uk.ac.ebi.intenz.biopax.level2
Class Biopax

java.lang.Object
  uk.ac.ebi.rhea.biopax.level2.Biopax
      uk.ac.ebi.intenz.biopax.level2.Biopax

public class Biopax
extends uk.ac.ebi.rhea.biopax.level2.Biopax

Utility class to dump IntEnz entries as BioPAX model.

Author:

rafalcan

Field Summary

static String	INTENZ_NS
static String	INTENZ_PREFIX

Fields inherited from class uk.ac.ebi.rhea.biopax.level2.Biopax

RHEA_NS, RHEA_PREFIX

Constructor Summary

Biopax()

Method Summary

static org.biopax.paxtools.model.Model	createModel() Creates an empty ontology model with the needed namespaces.
static void	write(Collection<EnzymeEntry> enzymes, OutputStream os) Writes a collection of enzyme entries to an output stream.

Methods inherited from class uk.ac.ebi.rhea.biopax.level2.Biopax

fixId, getBpDataSource, getBpPublicationXref, getBpPublicationXref, getBpXref, getBpXref, read, read, read, read, write, write, write

Methods inherited from class java.lang.Object

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

Field Detail

INTENZ_PREFIX

public static final String INTENZ_PREFIX

See Also:

Constant Field Values

INTENZ_NS

public static final String INTENZ_NS

See Also:

Constant Field Values

Constructor Detail

Biopax

public Biopax()

Method Detail

createModel

public static org.biopax.paxtools.model.Model createModel()

Creates an empty ontology model with the needed namespaces.

Returns:

an OWL model.

write

public static void write(Collection<EnzymeEntry> enzymes,
                         OutputStream os)
                  throws IOException,
                         IllegalAccessException,
                         InvocationTargetException

Writes a collection of enzyme entries to an output stream.

Parameters:

enzymes -

os -

Throws:

IOException

IllegalAccessException

InvocationTargetException