Uses of Interface
org.biopax.paxtools.model.level2.physicalEntityParticipant

Packages that use physicalEntityParticipant

Package	Description
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
org.biopax.paxtools.model.level2	This package contains the interfaces that maps to the BioPAX level 2 specification.

Uses of physicalEntityParticipant in org.biopax.paxtools.controller

Methods in org.biopax.paxtools.controller that return physicalEntityParticipant

Modifier and Type	Method and Description
physicalEntityParticipant	ConversionScore.getMatch(physicalEntityParticipant pep1)

Methods in org.biopax.paxtools.controller that return types with arguments of type physicalEntityParticipant

Modifier and Type	Method and Description
Set<physicalEntityParticipant>	ConversionScore.getMatchedPEPs()

Methods in org.biopax.paxtools.controller with parameters of type physicalEntityParticipant

Modifier and Type	Method and Description
Object	ReusedPEPHelper.fixReusedPEP(physicalEntityParticipant pep, BioPAXElement bpe)
physicalEntityParticipant	ConversionScore.getMatch(physicalEntityParticipant pep1)

Constructor parameters in org.biopax.paxtools.controller with type arguments of type physicalEntityParticipant

Constructor and Description
ConversionScore(conversion conv1, conversion conv2, Double score, Map<physicalEntityParticipant,physicalEntityParticipant> pepMap, boolean reverseMatch)
ConversionScore(conversion conv1, conversion conv2, Double score, Map<physicalEntityParticipant,physicalEntityParticipant> pepMap, boolean reverseMatch)

Uses of physicalEntityParticipant in org.biopax.paxtools.model.level2

Subinterfaces of physicalEntityParticipant in org.biopax.paxtools.model.level2

Modifier and Type	Interface and Description
interface	sequenceParticipant

Methods in org.biopax.paxtools.model.level2 that return physicalEntityParticipant

Modifier and Type	Method and Description
physicalEntityParticipant	experimentalForm.getPARTICIPANT()

Methods in org.biopax.paxtools.model.level2 that return types with arguments of type physicalEntityParticipant

Modifier and Type	Method and Description
Set<physicalEntityParticipant>	catalysis.getCOFACTOR()
Set<physicalEntityParticipant>	complex.getCOMPONENTS()
Set<physicalEntityParticipant>	control.getCONTROLLER()
Set<physicalEntityParticipant>	conversion.getLEFT()
Set<physicalEntityParticipant>	conversion.getRIGHT()
Set<physicalEntityParticipant>	physicalEntity.isPHYSICAL_ENTITYof()

Methods in org.biopax.paxtools.model.level2 with parameters of type physicalEntityParticipant

Modifier and Type	Method and Description
void	catalysis.addCOFACTOR(physicalEntityParticipant COFACTOR)
void	complex.addCOMPONENTS(physicalEntityParticipant COMPONENTS)
void	control.addCONTROLLER(physicalEntityParticipant CONTROLLER)
void	conversion.addLEFT(physicalEntityParticipant LEFT)
void	physicalEntity.addPHYSICAL_ENTITYof(physicalEntityParticipant pep)
void	conversion.addRIGHT(physicalEntityParticipant RIGHT)
boolean	physicalEntityParticipant.isInEquivalentState(physicalEntityParticipant that)
void	catalysis.removeCOFACTOR(physicalEntityParticipant COFACTOR)
void	complex.removeCOMPONENTS(physicalEntityParticipant COMPONENTS)
void	control.removeCONTROLLER(physicalEntityParticipant CONTROLLER)
void	conversion.removeLEFT(physicalEntityParticipant LEFT)
void	physicalEntity.removePHYSICAL_ENTITYof(physicalEntityParticipant pep)
void	conversion.removeRIGHT(physicalEntityParticipant RIGHT)
void	experimentalForm.setPARTICIPANT(physicalEntityParticipant PARTICIPANT)

Method parameters in org.biopax.paxtools.model.level2 with type arguments of type physicalEntityParticipant

Modifier and Type	Method and Description
void	catalysis.setCOFACTOR(Set<physicalEntityParticipant> COFACTOR)
void	complex.setCOMPONENTS(Set<physicalEntityParticipant> COMPONENTS)
void	control.setCONTROLLER(Set<physicalEntityParticipant> CONTROLLER)
void	conversion.setLEFT(Set<physicalEntityParticipant> LEFT)
void	conversion.setRIGHT(Set<physicalEntityParticipant> RIGHT)