A B C D E F G H I J K L M N O P R S T U V X

A

AbstractFilterSet<E> - Class in org.biopax.paxtools.util
Base class for implementing various filters
AbstractFilterSet(Set) - Constructor for class org.biopax.paxtools.util.AbstractFilterSet
 
AbstractSingleElementSet - Class in org.biopax.paxtools.util
 
AbstractSingleElementSet() - Constructor for class org.biopax.paxtools.util.AbstractSingleElementSet
 
add(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
add(BioPAXElement) - Method in interface org.biopax.paxtools.model.level2.Model
 
addAUTHORS(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
addAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
addAUTHORS(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
addAVAILABILITY(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
addAVAILABILITY(String) - Method in interface org.biopax.paxtools.model.level2.entity
This method adds the given text to the avaialability set.
addAVAILABILITY(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
addBiochemicalReaction(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addBiochemicalReaction(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addBioSource(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addBioSource(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addCatalysis(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addCatalysis(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addChemicalStructure(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addChemicalStructure(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addCOFACTOR(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
addCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis
 
addCOFACTOR(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
addCOMMENT(String) - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
addCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
addCOMMENT(String) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
addComplex(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addComplex(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addComplexAssembly(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addComplexAssembly(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addCOMPONENTS(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
addCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex
 
addCOMPONENTS(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
addCONFIDENCE(confidence) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
addConfidence(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence
 
addConfidence(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addCONFIDENCE(confidence) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
addControl(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addControl(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addCONTROLLED(process) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
addCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control
 
addCONTROLLED(process) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
addCONTROLLEDof(control) - Method in class org.biopax.paxtools.impl.level2.processImpl
 
addCONTROLLER(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
addCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control
 
addCONTROLLER(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
addConversion(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addConversion(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addDATA_SOURCE(dataSource) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
addDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity
This method adds the given value to the DATA_SOURCE set.
addDATA_SOURCE(dataSource) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
addDataSource(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addDataSource(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addDELTA_G(deltaGprimeO) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
addDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
addDELTA_G(deltaGprimeO) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
addDELTA_H(double) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
addDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
addDELTA_H(double) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
addDELTA_S(double) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
addDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
addDELTA_S(double) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
addDeltaGprimeO(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addDeltaGprimeO(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addDna(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addDna(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addEC_NUMBER(String) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
addEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
addEC_NUMBER(String) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
addElement(XReferrable) - Static method in class org.biopax.paxtools.controller.UnifiedCluster
 
addEvidence(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addEVIDENCE(evidence) - Method in class org.biopax.paxtools.impl.level2.processImpl
 
addEvidence(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process
 
addEVIDENCE(evidence) - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
addEVIDENCE_CODE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
addEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence
 
addEVIDENCE_CODE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
addEXPERIMENTAL_FORM(experimentalForm) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
addEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence
 
addEXPERIMENTAL_FORM(experimentalForm) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
addEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
addEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
addEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
addExperimentalForm(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addExperimentalForm(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addFEATURE_LOCATION(sequenceLocation) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
addFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
addFEATURE_LOCATION(sequenceLocation) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
addInteraction(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addInteraction(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addINTERACTION_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
addINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
 
addINTERACTION_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
addKEQ(kPrime) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
addKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
addKEQ(kPrime) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
addKPrime(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addKPrime(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addLEFT(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
addLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
 
addLEFT(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
addMaxCardinalityRestriction(Class, int) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
addMethod - Variable in class org.biopax.paxtools.controller.PropertyEditor
This variable stores the method to invoke for adding the given value to the property managed by this editor.
addModulation(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addModulation(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addNAME(String) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
addNAME(String) - Method in interface org.biopax.paxtools.model.level2.dataSource
 
addNAME(String) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
addNEXT_STEP(pathwayStep) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
addNEXT_STEP(pathwayStep) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
addNEXT_STEP(pathwayStep) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
addOpenControlledVocabulary(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addOpenControlledVocabulary(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.interactionImpl
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
addPARTICIPANTS(InteractionParticipant) - Method in interface org.biopax.paxtools.model.level2.interaction
 
addPARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
addPathway(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPathway(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPATHWAY_COMPONENTS(pathwayComponent) - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
addPATHWAY_COMPONENTS(pathwayComponent) - Method in interface org.biopax.paxtools.model.level2.pathway
 
addPATHWAY_COMPONENTS(pathwayComponent) - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
addPathwayStep(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPathwayStep(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPHYSICAL_ENTITYof(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
addPhysicalEntity(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPhysicalEntity(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPhysicalEntityParticipant(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPhysicalEntityParticipant(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPhysicalInteraction(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPhysicalInteraction(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addProtein(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addProtein(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addPublicationXref(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addPublicationXref(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addRangeRestriction(Class, Set<Class>) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
 
addRDFId(String) - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
addRelationshipXref(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addRelationshipXref(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addRIGHT(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
addRIGHT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
 
addRIGHT(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
addRna(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addRna(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
addSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
 
addSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in class org.biopax.paxtools.proxy.level2.sequenceParticipantProxy
 
addSequenceFeature(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addSequenceFeature(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSequenceInterval(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addSequenceInterval(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSequenceParticipant(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addSequenceParticipant(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSequenceSite(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addSequenceSite(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSmallMolecule(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addSmallMolecule(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addSOURCE(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
addSOURCE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
addSOURCE(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
addSTEP_INTERACTIONS(process) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
addSTEP_INTERACTIONS(process) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
addSTEP_INTERACTIONS(process) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
addSTEP_INTERACTIONSOf(pathwayStep) - Method in class org.biopax.paxtools.impl.level2.processImpl
 
addSTRUCTURE(chemicalStructure) - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
addSTRUCTURE(chemicalStructure) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
addSTRUCTURE(chemicalStructure) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
addSYNONYMS(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
addSYNONYMS(String) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
addSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.entity
This method adds the given value to the SYNONYMS set.
addSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
addSYNONYMS(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
addSYNONYMS(String) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
addTERM(String) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
addTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
 
addTERM(String) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
addTransport(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addTransport(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addTransportWithBiochemicalReaction(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addTransportWithBiochemicalReaction(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addUnificationXref(String) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
addUnificationXref(String) - Method in interface org.biopax.paxtools.model.level2.Model
 
addURL(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
addURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
addURL(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
addXREF(xref) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
addXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
addXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 

B

BaseSearch - Class in org.biopax.paxtools.persistence.level2
base search class
BaseSearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.BaseSearch
construct
biochemicalReaction - Interface in org.biopax.paxtools.model.level2
 
biochemicalReactionImpl - Class in org.biopax.paxtools.impl.level2
 
biochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
biochemicalReactionProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for biochemicalReaction
biochemicalReactionProxy() - Constructor for class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
BioPAXElement - Interface in org.biopax.paxtools.model.level2
 
bioPAXElementImpl - Class in org.biopax.paxtools.impl.level2
 
bioPAXElementImpl() - Constructor for class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
BioPAXElementProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for BioPAXElement
BioPAXElementProxy() - Constructor for class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
BioPAXFactory - Interface in org.biopax.paxtools.model.level2
 
BioPAXFactoryForPersistence - Class in org.biopax.paxtools.proxy.level2
User: root Date: Apr 26, 2006 Time: 3:06:08 PM_DOT
BioPAXFactoryForPersistence() - Constructor for class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
BioPAXFactoryImpl - Class in org.biopax.paxtools.impl.level2
User: root Date: Apr 26, 2006 Time: 3:06:08 PM_DOT
BioPAXFactoryImpl() - Constructor for class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
BioPaxIOException - Exception in org.biopax.paxtools.util
 
BioPaxIOException(Throwable) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException
 
BioPaxIOException(String) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException
 
BioPAXLevel - Enum in org.biopax.paxtools.model
 
bioSource - Interface in org.biopax.paxtools.model.level2
 
bioSourceImpl - Class in org.biopax.paxtools.impl.level2
Created by IntelliJ IDEA.
bioSourceImpl() - Constructor for class org.biopax.paxtools.impl.level2.bioSourceImpl
 
bioSourceProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for bioSource
bioSourceProxy() - Constructor for class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
BP_PREFIX - Static variable in interface org.biopax.paxtools.model.level2.Model
 
bPrintTime - Variable in class org.biopax.paxtools.persistence.level2.HiRDB
 
bPrintTime - Variable in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 
bShowSQL - Variable in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 
buildDDL(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
build DDL

