org.biopax.paxtools.impl.level2
Class interactionAdapter

java.lang.Object
  org.biopax.paxtools.impl.level2.bioPAXElementImpl
      org.biopax.paxtools.impl.level2.entityImpl
          org.biopax.paxtools.impl.level2.processImpl
              org.biopax.paxtools.impl.level2.interactionAdapter

All Implemented Interfaces:

BioPAXElement, entity, interaction, InteractionParticipant, pathwayComponent, process, XReferrable

Direct Known Subclasses:

interactionImpl, physicalInteractionAdapter

public abstract class interactionAdapter
extends processImpl
implements interaction

Field Summary

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Fields inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

interactionAdapter()

Method Summary

protected boolean	compareParticipantSets(java.util.Set<InteractionParticipant> set1, java.util.Set<InteractionParticipant> set2)
int	equivalenceCode()
java.util.Set<InteractionParticipant>	getPARTICIPANTS()
boolean	isEquivalent(BioPAXElement element)
protected void	setParticipantInverse(InteractionParticipant ip, boolean remove)
protected void	updatePARTICIPANTS(java.util.Set<? extends InteractionParticipant> oldSet, java.util.Set<? extends InteractionParticipant> newSet)

Methods inherited from class org.biopax.paxtools.impl.level2.processImpl

addCONTROLLEDof, addEVIDENCE, addSTEP_INTERACTIONSOf, getEVIDENCE, isCONTROLLEDOf, isPATHWAY_COMPONENTSof, isSTEP_INTERACTIONSOf, removeEVIDENCE, setEVIDENCE

Methods inherited from class org.biopax.paxtools.impl.level2.entityImpl

addAVAILABILITY, addDATA_SOURCE, addSYNONYMS, addXREF, getAVAILABILITY, getDATA_SOURCE, getNAME, getSHORT_NAME, getSYNONYMS, getXREF, isPARTICIPANTSof, removeAVAILABILITY, removeDATA_SOURCE, removeSYNONYMS, removeXREF, setAVAILABILITY, setDATA_SOURCE, setNAME, setSHORT_NAME, setSYNONYMS, setXREF

Methods inherited from class org.biopax.paxtools.impl.level2.bioPAXElementImpl

addCOMMENT, equals, getCOMMENT, getRDFId, hashCode, removeCOMMENT, setCOMMENT, setRDFId

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.model.level2.interaction

addPARTICIPANTS, removePARTICIPANTS, setPARTICIPANTS

Methods inherited from interface org.biopax.paxtools.model.level2.process

addEVIDENCE, getEVIDENCE, isCONTROLLEDOf, isSTEP_INTERACTIONSOf, removeEVIDENCE, setEVIDENCE

Methods inherited from interface org.biopax.paxtools.model.level2.entity

addAVAILABILITY, addDATA_SOURCE, addSYNONYMS, getAVAILABILITY, getDATA_SOURCE, getNAME, getSHORT_NAME, getSYNONYMS, removeAVAILABILITY, removeDATA_SOURCE, removeSYNONYMS, setAVAILABILITY, setDATA_SOURCE, setNAME, setSHORT_NAME, setSYNONYMS

Methods inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

addCOMMENT, getCOMMENT, getModelInterface, getRDFId, removeCOMMENT, setCOMMENT, setRDFId

Methods inherited from interface org.biopax.paxtools.model.level2.XReferrable

addXREF, getXREF, removeXREF, setXREF

Methods inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

addCOMMENT, getCOMMENT, getModelInterface, getRDFId, removeCOMMENT, setCOMMENT, setRDFId

Methods inherited from interface org.biopax.paxtools.model.level2.InteractionParticipant

isPARTICIPANTSof

Methods inherited from interface org.biopax.paxtools.model.level2.BioPAXElement

addCOMMENT, getCOMMENT, getModelInterface, getRDFId, removeCOMMENT, setCOMMENT, setRDFId

Methods inherited from interface org.biopax.paxtools.model.level2.pathwayComponent

isPATHWAY_COMPONENTSof

Constructor Detail

interactionAdapter

public interactionAdapter()

Method Detail

getPARTICIPANTS

public java.util.Set<InteractionParticipant> getPARTICIPANTS()

Specified by:

getPARTICIPANTS in interface interaction

compareParticipantSets

protected boolean compareParticipantSets(java.util.Set<InteractionParticipant> set1,
                                         java.util.Set<InteractionParticipant> set2)

isEquivalent

public boolean isEquivalent(BioPAXElement element)

Specified by:

isEquivalent in interface BioPAXElement

equivalenceCode

public int equivalenceCode()

Specified by:

equivalenceCode in interface BioPAXElement

updatePARTICIPANTS

protected void updatePARTICIPANTS(java.util.Set<? extends InteractionParticipant> oldSet,
                                  java.util.Set<? extends InteractionParticipant> newSet)

setParticipantInverse

protected void setParticipantInverse(InteractionParticipant ip,
                                     boolean remove)