org.coode.owlapi.obo.renderer

Class OBOFlatFileRenderer

java.lang.Object

org.semanticweb.owlapi.io.AbstractOWLRenderer

org.coode.owlapi.obo.renderer.OBOFlatFileRenderer

All Implemented Interfaces:

OBOExceptionHandler, OWLRenderer

public class OBOFlatFileRenderer
extends AbstractOWLRenderer
implements OBOExceptionHandler

Renders OBO 1.2 flat file format. OBO 1.2 is a subset of OWL, so a rendering of an arbitrary OWL ontology may be incomplete in OBO. Several features are currently not implemented: - Exception handling for unsupported constructs - these are currently reported in stderr - axiom annotations (these might be serialisable as inline comments - although OBO parsers provide no guarantees these will be roundtripped) - anonymous classes/properties - it is not clear what this means in OBO - datatype restrictions - namespace and derived tags for relationships etc - it is not clear what this means in OBO - preservation of ordering on roundtripping exercises - Stanzas are ordered (classes, obj/data props then instances) - Entities are ordered by ID in each Stanza type - OBO tags are ordered WRT the OBO specifications Additional points: - cardinality is expressed as an '=' separated tag value pair in [1] and underspecified in [2]. OBOEdit 2 does not parse this (at the time of writing) so this has been changed to standard TVP syntax - OBO 1.2 currently specifies pairwise disjointness which this renderer follows so files may get large - Exceptions are caught along the way and then wrapped in an OBOStorageIncompleteException which is thrown after serialisation ends References: [1] http://www.cs.man.ac.uk/~horrocks/obo/ [2] http://www.geneontology.org/GO.format.obo-1_2.shtml

Author:

Nick Drummond, The University Of Manchester, Bio Health Informatics Group, Date: Dec 17, 2008

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	OBOFlatFileRenderer()
protected	OBOFlatFileRenderer(OWLOntologyManager owlOntologyManager) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
void	addException(OBOStorageException exception) Adds the exception.
List<OBOStorageException>	getExceptions() Gets the exceptions.
void	render(OWLOntology ontology, Writer writer) Renders the specified ontology using the specified writer.

Methods inherited from class org.semanticweb.owlapi.io.AbstractOWLRenderer

getOWLOntologyManager, render, setOWLOntologyManager

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OBOFlatFileRenderer

@Deprecated
protected OBOFlatFileRenderer(OWLOntologyManager owlOntologyManager)

Deprecated.

OBOFlatFileRenderer

protected OBOFlatFileRenderer()

Method Detail

render

public void render(OWLOntology ontology,
          Writer writer)
            throws OWLRendererException

Description copied from class: AbstractOWLRenderer

Renders the specified ontology using the specified writer.

Specified by:

render in class AbstractOWLRenderer

Parameters:

ontology - the ontology to render

writer - The writer that should be used to write the ontology. Note that this writer need not be wrapped with a BufferedWriter because this is taken care of by this abstract implementation.

Throws:

OWLRendererException - if exceptions arise

addException

public void addException(OBOStorageException exception)

Description copied from interface: OBOExceptionHandler

Adds the exception.

Specified by:

addException in interface OBOExceptionHandler

Parameters:

exception - the exception

getExceptions

public List<OBOStorageException> getExceptions()

Description copied from interface: OBOExceptionHandler

Gets the exceptions.

Specified by:

getExceptions in interface OBOExceptionHandler

Returns:

the exceptions