C

call_setPARTICIPANTS_x(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
call_setPARTICIPANTS_x(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
canInstantiate(String) - Method in interface org.biopax.paxtools.controller.EditorMap
 
canInstantiate(String) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
catalysis - Interface in org.biopax.paxtools.model.level2
 
catalysisImpl - Class in org.biopax.paxtools.impl.level2
 
catalysisImpl() - Constructor for class org.biopax.paxtools.impl.level2.catalysisImpl
 
catalysisProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for catalysis
catalysisProxy() - Constructor for class org.biopax.paxtools.proxy.level2.catalysisProxy
 
checkCONTROLLED(process) - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
checkCONTROLLED(process) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
checkCONTROLLED(entity) - Method in class org.biopax.paxtools.impl.level2.modulationImpl
 
checkCONTROLLED(process) - Method in class org.biopax.paxtools.impl.level2.modulationImpl
 
checkRestrictions(Object, Object) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
 
checkRestrictions(Object, Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
chemicalStructure - Interface in org.biopax.paxtools.model.level2
 
chemicalStructureImpl - Class in org.biopax.paxtools.impl.level2
 
chemicalStructureImpl() - Constructor for class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
chemicalStructureProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for chemicalStructure
chemicalStructureProxy() - Constructor for class org.biopax.paxtools.proxy.level2.chemicalStructureProxy
 
ClassFilterSet<E> - Class in org.biopax.paxtools.util
User: root Date: Aug 30, 2006 Time: 3:05:58 PM
ClassFilterSet(Set, Class) - Constructor for class org.biopax.paxtools.util.ClassFilterSet
Constructor
close() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
close entity manager
compareParticipantSets(Set<InteractionParticipant>, Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
complex - Interface in org.biopax.paxtools.model.level2
 
complexAssembly - Interface in org.biopax.paxtools.model.level2
 
complexAssemblyImpl - Class in org.biopax.paxtools.impl.level2
User: root Date: Apr 13, 2006 Time: 2:22:39 PM_DOT
complexAssemblyImpl() - Constructor for class org.biopax.paxtools.impl.level2.complexAssemblyImpl
 
complexAssemblyProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for complexAssembly
complexAssemblyProxy() - Constructor for class org.biopax.paxtools.proxy.level2.complexAssemblyProxy
 
complexImpl - Class in org.biopax.paxtools.impl.level2
 
complexImpl() - Constructor for class org.biopax.paxtools.impl.level2.complexImpl
 
complexProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for complex
complexProxy() - Constructor for class org.biopax.paxtools.proxy.level2.complexProxy
 
confidence - Interface in org.biopax.paxtools.model.level2
 
confidenceImpl - Class in org.biopax.paxtools.impl.level2
 
confidenceImpl() - Constructor for class org.biopax.paxtools.impl.level2.confidenceImpl
 
confidenceProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for confidence
confidenceProxy() - Constructor for class org.biopax.paxtools.proxy.level2.confidenceProxy
 
contains(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
This method returns true if only the parameter is actually contained within this level2
contains(BioPAXElement) - Method in interface org.biopax.paxtools.model.level2.Model
This method returns true if only the parameter is actually contained within this level2
contains(Object) - Method in class org.biopax.paxtools.util.AbstractFilterSet
 
containsEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
THis method returns true if the paramter or an equalivant object as defined by the method exists in the level2.
containsEquivalent(BioPAXElement) - Method in interface org.biopax.paxtools.model.level2.Model
THis method returns true if the paramter or an equalivant object as defined by the method exists in the level2.
control - Interface in org.biopax.paxtools.model.level2
 
controlImpl - Class in org.biopax.paxtools.impl.level2
 
controlImpl() - Constructor for class org.biopax.paxtools.impl.level2.controlImpl
 
controlProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for control
controlProxy() - Constructor for class org.biopax.paxtools.proxy.level2.controlProxy
 
ControlType - Enum in org.biopax.paxtools.model.level2
User: root Date: Aug 1, 2006 Time: 5:37:34 PM_DOT
conversion - Interface in org.biopax.paxtools.model.level2
 
conversionImpl - Class in org.biopax.paxtools.impl.level2
 
conversionImpl() - Constructor for class org.biopax.paxtools.impl.level2.conversionImpl
 
conversionProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for conversion
conversionProxy() - Constructor for class org.biopax.paxtools.proxy.level2.conversionProxy
 
convertFromOWL(InputStream) - Method in class org.biopax.paxtools.io.jena.JenaIOHandler
 
convertToOWL(Model, OutputStream) - Method in class org.biopax.paxtools.io.jena.JenaIOHandler
 
copyPEPFields() - Method in class org.biopax.paxtools.io.ReusedPEPHelper
 
createBiochemicalReaction() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createBiochemicalReaction() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createBiochemicalReaction() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createBioSource() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createBioSource() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createBioSource() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createCatalysis() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createCatalysis() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createCatalysis() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createChemicalStructure() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createChemicalStructure() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createChemicalStructure() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createComplex() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createComplex() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createComplex() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createComplexAssembly() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createComplexAssembly() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createComplexAssembly() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createConfidence() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createConfidence() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createConfidence() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createControl() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createControl() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createControl() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createConversion() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createConversion() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createConversion() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createDataSource() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createDataSource() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createDataSource() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createDeltaGprimeO() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createDeltaGprimeO() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createDeltaGprimeO() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createDna() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createDna() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createDna() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createEntityManager() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 
createEvidence() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createEvidence() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createEvidence() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createExperimentalForm() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createExperimentalForm() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createExperimentalForm() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createInteraction() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createInteraction() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createInteraction() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createInteractionSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
create interaction search
createInteractionSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
create interaction search
createKeywordSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
create keyword search
createKeywordSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
create keyword search
createKPrime() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createKPrime() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createKPrime() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createMiscSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
create misc search
createMiscSearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
create misc search
createModel() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createModel() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createModel() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createModulation() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createModulation() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createModulation() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createNewInstance(String) - Method in interface org.biopax.paxtools.controller.EditorMap
 
createNewInstance(Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
createNewInstance(String) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
createNewInstance(Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
createOpenControlledVocabulary() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createOpenControlledVocabulary() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createOpenControlledVocabulary() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPathway() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPathway() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPathway() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPathwaySearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
create pathway search
createPathwaySearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
create pathway search
createPathwayStep() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPathwayStep() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPathwayStep() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPhysicalEntity() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPhysicalEntity() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPhysicalEntity() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPhysicalEntityParticipant() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPhysicalEntityParticipant() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPhysicalEntityParticipant() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPhysicalEntitySearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
create physicalEntity search
createPhysicalEntitySearch() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
create physicalEntity search
createPhysicalInteraction() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPhysicalInteraction() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPhysicalInteraction() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPropertyEditor(Class, String) - Static method in class org.biopax.paxtools.controller.PropertyEditor
This method creates a property reflecting on the domain and property.
createProtein() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createProtein() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createProtein() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createPublicationXref() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createPublicationXref() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createPublicationXref() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createRelationshipXref() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createRelationshipXref() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createRelationshipXref() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createRna() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createRna() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createRna() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createSequenceFeature() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createSequenceFeature() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createSequenceFeature() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createSequenceInterval() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createSequenceInterval() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createSequenceInterval() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createSequenceParticipant() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createSequenceParticipant() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createSequenceParticipant() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createSequenceSite() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createSequenceSite() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createSequenceSite() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createSmallMolecule() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createSmallMolecule() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createSmallMolecule() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createTransport() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createTransport() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createTransport() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createTransportWithBiochemicalReaction() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createTransportWithBiochemicalReaction() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createTransportWithBiochemicalReaction() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 
createUnificationXref() - Method in class org.biopax.paxtools.impl.level2.BioPAXFactoryImpl
 
createUnificationXref() - Method in interface org.biopax.paxtools.model.level2.BioPAXFactory
 
createUnificationXref() - Method in class org.biopax.paxtools.proxy.level2.BioPAXFactoryForPersistence
 

