org.biopax.paxtools.model.level3
Interface Pathway

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Controller, Entity, Level3Element, Named, Observable, Process, java.io.Serializable, XReferrable

All Known Implementing Classes:

PathwayImpl

public interface Pathway
extends Process, Controller

Method Summary

void	addPathwayComponent(Process components)
void	addPathwayOrder(PathwayStep order)
BioSource	getOrganism() An organism, e.g.
java.util.Set<Process>	getPathwayComponent()
java.util.Set<PathwayStep>	getPathwayOrder()
void	removePathwayComponent(Process components)
void	removePathwayOrder(PathwayStep order)
void	setOrganism(BioSource source) An organism, e.g.

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Controller

getControllerOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Method Detail

getPathwayComponent

java.util.Set<Process> getPathwayComponent()

addPathwayComponent

void addPathwayComponent(Process components)

removePathwayComponent

void removePathwayComponent(Process components)

getPathwayOrder

java.util.Set<PathwayStep> getPathwayOrder()

addPathwayOrder

void addPathwayOrder(PathwayStep order)

removePathwayOrder

void removePathwayOrder(PathwayStep order)

getOrganism

BioSource getOrganism()

An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.

Returns:

the organism for this gene.

setOrganism

void setOrganism(BioSource source)

An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.

Parameters:

source - new organism for this gene