uk.ac.ebi.intenz.biopax.level2

Class BiopaxCatalysis

java.lang.Object

uk.ac.ebi.intenz.biopax.level2.BiopaxCatalysis

public class BiopaxCatalysis
extends Object

Adapter class to convert IntEnz EnzymeEntrys into BioPAX catalysys objects and viceversa.
Note that one IntEnz EnzymeEntry may catalyze more than one reaction. As BioPAX catalysis allows one CONTROLLED property at most, several catalysis may be generated per IntEnz entry.

Constructor Summary

Constructors

Constructor and Description
BiopaxCatalysis(org.biopax.paxtools.model.level2.catalysis cat) Not yet implemented.
BiopaxCatalysis(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry enzymeEntry, org.biopax.paxtools.model.Model model) Constructor from an IntEnz EnzymeEntry.

Method Summary

Methods

Modifier and Type	Method and Description
Collection<org.biopax.paxtools.model.level2.catalysis>	getBiopaxCatalysis()
uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry	getIntEnzEnzyme()

Methods inherited from class java.lang.Object

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

Constructor Detail

BiopaxCatalysis

public BiopaxCatalysis(uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry enzymeEntry,
               org.biopax.paxtools.model.Model model)

Constructor from an IntEnz EnzymeEntry.
The following BioPAX properties are currently ignored:

• CONTROL-TYPE: ACTIVATION by default
• PARTICIPANTS: defined in the enclosed reaction (CONTROLLED)
• AVAILABILITY
• EVIDENCE
• INTERACTION-TYPE

Notes about enzyme names:

• the systematic name is mapped to BioPAX' NAME.
• the common/accepted/recommended name is mapped to BioPAX' SHORT-NAME.
• BioPAX' SYNONYMS include both of them, following the specification.

Notes about xrefs:

• GO xrefs are assigned to BioPAX catalysis.
• PROSITE xrefs are assigned to BioPAX' CONTROLLER property, as relationshipXref.
• Any other xrefs are assigned to BioPAX' CONTROLLER property, as unificationXrefs

IntEnz citations are exported as publicationXref assigned to the BioPAX' catalysis.

Parameters:

enzymeEntry - an IntEnz enzyme.

model - A BioPAX model to add the catalysis to.

BiopaxCatalysis

public BiopaxCatalysis(org.biopax.paxtools.model.level2.catalysis cat)

Not yet implemented. Throws an exception.

Parameters:

cat -

Method Detail

getIntEnzEnzyme

public uk.ac.ebi.intenz.domain.enzyme.EnzymeEntry getIntEnzEnzyme()

Returns:

the IntEnz side of this apapter.

getBiopaxCatalysis

public Collection<org.biopax.paxtools.model.level2.catalysis> getBiopaxCatalysis()

Returns:

the BioPAX side of this adapter.