D

dataSource - Interface in org.biopax.paxtools.model.level2
XREF Should be only unification and publication xrefs
dataSourceImpl - Class in org.biopax.paxtools.impl.level2
 
dataSourceImpl() - Constructor for class org.biopax.paxtools.impl.level2.dataSourceImpl
 
dataSourceProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for dataSource
dataSourceProxy() - Constructor for class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
defaultProperties - Static variable in class org.biopax.paxtools.model.level2.PaxtoolsProperties
 
deleteOWL(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
delete owl data
deltaGprimeO - Interface in org.biopax.paxtools.model.level2
 
deltaGprimeOImpl - Class in org.biopax.paxtools.impl.level2
 
deltaGprimeOImpl() - Constructor for class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
deltaGprimeOProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for deltaGprimeO
deltaGprimeOProxy() - Constructor for class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
Direction - Enum in org.biopax.paxtools.model.level2
Catalysis direction controlled vocabulary
dna - Interface in org.biopax.paxtools.model.level2
 
dnaImpl - Class in org.biopax.paxtools.impl.level2
 
dnaImpl() - Constructor for class org.biopax.paxtools.impl.level2.dnaImpl
 
dnaProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for dna
dnaProxy() - Constructor for class org.biopax.paxtools.proxy.level2.dnaProxy
 
domain - Variable in class org.biopax.paxtools.controller.PropertyEditor
This is the Class representing the domain of the property.
doubleSetToStringSet(Set<Double>) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
doubleToString(Double) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
downloadOWL(String, OutputStream) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
download owl data

E

EditorMap - Interface in org.biopax.paxtools.controller
User: root Date: Aug 24, 2006 Time: 5:44:41 PM
entity - Interface in org.biopax.paxtools.model.level2
This class represents a discrete biological unit used when describing pathways.
entityImpl - Class in org.biopax.paxtools.impl.level2
 
entityImpl() - Constructor for class org.biopax.paxtools.impl.level2.entityImpl
 
entityProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for entity
entityProxy() - Constructor for class org.biopax.paxtools.proxy.level2.entityProxy
 
EnumeratedPropertyEditor - Class in org.biopax.paxtools.controller
User: root Date: Aug 22, 2006 Time: 5:46:22 PM
EnumeratedPropertyEditor(String, Method, Class, Class, boolean) - Constructor for class org.biopax.paxtools.controller.EnumeratedPropertyEditor
 
equals(Object) - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
equals(Object) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
EquivalanceChecker - Class in org.biopax.paxtools.util
User: demir Date: Mar 26, 2007 Time: 10:35:26 PM
EquivalanceChecker() - Constructor for class org.biopax.paxtools.util.EquivalanceChecker
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
equivalenceCode() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
equivalenceCode() - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
equivalenceCode() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
evidence - Interface in org.biopax.paxtools.model.level2
 
evidenceImpl - Class in org.biopax.paxtools.impl.level2
 
evidenceImpl() - Constructor for class org.biopax.paxtools.impl.level2.evidenceImpl
 
evidenceProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for evidence
evidenceProxy() - Constructor for class org.biopax.paxtools.proxy.level2.evidenceProxy
 
experimentalForm - Interface in org.biopax.paxtools.model.level2
 
experimentalFormImpl - Class in org.biopax.paxtools.impl.level2
 
experimentalFormImpl() - Constructor for class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
experimentalFormProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for experimentalForm
experimentalFormProxy() - Constructor for class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
externalReferenceUtilityClass - Interface in org.biopax.paxtools.model.level2
 
externalReferenceUtilityClassProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for externalReferenceUtilityClass
externalReferenceUtilityClassProxy() - Constructor for class org.biopax.paxtools.proxy.level2.externalReferenceUtilityClassProxy
 

F

fetch(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.Fetcher
 
fetch(EntityManager, String, String) - Method in class org.biopax.paxtools.persistence.level2.KeywordSearch
 
fetch(EntityManager, String, String, Class) - Method in class org.biopax.paxtools.persistence.level2.KeywordSearch
 
fetchAllNEXT_STEPOfPathway(pathwayComponent, HashSet<pathwayStep>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchAllPreviousStepOfPathway(EntityManager, pathwayComponent, HashSet<pathwayStep>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchAllSubPathway(pathwayComponent, HashSet<pathway>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchAllSuperPathway(EntityManager, pathway, HashSet<pathway>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchBackStep(EntityManager, pathwayStep) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchChildPathwayComponentOrProcess(pathwayComponent) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchControlByCONTROLLED(EntityManager, String, boolean) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
 
fetchEC_NUMBERInPathwayComponent(pathwayComponent, HashSet<String>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
Fetcher - Class in org.biopax.paxtools.controller
 
Fetcher(EditorMap) - Constructor for class org.biopax.paxtools.controller.Fetcher
 
fetchEvidence(pathwayComponent, HashSet<evidence>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchInteraction(pathwayComponent, HashSet<interaction>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchNEXT_STEPOfPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchOpenControlledVocabularyByTerm(EntityManager, String) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchPathwayByPathwayComonent(EntityManager, pathwayComponent) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchPathwayStepByProcess(EntityManager, process) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchPhysicalEntity(BioPAXElement, HashSet<physicalEntity>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchPhysicalInteractionByINTERACTION_TYPE(EntityManager, String) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
 
fetchPreviousStepOfPathway(EntityManager, pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchSubPathwayComponent(pathwayComponent) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchSuperPathway(EntityManager, pathwayComponent) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
fetchXref(BioPAXElement, HashSet<xref>) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
 
filter(Object) - Method in class org.biopax.paxtools.util.AbstractFilterSet
 
filter(Object) - Method in class org.biopax.paxtools.util.ClassFilterSet
 
fixReusedPEP(Object, BioPAXElement) - Method in class org.biopax.paxtools.io.ReusedPEPHelper
 
floatToString(Float) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 

G

getAddMethod() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getAllEvidenceListInPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all evidence in pathway
getAllNEXT_STEPListOfPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all NEXT_STEP of pathway
getAllPreviousStepListOfPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all previous steps of pathway
getAllSubPathwayList(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all sub pathway
getAllSuperPathwayList(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all super pathway
getAnalyzer() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
text analyzer for lucene
getAUTHORS() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getAUTHORS() - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
getAUTHORS() - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
getAVAILABILITY() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getAVAILABILITY() - Method in interface org.biopax.paxtools.model.level2.entity
The contents of this set can be modified but semantic consistency is not guaranteed.
getAVAILABILITY() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getBiochemicalReactionList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all biochemicalReaction
getBiochemicalReactionListByEC_NUMBER(String) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get biochemicalReaction by EC_NUMBER
getBioPAXClassFor(Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getBioPAXClassFor(Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getCatalysisList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all catalysis
getCELLTYPE() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
getCELLTYPE() - Method in interface org.biopax.paxtools.model.level2.bioSource
 
getCELLTYPE() - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
getCELLULAR_LOCATION() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
getCELLULAR_LOCATION() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
getCELLULAR_LOCATION() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
getCHEMICAL_FORMULA() - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
getCHEMICAL_FORMULA() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
getCHEMICAL_FORMULA() - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
getCOFACTOR() - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
getCOFACTOR() - Method in interface org.biopax.paxtools.model.level2.catalysis
 
getCOFACTOR() - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
getCOMMENT() - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
getCOMMENT() - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
getCOMMENT() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
getComplexAssemblyList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all complexAssembly
getComplexList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all complex
getCOMPONENTS() - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
getCOMPONENTS() - Method in interface org.biopax.paxtools.model.level2.complex
 
getCOMPONENTS() - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
getCONFIDENCE() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
getCONFIDENCE() - Method in interface org.biopax.paxtools.model.level2.evidence
 
getCONFIDENCE() - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
getCONFIDENCE_VALUE() - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
getCONFIDENCE_VALUE() - Method in interface org.biopax.paxtools.model.level2.confidence
 
getCONFIDENCE_VALUE() - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
getConnect() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
connect
getConnect() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
connect
getConnectionURL() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
connection URL (JDBC path)
getCONTROL_TYPE() - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
getCONTROL_TYPE() - Method in interface org.biopax.paxtools.model.level2.control
 
getCONTROL_TYPE() - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
getCONTROLLED() - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
getCONTROLLED() - Method in interface org.biopax.paxtools.model.level2.control
 
getCONTROLLED() - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
getCONTROLLER() - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
getCONTROLLER() - Method in interface org.biopax.paxtools.model.level2.control
 
