)

Parameters:

id - the id

Returns:

the typedef frame

getTypedefFrame

public Frame getTypedefFrame(String id,
                    boolean followImports)

Parameters:

id - the id

followImports - the follow imports

Returns:

the typedef frame

getInstanceFrame

public Frame getInstanceFrame(String id)

Parameters:

id - the id

Returns:

the instance frame

getImportedOBODocs

public Collection<OBODoc> getImportedOBODocs()

Returns:

the imported obo docs

setImportedOBODocs

public void setImportedOBODocs(Collection<OBODoc> importedOBODocs)

Parameters:

importedOBODocs - the new imported obo docs

addImportedOBODoc

public void addImportedOBODoc(OBODoc doc)

Adds the imported obo doc.

Parameters:

doc - the doc

addFrame

public void addFrame(Frame f)
              throws FrameMergeException

Adds the frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addTermFrame

public void addTermFrame(Frame f)
                  throws FrameMergeException

Adds the term frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addTypedefFrame

public void addTypedefFrame(Frame f)
                     throws FrameMergeException

Adds the typedef frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

addInstanceFrame

public void addInstanceFrame(Frame f)
                      throws FrameMergeException

Adds the instance frame.

Parameters:

f - the frame

Throws:

FrameMergeException - the frame merge exception

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)

Parameters:

prefix - the prefix

Returns:

true, if is treat xrefs as equivalent

mergeContents

public void mergeContents(OBODoc extDoc)
                   throws FrameMergeException

Merge contents.

Parameters:

extDoc - the external doc

Throws:

FrameMergeException - the frame merge exception

addDefaultOntologyHeader

public void addDefaultOntologyHeader(String defaultOnt)

Adds the default ontology header.

Parameters:

defaultOnt - the default ont

check

public void check()
           throws FrameStructureException

Check this document for violations, i.e. cardinality constraint violations.

Throws:

FrameStructureException - the frame structure exception

See Also:

for equivalent checks in OWL

toString

public String toString()

Overrides:

toString in class Object