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

Packages that use physicalEntityParticipant

org.biopax.paxtools.controller
org.biopax.paxtools.model.level2
org.biopax.paxtools.util

Uses of physicalEntityParticipant in org.biopax.paxtools.controller

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

physicalEntityParticipant

ConversionScore.getMatch(physicalEntityParticipant pep1)

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

java.util.Set<physicalEntityParticipant>

ConversionScore.getMatchedPEPs()

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

java.lang.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

ConversionScore(conversion conv1, conversion conv2, java.lang.Double score, java.util.Map<physicalEntityParticipant,physicalEntityParticipant> pepMap, boolean reverseMatch)

ConversionScore(conversion conv1, conversion conv2, java.lang.Double score, java.util.Map<physicalEntityParticipant,physicalEntityParticipant> pepMap, boolean reverseMatch)

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

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

interface

sequenceParticipant

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

physicalEntityParticipant

experimentalForm.getPARTICIPANT()

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

java.util.Set<physicalEntityParticipant>	catalysis.getCOFACTOR()
java.util.Set<physicalEntityParticipant>	complex.getCOMPONENTS()
java.util.Set<physicalEntityParticipant>	control.getCONTROLLER()
java.util.Set<physicalEntityParticipant>	conversion.getLEFT()
java.util.Set<physicalEntityParticipant>	conversion.getRIGHT()
java.util.Set<physicalEntityParticipant>	physicalEntity.isPHYSICAL_ENTITYof()

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

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

void	catalysis.setCOFACTOR(java.util.Set<physicalEntityParticipant> COFACTOR)
void	complex.setCOMPONENTS(java.util.Set<physicalEntityParticipant> COMPONENTS)
void	control.setCONTROLLER(java.util.Set<physicalEntityParticipant> CONTROLLER)
void	conversion.setLEFT(java.util.Set<physicalEntityParticipant> LEFT)
void	conversion.setRIGHT(java.util.Set<physicalEntityParticipant> RIGHT)

Uses of physicalEntityParticipant in org.biopax.paxtools.util

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

static java.util.Collection<java.util.List<physicalEntityParticipant>>	Level2Helper.groupParticipants(physicalEntity pe, boolean includeComplexMemberships)
static java.util.Collection<java.util.List<physicalEntityParticipant>>	Level2Helper.selectFunctionalSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)
static java.util.Collection<java.util.List<physicalEntityParticipant>>	Level2Helper.selectInactiveSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)

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

static java.util.Collection<java.util.List<physicalEntityParticipant>>	Level2Helper.selectFunctionalSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)
static java.util.Collection<java.util.List<physicalEntityParticipant>>	Level2Helper.selectInactiveSets(java.util.Collection<java.util.List<physicalEntityParticipant>> parts)