getCONTROLLER() - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
getCONTROLLERListByCONTROLLED(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get CONTROLLER By CONTROLLED
getControlList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all control
getControlListByCONTROLLED(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get control by CONTROLLED
getConversionList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all conversion
getDATA_SOURCE() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getDATA_SOURCE() - Method in interface org.biopax.paxtools.model.level2.entity
This method returns a set of free text descriptions of the source of this data, e.g.
getDATA_SOURCE() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getDataSourceList() - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get data source
getDataTypeFor(PropertyEditor) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getDB() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
getDB() - Method in interface org.biopax.paxtools.model.level2.xref
 
getDB() - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
getDB_VERSION() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
getDB_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref
 
getDB_VERSION() - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
getDELTA_G() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getDELTA_G() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
getDELTA_G() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getDELTA_G_PRIME_O() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getDELTA_G_PRIME_O() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
getDELTA_G_PRIME_O() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getDELTA_G_PRIME_O_x() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getDELTA_H() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getDELTA_H() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
getDELTA_H() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getDELTA_H_x() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getDELTA_S() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getDELTA_S() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
getDELTA_S() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getDELTA_S_x() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getDIRECTION() - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
getDIRECTION() - Method in interface org.biopax.paxtools.model.level2.catalysis
 
getDIRECTION() - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
getDnaList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all dna
getDomain() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getEC_NUMBER() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getEC_NUMBER() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
getEC_NUMBER() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getEC_NUMBERListInPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get EC_NUMBER in pathway
getEditorForProperty(String, Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getEditorForProperty(String, Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getEditorsForProperty(String) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getEditorsForProperty(String) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getEditorsOf(Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getEditorsOf(Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getElementByRDFID(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDB
get element by rdf:ID
getElementByRDFID(EntityManager, String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
get element by rdf:ID
getElementByRDFID(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
get element by rdf:ID
getEntityListByAVAIRABILITY(String) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get entity by AVAIRABILITY
getEntityListByCOMMENT(String) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get entity by COMMENT
getEntityListByDATA_SOURCE(String) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get entity by DATA_SOURCE
getEntityListByDBAndIDOfXREF(String, String) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get entity by DB and ID of xref
getEntityListByNAME(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get entity by NAME
getEntityManager() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
 
getEntityManager() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
get entity manager
getEVIDENCE() - Method in class org.biopax.paxtools.impl.level2.processImpl
 
getEVIDENCE() - Method in interface org.biopax.paxtools.model.level2.process
 
getEVIDENCE() - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
getEVIDENCE_CODE() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
getEVIDENCE_CODE() - Method in interface org.biopax.paxtools.model.level2.evidence
 
getEVIDENCE_CODE() - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
getEXPERIMENTAL_FORM() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
getEXPERIMENTAL_FORM() - Method in interface org.biopax.paxtools.model.level2.evidence
 
getEXPERIMENTAL_FORM() - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
getEXPERIMENTAL_FORM_TYPE() - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
getEXPERIMENTAL_FORM_TYPE() - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
getEXPERIMENTAL_FORM_TYPE() - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
getFEATURE_LOCATION() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getFEATURE_LOCATION() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
getFEATURE_LOCATION() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getFEATURE_TYPE() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getFEATURE_TYPE() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
getFEATURE_TYPE() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getFieldNames() - Method in class org.biopax.paxtools.persistence.level2.KeywordSearch
get field names
getGetMethod() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getID() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
getID() - Method in interface org.biopax.paxtools.model.level2.xref
 
getID() - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
getID_VERSION() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
getID_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref
 
getID_VERSION() - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
getIdMap() - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
getIdMap() - Method in interface org.biopax.paxtools.model.level2.Model
 
getIndexBase() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
index base
getInstance() - Static method in class org.biopax.paxtools.model.level2.PaxtoolsProperties
 
getINTERACTION_TYPE() - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
getINTERACTION_TYPE() - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
 
getINTERACTION_TYPE() - Method in class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
getInteractionList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all interaction
getInteractionListByINTERACTION_TYPE(String) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get interaction by INTERACTION_TYPE
getInteractionListByNAME(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get interaction by NAME
getInteractionListInPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get interaction in pathway
getIONIC_STRENGTH() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getIONIC_STRENGTH() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getIONIC_STRENGTH() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
getIONIC_STRENGTH() - Method in interface org.biopax.paxtools.model.level2.kPrime
 
getIONIC_STRENGTH() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getIONIC_STRENGTH() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getIONIC_STRENGTH_x() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getIONIC_STRENGTH_x() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getK_PRIME() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getK_PRIME() - Method in interface org.biopax.paxtools.model.level2.kPrime
 
getK_PRIME() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getK_PRIME_x() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getKEQ() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getKEQ() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
getKEQ() - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
getKeyName() - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
getKnownSubClassesOf(Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getKnownSubClassesOf(Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getLEFT() - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
getLEFT() - Method in interface org.biopax.paxtools.model.level2.conversion
 
getLEFT() - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
getLEFT_x() - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
getLevelFileAsStream() - Method in enum org.biopax.paxtools.model.BioPAXLevel
 
getLocalName(Class) - Method in interface org.biopax.paxtools.controller.EditorMap
 
getLocalName(Class) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
getLocator() - Method in enum org.biopax.paxtools.model.BioPAXLevel
 
getMaxCardinality(Class) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getMethod - Variable in class org.biopax.paxtools.controller.PropertyEditor
This variable stores the method to invoke for getting the value of the property on a given bean.
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.complexAssemblyImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.dnaImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.interactionImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.modulationImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.proteinImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.relationshipXrefImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.rnaImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.transportImpl
 
getModelInterface() - Method in class org.biopax.paxtools.impl.level2.unificationXrefImpl
 
getModelInterface() - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
getModelInterface() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
getModulationList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all modulation
getMOLECULAR_WEIGHT() - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
getMOLECULAR_WEIGHT() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
getMOLECULAR_WEIGHT() - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
getMOLECULAR_WEIGHT_x() - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
getNAME() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
getNAME() - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
getNAME() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getNAME() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getNAME() - Method in interface org.biopax.paxtools.model.level2.bioSource
 
getNAME() - Method in interface org.biopax.paxtools.model.level2.dataSource
 
getNAME() - Method in interface org.biopax.paxtools.model.level2.entity
This method returns the preferred full name for this entity.
getNAME() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
getNAME() - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
getNAME() - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
getNAME() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getNAME() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getNameSpace() - Method in enum org.biopax.paxtools.model.BioPAXLevel
 
getNameSpacePrefixMap() - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
getNameSpacePrefixMap() - Method in interface org.biopax.paxtools.model.level2.Model
 
getNEXT_STEP() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
getNEXT_STEP() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
getNEXT_STEP() - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
getNEXT_STEPListOfPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get NEXT_STEP of pathway
getObjects() - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
getObjects(Class) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
getObjects() - Method in interface org.biopax.paxtools.model.level2.Model
 
getObjects(Class) - Method in interface org.biopax.paxtools.model.level2.Model
 
getORGANISM() - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
getORGANISM() - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
getORGANISM() - Method in interface org.biopax.paxtools.model.level2.complex
 
getORGANISM() - Method in interface org.biopax.paxtools.model.level2.pathway
 
getORGANISM() - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
 
getORGANISM() - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
getORGANISM() - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
getORGANISM() - Method in class org.biopax.paxtools.proxy.level2.sequenceEntityProxy
 
getPARTICIPANT() - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
getPARTICIPANT() - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
getPARTICIPANT() - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
getPARTICIPANTS() - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
getPARTICIPANTS() - Method in class org.biopax.paxtools.impl.level2.interactionImpl
 
getPARTICIPANTS() - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
getPARTICIPANTS() - Method in interface org.biopax.paxtools.model.level2.interaction
 
getPARTICIPANTS() - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
getPARTICIPANTS_x() - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
getPassword() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
database user password
getPATHWAY_COMPONENTS() - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
getPATHWAY_COMPONENTS() - Method in interface org.biopax.paxtools.model.level2.pathway
 
