org.biopax.paxtools.impl.level3
Class PathwayImpl

java.lang.Object
  org.biopax.paxtools.impl.BioPAXElementImpl
      org.biopax.paxtools.impl.level3.L3ElementImpl
          org.biopax.paxtools.impl.level3.XReferrableImpl
              org.biopax.paxtools.impl.level3.NamedImpl
                  org.biopax.paxtools.impl.level3.EntityImpl
                      org.biopax.paxtools.impl.level3.ProcessImpl
                          org.biopax.paxtools.impl.level3.PathwayImpl

All Implemented Interfaces:

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

@Entity
@Indexed
public class PathwayImpl
extends ProcessImpl
implements Pathway

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

Constructor Summary

PathwayImpl()

Method Summary

void	addPathwayComponent(Process component)
void	addPathwayOrder(PathwayStep pathwayOrder)
java.util.Set<Control>	getControllerOf() This method returns the list of Control interactions that this entity controls.
java.lang.Class<? extends Pathway>	getModelInterface() This method returns the actual model interface that a class implements.
BioSource	getOrganism() An organism, e.g.
java.util.Set<Process>	getPathwayComponent()
java.util.Set<PathwayStep>	getPathwayOrder()
void	removePathwayComponent(Process component)
void	removePathwayOrder(PathwayStep pathwayOrder)
protected void	setControllerOf(java.util.Set<Control> controllerOf)
void	setOrganism(BioSource organism) An organism, e.g.
protected void	setPathwayComponent(java.util.Set<Process> pathwayComponent)
protected void	setPathwayOrder(java.util.Set<PathwayStep> pathwayOrder)

Methods inherited from class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, semanticallyEquivalent, setAvailability, setDataSource, setEvidence, setParticipantOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getNameX, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setNameX, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, hasCommonUnificationXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

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

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

getControlledOf, getPathwayComponentOf, getStepProcessOf

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

Constructor Detail

PathwayImpl

public PathwayImpl()

Method Detail

getModelInterface

public java.lang.Class<? extends Pathway> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getPathwayComponent

public java.util.Set<Process> getPathwayComponent()

Specified by:

getPathwayComponent in interface Pathway

setPathwayComponent

protected void setPathwayComponent(java.util.Set<Process> pathwayComponent)

addPathwayComponent

public void addPathwayComponent(Process component)

Specified by:

addPathwayComponent in interface Pathway

removePathwayComponent

public void removePathwayComponent(Process component)

Specified by:

removePathwayComponent in interface Pathway

getPathwayOrder

public java.util.Set<PathwayStep> getPathwayOrder()

Specified by:

getPathwayOrder in interface Pathway

setPathwayOrder

protected void setPathwayOrder(java.util.Set<PathwayStep> pathwayOrder)

addPathwayOrder

public void addPathwayOrder(PathwayStep pathwayOrder)

Specified by:

addPathwayOrder in interface Pathway

removePathwayOrder

public void removePathwayOrder(PathwayStep pathwayOrder)

Specified by:

removePathwayOrder in interface Pathway

getOrganism

public BioSource getOrganism()

Description copied from interface: Pathway

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.

Specified by:

getOrganism in interface Pathway

Returns:

the organism for this gene.

setOrganism

public void setOrganism(BioSource organism)

Description copied from interface: Pathway

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.

Specified by:

setOrganism in interface Pathway

Parameters:

organism - new organism for this gene

getControllerOf

public java.util.Set<Control> getControllerOf()

Description copied from interface: Controller

This method returns the list of Control interactions that this entity controls. Reverse method of Control.getController(). Contents of this set is automatically maintained and should not be modified.

Specified by:

getControllerOf in interface Controller

Returns:

list of Control interactions that this entity controls.

setControllerOf

protected void setControllerOf(java.util.Set<Control> controllerOf)