getPATHWAY_COMPONENTS() - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
getPathwayList() - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get all pathway
getPathwayListByNAME(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get pathway by NAME
getPathwayListByORGANISM(String) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get pathway by ORGANISM
getPathwayListByTERMOfEVIDENCE_CODE(String) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get pathway by TERM of EVIDENCE_CODE
getPH() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getPH() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getPH() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
getPH() - Method in interface org.biopax.paxtools.model.level2.kPrime
 
getPH() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getPH() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getPH_x() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getPH_x() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getPHYSICAL_ENTITY() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
getPHYSICAL_ENTITY() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
getPHYSICAL_ENTITY() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
getPhysicalEntityList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all physical entity
getPhysicalEntityListByNAME(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get physicalEntity by NAME
getPhysicalEntityListByORGANISM(String) - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get physicalEntity by ORGANISM
getPhysicalEntityListInPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get physicalEntity in pathway
getPMG() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getPMG() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getPMG() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
getPMG() - Method in interface org.biopax.paxtools.model.level2.kPrime
 
getPMG() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getPMG() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getPMG_x() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getPMG_x() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getPOSITION_STATUS() - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
getPOSITION_STATUS() - Method in interface org.biopax.paxtools.model.level2.sequenceSite
 
getPOSITION_STATUS() - Method in class org.biopax.paxtools.proxy.level2.sequenceSiteProxy
 
getPreviousStepListOfPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get previous steps of pathway
getPrimarySetMethod() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getProperty() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getProteinList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all protein
getProxyId() - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
getProxyId() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
getPUName() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
persistence unit name
getRange() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getRDFId() - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
getRDFId() - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
getRDFId() - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
getRDFId() - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
getRDFId() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
getRELATIONSHIP_TYPE() - Method in class org.biopax.paxtools.impl.level2.relationshipXrefImpl
 
getRELATIONSHIP_TYPE() - Method in interface org.biopax.paxtools.model.level2.relationshipXref
 
getRELATIONSHIP_TYPE() - Method in class org.biopax.paxtools.proxy.level2.relationshipXrefProxy
 
getRemoveMethod() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getRestrictedRanges() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
 
getRestrictedRangesFor(Class) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
 
getRIGHT() - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
getRIGHT() - Method in interface org.biopax.paxtools.model.level2.conversion
 
getRIGHT() - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
getRIGHT_x() - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
getRnaList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all rna
getSEQUENCE() - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
 
getSEQUENCE() - Method in class org.biopax.paxtools.proxy.level2.sequenceEntityProxy
 
getSEQUENCE_FEATURE_LIST() - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
getSEQUENCE_FEATURE_LIST() - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
 
getSEQUENCE_FEATURE_LIST() - Method in class org.biopax.paxtools.proxy.level2.sequenceParticipantProxy
 
getSEQUENCE_INTERVAL_BEGIN() - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
getSEQUENCE_INTERVAL_BEGIN() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
 
getSEQUENCE_INTERVAL_BEGIN() - Method in class org.biopax.paxtools.proxy.level2.sequenceIntervalProxy
 
getSEQUENCE_INTERVAL_END() - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
getSEQUENCE_INTERVAL_END() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
 
getSEQUENCE_INTERVAL_END() - Method in class org.biopax.paxtools.proxy.level2.sequenceIntervalProxy
 
getSEQUENCE_POSITION() - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
getSEQUENCE_POSITION() - Method in interface org.biopax.paxtools.model.level2.sequenceSite
 
getSEQUENCE_POSITION() - Method in class org.biopax.paxtools.proxy.level2.sequenceSiteProxy
 
getSequenceEntityListBySEQUENCE(String, boolean) - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get sequenceEntity by SEQUENCE
getSession() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
session
getSetMethod() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getSHORT_NAME() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getSHORT_NAME() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getSHORT_NAME() - Method in interface org.biopax.paxtools.model.level2.entity
This method sets an abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
getSHORT_NAME() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
getSHORT_NAME() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getSHORT_NAME() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getSmallMoleculeList() - Method in class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
get all smallMolecule
getSOURCE() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getSOURCE() - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
getSOURCE() - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
getSPONTANEOUS() - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
getSPONTANEOUS() - Method in interface org.biopax.paxtools.model.level2.conversion
 
getSPONTANEOUS() - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
getSTEP_INTERACTIONS() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
getSTEP_INTERACTIONS() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
getSTEP_INTERACTIONS() - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
getSTOICHIOMETRIC_COEFFICIENT() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
getSTOICHIOMETRIC_COEFFICIENT() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
getSTOICHIOMETRIC_COEFFICIENT() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
getSTOICHIOMETRIC_COEFFICIENT_x() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
getSTRUCTURE() - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
getSTRUCTURE() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
getSTRUCTURE() - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
getSTRUCTURE_DATA() - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
getSTRUCTURE_DATA() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
 
getSTRUCTURE_DATA() - Method in class org.biopax.paxtools.proxy.level2.chemicalStructureProxy
 
getSTRUCTURE_FORMAT() - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
getSTRUCTURE_FORMAT() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
 
getSTRUCTURE_FORMAT() - Method in class org.biopax.paxtools.proxy.level2.chemicalStructureProxy
 
getSuperPathwayList(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get super pathway
getSYNONYMS() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getSYNONYMS() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getSYNONYMS() - Method in interface org.biopax.paxtools.model.level2.entity
The contents of this set can be modified but semantic consistency is not guaranteed.
getSYNONYMS() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
getSYNONYMS() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getSYNONYMS() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getTAXON_XREF() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
getTAXON_XREF() - Method in interface org.biopax.paxtools.model.level2.bioSource
 
getTAXON_XREF() - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
getTEMPERATURE() - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
getTEMPERATURE() - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.kPrime
 
getTEMPERATURE() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getTEMPERATURE() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getTEMPERATURE_x() - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
getTEMPERATURE_x() - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
getTERM() - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
getTERM() - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
 
getTERM() - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
getTISSUE() - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
getTISSUE() - Method in interface org.biopax.paxtools.model.level2.bioSource
 
getTISSUE() - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
getTITLE() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getTITLE() - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
getTITLE() - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
getTopLevelPathway(pathway) - Method in class org.biopax.paxtools.persistence.level2.PathwaySearch
get top level pathway
getTransportList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all transport
getTransportWithBiochemicalReactionList() - Method in class org.biopax.paxtools.persistence.level2.InteractionSearch
get all transportWithBiochemicalReaction
getUploadDate() - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
getUploadDate() - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
getURL() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getURL() - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
getURL() - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
getUser() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
database user
getValue() - Method in enum org.biopax.paxtools.model.Unknown
 
getValue() - Method in class org.biopax.paxtools.util.AbstractSingleElementSet
 
getValueFromBean(Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
getXREF() - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
getXREF() - Method in interface org.biopax.paxtools.model.level2.XReferrable
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
getXREF() - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
getYEAR() - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
getYEAR() - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
getYEAR() - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
GOUnificationXREFtoRelationshipXREFConverter - Class in org.biopax.paxtools.examples
User: root Date: Jan 18, 2007 Time: 4:56:53 PM
GOUnificationXREFtoRelationshipXREFConverter() - Constructor for class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
 

H

hashCode() - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
hashCode() - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
HiRDB - Class in org.biopax.paxtools.persistence.level2
RDB hibernation context class
HiRDB() - Constructor for class org.biopax.paxtools.persistence.level2.HiRDB
contructor
HiRDB(String, String, String, String, String) - Constructor for class org.biopax.paxtools.persistence.level2.HiRDB
contructor
HiRDBConnect - Class in org.biopax.paxtools.persistence.level2
RDB hibernation connect class
HiRDBConnect() - Constructor for class org.biopax.paxtools.persistence.level2.HiRDBConnect
contructor
HiRDBConnect(String, String, String, String, String) - Constructor for class org.biopax.paxtools.persistence.level2.HiRDBConnect
contructor
HiRDBSession - Class in org.biopax.paxtools.persistence.level2
RDB hibernation context class
HiRDBSession() - Constructor for class org.biopax.paxtools.persistence.level2.HiRDBSession
contructor
HiRDBSession(HiRDBConnect) - Constructor for class org.biopax.paxtools.persistence.level2.HiRDBSession
contructor
HiRDBTrial - Class in org.biopax.paxtools.persistence.level2
HiRDB sample program
HiRDBTrial() - Constructor for class org.biopax.paxtools.persistence.level2.HiRDBTrial
 

I

IllegalBioPAXArgumentException - Exception in org.biopax.paxtools.util
 
IllegalBioPAXArgumentException() - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException
 
IllegalBioPAXArgumentException(Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException
 
IllegalBioPAXArgumentException(String) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException
 
IllegalBioPAXArgumentException(String, Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException
 
IllegalRDFIDException - Exception in org.biopax.paxtools.util
 
IllegalRDFIDException() - Constructor for exception org.biopax.paxtools.util.IllegalRDFIDException
 
IllegalRDFIDException(Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalRDFIDException
 
IllegalRDFIDException(String) - Constructor for exception org.biopax.paxtools.util.IllegalRDFIDException
 
IllegalRDFIDException(String, Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalRDFIDException
 
insertStatement(PropertyEditor, Object, OntModel) - Method in class org.biopax.paxtools.io.jena.JenaIOHandler
 
interaction - Interface in org.biopax.paxtools.model.level2
 
interactionAdapter - Class in org.biopax.paxtools.impl.level2
 
interactionAdapter() - Constructor for class org.biopax.paxtools.impl.level2.interactionAdapter
 
interactionImpl - Class in org.biopax.paxtools.impl.level2
 
interactionImpl() - Constructor for class org.biopax.paxtools.impl.level2.interactionImpl
 
InteractionParticipant - Interface in org.biopax.paxtools.model.level2
marker interface for entities and PEPs
InteractionParticipantProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for InteractionParticipant
InteractionParticipantProxy() - Constructor for class org.biopax.paxtools.proxy.level2.InteractionParticipantProxy
 
InteractionParticipantUtilityClassProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for utilityClass
InteractionParticipantUtilityClassProxy() - Constructor for class org.biopax.paxtools.proxy.level2.InteractionParticipantUtilityClassProxy
 
interactionProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for interaction
interactionProxy() - Constructor for class org.biopax.paxtools.proxy.level2.interactionProxy
 
InteractionSearch - Class in org.biopax.paxtools.persistence.level2
interaction search class
InteractionSearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.InteractionSearch
construct
interfaceFor(BioPAXElement) - Method in interface org.biopax.paxtools.controller.EditorMap
 
interfaceFor(BioPAXElement) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
 
invokeMethod(Method, Object, Object) - Method in class org.biopax.paxtools.controller.EnumeratedPropertyEditor
 
invokeMethod(Method, Object, Object) - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor
 
invokeMethod(Method, Object, Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
is(String) - Static method in class org.biopax.paxtools.model.level2.PaxtoolsProperties
 
isCOMPONENTof() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
isCOMPONENTof() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
isCOMPONENTof() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
isCOMPONENTSof(physicalEntityParticipant) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of COMPONENTS
isCONTROLLEDOf() - Method in class org.biopax.paxtools.impl.level2.processImpl
 
isCONTROLLEDOf() - Method in interface org.biopax.paxtools.model.level2.process
 
isCONTROLLEDOf() - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
Not possible to implement - needs to be done manually TODO: think about this.
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
isEquivalent(BioPAXElement) - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
isEquivalentState(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
isEquivalentState(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
isInBioPAXNameSpace(String) - Method in enum org.biopax.paxtools.model.BioPAXLevel
 
isInstanceOfAtLeastOne(Set<Class>, Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
isMultipleCardinality() - Method in class org.biopax.paxtools.controller.PropertyEditor
 
isNEXT_STEPof() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
isNEXT_STEPof() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
isNEXT_STEPof(pathwayStep) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of NEXT_STEP
isNEXT_STEPof() - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
isPARTICIPANTSof() - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
isPARTICIPANTSof() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
isPARTICIPANTSof() - Method in interface org.biopax.paxtools.model.level2.InteractionParticipant
This method returns the interaction that this entity/pep takes part in.
isPARTICIPANTSof(InteractionParticipant) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
 
isPARTICIPANTSof() - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
isPARTICIPANTSof() - Method in class org.biopax.paxtools.proxy.level2.InteractionParticipantProxy
 
isPARTICIPANTSof() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
isPATHWAY_COMPONENTSof() - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
isPATHWAY_COMPONENTSof() - Method in class org.biopax.paxtools.impl.level2.processImpl
 
isPATHWAY_COMPONENTSof() - Method in interface org.biopax.paxtools.model.level2.pathwayComponent
 
isPATHWAY_COMPONENTSof(pathwayComponent) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of PATHWAY_COMPONENT
isPATHWAY_COMPONENTSof() - Method in class org.biopax.paxtools.proxy.level2.pathwayComponentProxy
 
isPATHWAY_COMPONENTSof() - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
isPHYSICAL_ENTITYof() - Method in class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
isPHYSICAL_ENTITYof() - Method in interface org.biopax.paxtools.model.level2.physicalEntity
 
isPHYSICAL_ENTITYof(physicalEntity) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of PHYSICAL_ENTITY
isPHYSICAL_ENTITYof() - Method in class org.biopax.paxtools.proxy.level2.physicalEntityProxy
 
isSetupOK() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 
isSTEP_INTERACTIONSOf() - Method in class org.biopax.paxtools.impl.level2.processImpl
 
isSTEP_INTERACTIONSOf() - Method in interface org.biopax.paxtools.model.level2.process
 
isSTEP_INTERACTIONSof(process) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of STEP_INTERACTIONS
isSTEP_INTERACTIONSOf() - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
isTokenChar(char) - Method in class org.biopax.paxtools.persistence.PaxtoolsTextTokenizer
 
isUnknown(Object) - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor
 
isUnknown(Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
isXREFof() - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
isXREFof() - Method in interface org.biopax.paxtools.model.level2.xref
 
isXREFof(xref) - Method in class org.biopax.paxtools.persistence.level2.MiscSearch
get back pointer of XREF
isXREFof() - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
iterator() - Method in class org.biopax.paxtools.util.AbstractFilterSet
 
iterator() - Method in class org.biopax.paxtools.util.AbstractSingleElementSet
 

J

JenaEditorMap - Class in org.biopax.paxtools.io.jena
This class is a reflection based controller on the level2.
JenaEditorMap() - Constructor for class org.biopax.paxtools.io.jena.JenaEditorMap
 
JenaEditorMap(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.jena.JenaEditorMap
 
JenaIOHandler - Class in org.biopax.paxtools.io.jena
 
JenaIOHandler() - Constructor for class org.biopax.paxtools.io.jena.JenaIOHandler
 
JenaIOHandler(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.jena.JenaIOHandler
 

K

KeywordSearch - Class in org.biopax.paxtools.persistence.level2
keyword search class
KeywordSearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.KeywordSearch
construct
kPrime - Interface in org.biopax.paxtools.model.level2
 
kPrimeImpl - Class in org.biopax.paxtools.impl.level2
 
kPrimeImpl() - Constructor for class org.biopax.paxtools.impl.level2.kPrimeImpl
 
kPrimeProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for kPrime
kPrimeProxy() - Constructor for class org.biopax.paxtools.proxy.level2.kPrimeProxy
 

L

listOWL() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
list owl data
listProteinUnificationXrefsPerPathway(Model) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
 
log - Static variable in class org.biopax.paxtools.controller.PropertyEditor
 

M

main(String[]) - Static method in class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
 
main(String[]) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
 
main(String[]) - Static method in class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
 
main(String[]) - Static method in class org.biopax.paxtools.persistence.level2.HiRDBTrial
main
merge(Model, Collection<? extends Model>) - Method in class org.biopax.paxtools.controller.Merger
 
Merger - Class in org.biopax.paxtools.controller
Utility class to merge multiple biopax models into one
Merger(EditorMap) - Constructor for class org.biopax.paxtools.controller.Merger
 
MiscSearch - Class in org.biopax.paxtools.persistence.level2
misc search class
MiscSearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.MiscSearch
construct
Model - Interface in org.biopax.paxtools.model.level2
This is the interface for container classes for BioPAX models.
ModelImpl - Class in org.biopax.paxtools.impl.level2
Main container class to access BioPAX objects.
ModelImpl() - Constructor for class org.biopax.paxtools.impl.level2.ModelImpl
 
modulation - Interface in org.biopax.paxtools.model.level2
get controlled should be catalysis
modulationImpl - Class in org.biopax.paxtools.impl.level2
 
modulationImpl() - Constructor for class org.biopax.paxtools.impl.level2.modulationImpl
 
modulationProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for modulation
modulationProxy() - Constructor for class org.biopax.paxtools.proxy.level2.modulationProxy
 
multipleCardinality - Variable in class org.biopax.paxtools.controller.PropertyEditor
This is false if there is a cardinality restriction of one on the property.

N

normalize(char) - Method in class org.biopax.paxtools.persistence.PaxtoolsTextTokenizer
 

O

ObjectPropertyEditor - Class in org.biopax.paxtools.controller
User: root Date: Aug 22, 2006 Time: 5:46:44 PM
ObjectPropertyEditor(String, Method, Class, Class, boolean) - Constructor for class org.biopax.paxtools.controller.ObjectPropertyEditor
 
open() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
open entity manager
openControlledVocabulary - Interface in org.biopax.paxtools.model.level2
 
openControlledVocabularyImpl - Class in org.biopax.paxtools.impl.level2
 
openControlledVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
openControlledVocabularyProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for openControlledVocabulary
openControlledVocabularyProxy() - Constructor for class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
org.biopax.paxtools.controller - package org.biopax.paxtools.controller
 
org.biopax.paxtools.examples - package org.biopax.paxtools.examples
 
org.biopax.paxtools.impl.level2 - package org.biopax.paxtools.impl.level2
 
org.biopax.paxtools.io - package org.biopax.paxtools.io
 
org.biopax.paxtools.io.jena - package org.biopax.paxtools.io.jena
 
org.biopax.paxtools.model - package org.biopax.paxtools.model
 
org.biopax.paxtools.model.level2 - package org.biopax.paxtools.model.level2
 
org.biopax.paxtools.persistence - package org.biopax.paxtools.persistence
 
org.biopax.paxtools.persistence.level2 - package org.biopax.paxtools.persistence.level2
 
org.biopax.paxtools.proxy.level2 - package org.biopax.paxtools.proxy.level2
 
org.biopax.paxtools.util - package org.biopax.paxtools.util
 
OwlFileInfo - Class in org.biopax.paxtools.persistence.level2
OWL file information record for RDB
OwlFileInfo() - Constructor for class org.biopax.paxtools.persistence.level2.OwlFileInfo
Creates a new instance of OwlFileInfo

P

pathway - Interface in org.biopax.paxtools.model.level2
 
pathwayComponent - Interface in org.biopax.paxtools.model.level2
Interface for pathway steps and processes
pathwayComponentProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for pathwayComponent
pathwayComponentProxy() - Constructor for class org.biopax.paxtools.proxy.level2.pathwayComponentProxy
 
pathwayImpl - Class in org.biopax.paxtools.impl.level2
 
pathwayImpl() - Constructor for class org.biopax.paxtools.impl.level2.pathwayImpl
 
pathwayProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for pathway
pathwayProxy() - Constructor for class org.biopax.paxtools.proxy.level2.pathwayProxy
 
PathwaySearch - Class in org.biopax.paxtools.persistence.level2
pathway search class
PathwaySearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.PathwaySearch
construct
pathwayStep - Interface in org.biopax.paxtools.model.level2
This represents a set of pathway events.
pathwayStepImpl - Class in org.biopax.paxtools.impl.level2
 
pathwayStepImpl() - Constructor for class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
pathwayStepProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for pathwayStep
pathwayStepProxy() - Constructor for class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
PaxtoolsProperties - Class in org.biopax.paxtools.model.level2
 
PaxtoolsProperties() - Constructor for class org.biopax.paxtools.model.level2.PaxtoolsProperties
 
PaxtoolsTextAnalyzer - Class in org.biopax.paxtools.persistence
 
PaxtoolsTextAnalyzer() - Constructor for class org.biopax.paxtools.persistence.PaxtoolsTextAnalyzer
 
PaxtoolsTextTokenizer - Class in org.biopax.paxtools.persistence
 
PaxtoolsTextTokenizer(Reader) - Constructor for class org.biopax.paxtools.persistence.PaxtoolsTextTokenizer
 
physicalEntity - Interface in org.biopax.paxtools.model.level2
 
physicalEntityImpl - Class in org.biopax.paxtools.impl.level2
 
physicalEntityImpl() - Constructor for class org.biopax.paxtools.impl.level2.physicalEntityImpl
 
physicalEntityParticipant - Interface in org.biopax.paxtools.model.level2
 
physicalEntityParticipantImpl - Class in org.biopax.paxtools.impl.level2
 
physicalEntityParticipantImpl() - Constructor for class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
physicalEntityParticipantProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for physicalEntityParticipant
physicalEntityParticipantProxy() - Constructor for class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
physicalEntityProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for physicalEntity
physicalEntityProxy() - Constructor for class org.biopax.paxtools.proxy.level2.physicalEntityProxy
 
PhysicalEntitySearch - Class in org.biopax.paxtools.persistence.level2
physicalEntity search class
PhysicalEntitySearch(HiRDBSession) - Constructor for class org.biopax.paxtools.persistence.level2.PhysicalEntitySearch
construct
physicalInteraction - Interface in org.biopax.paxtools.model.level2
 
physicalInteractionAdapter - Class in org.biopax.paxtools.impl.level2
 
physicalInteractionAdapter() - Constructor for class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
physicalInteractionImpl - Class in org.biopax.paxtools.impl.level2
 
physicalInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
physicalInteractionProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for physicalInteraction
physicalInteractionProxy() - Constructor for class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
PM - Static variable in interface org.biopax.paxtools.controller.EditorMap
 
PM - Static variable in class org.biopax.paxtools.io.jena.JenaIOHandler
 
PM_DOT - Static variable in interface org.biopax.paxtools.controller.EditorMap
 
PM_DOT - Static variable in class org.biopax.paxtools.io.jena.JenaIOHandler
 
PositionStatusType - Enum in org.biopax.paxtools.model.level2
 
PrimitivePropertyEditor - Class in org.biopax.paxtools.controller
User: root Date: Aug 22, 2006 Time: 5:46:22 PM
PrimitivePropertyEditor(String, Method, Class, Class, boolean) - Constructor for class org.biopax.paxtools.controller.PrimitivePropertyEditor
 
process - Interface in org.biopax.paxtools.model.level2
Tagging interface for entities that needs evidence and can be targeted by a control : Pathway and Interaction
processImpl - Class in org.biopax.paxtools.impl.level2
 
processImpl() - Constructor for class org.biopax.paxtools.impl.level2.processImpl
 
processProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for process
processProxy() - Constructor for class org.biopax.paxtools.proxy.level2.processProxy
 
property - Variable in class org.biopax.paxtools.controller.PropertyEditor
Local OWL name of the property
PropertyEditor - Class in org.biopax.paxtools.controller
This is the base class for all property editors.
PropertyEditor(String, Method, Class, Class, boolean) - Constructor for class org.biopax.paxtools.controller.PropertyEditor
 
protein - Interface in org.biopax.paxtools.model.level2
 
proteinImpl - Class in org.biopax.paxtools.impl.level2
 
proteinImpl() - Constructor for class org.biopax.paxtools.impl.level2.proteinImpl
 
ProteinNameLister - Class in org.biopax.paxtools.examples
 
ProteinNameLister() - Constructor for class org.biopax.paxtools.examples.ProteinNameLister
 
proteinProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for protein
proteinProxy() - Constructor for class org.biopax.paxtools.proxy.level2.proteinProxy
 
ProxyIdInfo - Class in org.biopax.paxtools.persistence.level2
proxy ID and rdf:ID information record for RDB
ProxyIdInfo() - Constructor for class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
publicationXref - Interface in org.biopax.paxtools.model.level2
 
publicationXrefImpl - Class in org.biopax.paxtools.impl.level2
 
publicationXrefImpl() - Constructor for class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
publicationXrefProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for publicationXref
publicationXrefProxy() - Constructor for class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
PUNAME_MYSQL - Static variable in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 
PUNAME_POSTGRESQL - Static variable in class org.biopax.paxtools.persistence.level2.HiRDBConnect
 

R

range - Variable in class org.biopax.paxtools.controller.PropertyEditor
This is the Class representing the range of the property.
relationshipXref - Interface in org.biopax.paxtools.model.level2
 
relationshipXrefImpl - Class in org.biopax.paxtools.impl.level2
 
relationshipXrefImpl() - Constructor for class org.biopax.paxtools.impl.level2.relationshipXrefImpl
 
relationshipXrefProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for relationshipXref
relationshipXrefProxy() - Constructor for class org.biopax.paxtools.proxy.level2.relationshipXrefProxy
 
remove(BioPAXElement) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
This method removes the element without dependency checking.
remove(BioPAXElement) - Method in interface org.biopax.paxtools.model.level2.Model
 
removeAUTHORS(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
removeAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
removeAUTHORS(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
removeAVAILABILITY(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
removeAVAILABILITY(String) - Method in interface org.biopax.paxtools.model.level2.entity
This method removes the given text from the avaialability set.
removeAVAILABILITY(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
removeCOFACTOR(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
removeCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis
 
removeCOFACTOR(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
removeCOMMENT(String) - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
removeCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
removeCOMMENT(String) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
removeCOMPONENTS(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
removeCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex
 
removeCOMPONENTS(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
removeCONFIDENCE(confidence) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
removeCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence
 
removeCONFIDENCE(confidence) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
removeCONTROLLED(process) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
removeCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control
 
removeCONTROLLED(process) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
removeCONTROLLER(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
removeCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control
 
removeCONTROLLER(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
removeDATA_SOURCE(dataSource) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
removeDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity
This method removes the given value from the DATA_SOURCE set.
removeDATA_SOURCE(dataSource) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
removeDELTA_G(deltaGprimeO) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
removeDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
removeDELTA_G(deltaGprimeO) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
removeDELTA_H(double) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
removeDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
removeDELTA_H(double) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
removeDELTA_S(double) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
removeDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
removeDELTA_S(double) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
removeEC_NUMBER(String) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
removeEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
removeEC_NUMBER(String) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
removeEVIDENCE(evidence) - Method in class org.biopax.paxtools.impl.level2.processImpl
 
removeEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process
 
removeEVIDENCE(evidence) - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
removeEVIDENCE_CODE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
removeEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence
 
removeEVIDENCE_CODE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
removeEXPERIMENTAL_FORM(experimentalForm) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
removeEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence
 
removeEXPERIMENTAL_FORM(experimentalForm) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
removeEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
removeEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
removeEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
removeFEATURE_LOCATION(sequenceLocation) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
removeFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
removeFEATURE_LOCATION(sequenceLocation) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
removeINTERACTION_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
removeINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
 
removeINTERACTION_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
removeKEQ(kPrime) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
removeKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
removeKEQ(kPrime) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
removeLEFT(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
removeLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
 
removeLEFT(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
removeMethod - Variable in class org.biopax.paxtools.controller.PropertyEditor
This variable stores the method for removing the value of the property on a given bean.
removeNAME(String) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
removeNAME(String) - Method in interface org.biopax.paxtools.model.level2.dataSource
 
removeNAME(String) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
removeNEXT_STEP(pathwayStep) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
removeNEXT_STEP(pathwayStep) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
removeNEXT_STEP(pathwayStep) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.interactionImpl
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
removePARTICIPANTS(InteractionParticipant) - Method in interface org.biopax.paxtools.model.level2.interaction
 
removePARTICIPANTS(InteractionParticipant) - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
removePATHWAY_COMPONENTS(pathwayComponent) - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
removePATHWAY_COMPONENTS(pathwayComponent) - Method in interface org.biopax.paxtools.model.level2.pathway
 
removePATHWAY_COMPONENTS(pathwayComponent) - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
removePropertyFromBean(Object, Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
removeRIGHT(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
removeRIGHT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
 
removeRIGHT(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
removeSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
removeSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
 
removeSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in class org.biopax.paxtools.proxy.level2.sequenceParticipantProxy
 
removeSOURCE(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
removeSOURCE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
removeSOURCE(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
removeSTEP_INTERACTIONS(process) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
removeSTEP_INTERACTIONS(process) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
removeSTEP_INTERACTIONS(process) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
removeSTRUCTURE(chemicalStructure) - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
removeSTRUCTURE(chemicalStructure) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
removeSTRUCTURE(chemicalStructure) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
removeSYNONYMS(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
removeSYNONYMS(String) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
removeSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.entity
This method removes the given value from the SYNONYMS set.
removeSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
removeSYNONYMS(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
removeSYNONYMS(String) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
removeTERM(String) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
removeTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
 
removeTERM(String) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
removeURL(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
removeURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
removeURL(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
removeValue() - Method in class org.biopax.paxtools.util.AbstractSingleElementSet
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
removeXREF(xref) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
removeXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
removeXREF(xref) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
ReusedPEPHelper - Class in org.biopax.paxtools.io
This class contains methods for handling reused PEPs
ReusedPEPHelper(Model, BioPAXFactory) - Constructor for class org.biopax.paxtools.io.ReusedPEPHelper
 
rna - Interface in org.biopax.paxtools.model.level2
 
rnaImpl - Class in org.biopax.paxtools.impl.level2
 
rnaImpl() - Constructor for class org.biopax.paxtools.impl.level2.rnaImpl
 
rnaProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for dna
rnaProxy() - Constructor for class org.biopax.paxtools.proxy.level2.rnaProxy
 

S

search(String) - Method in class org.biopax.paxtools.persistence.level2.KeywordSearch
keyword search
search(String, String) - Method in class org.biopax.paxtools.persistence.level2.KeywordSearch
keyword search
SEARCH_FIELD_AVAILABILITY - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_COMMENT - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_EC_NUMBER - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_KEYWORD - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_NAME - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_SEQUENCE - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_SYNONYMS - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_TERM - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_XREF_DB - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_FIELD_XREF_ID - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
SEARCH_INDEX_NAME - Static variable in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
sequenceEntity - Interface in org.biopax.paxtools.model.level2
User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
sequenceEntityProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceEntity
sequenceEntityProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceEntityProxy
 
sequenceFeature - Interface in org.biopax.paxtools.model.level2
 
sequenceFeatureImpl - Class in org.biopax.paxtools.impl.level2
 
sequenceFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
sequenceFeatureProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceFeature
sequenceFeatureProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
sequenceInterval - Interface in org.biopax.paxtools.model.level2
 
sequenceIntervalImpl - Class in org.biopax.paxtools.impl.level2
 
sequenceIntervalImpl() - Constructor for class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
sequenceIntervalProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceInterval
sequenceIntervalProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceIntervalProxy
 
sequenceLocation - Interface in org.biopax.paxtools.model.level2
 
sequenceLocationProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceLocation
sequenceLocationProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceLocationProxy
 
sequenceParticipant - Interface in org.biopax.paxtools.model.level2
 
sequenceParticipantImpl - Class in org.biopax.paxtools.impl.level2
 
sequenceParticipantImpl() - Constructor for class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
sequenceParticipantProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceParticipant
sequenceParticipantProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceParticipantProxy
 
sequenceSite - Interface in org.biopax.paxtools.model.level2
 
sequenceSiteImpl - Class in org.biopax.paxtools.impl.level2
 
sequenceSiteImpl() - Constructor for class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
sequenceSiteProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for sequenceSite
sequenceSiteProxy() - Constructor for class org.biopax.paxtools.proxy.level2.sequenceSiteProxy
 
set(String, Object, Document, Field.Store, Field.Index, Float) - Method in class org.biopax.paxtools.proxy.level2.StringSetBridge
 
setAUTHORS(Set<String>) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
setAUTHORS(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
setAUTHORS(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
setAVAILABILITY(Set<String>) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setAVAILABILITY(Set<String>) - Method in interface org.biopax.paxtools.model.level2.entity
This method overrides existing set with the new set.
setAVAILABILITY(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setCELLTYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
setCELLTYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.bioSource
 
setCELLTYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
setCELLULAR_LOCATION(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
setCELLULAR_LOCATION(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
setCELLULAR_LOCATION(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
setCHEMICAL_FORMULA(String) - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
A string representing the Chemical Formula of this small molecule.
setCHEMICAL_FORMULA(String) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
setCHEMICAL_FORMULA(String) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
setCOFACTOR(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
setCOFACTOR(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.catalysis
 
setCOFACTOR(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
setCOMMENT(Set<String>) - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
setCOMMENT(Set<String>) - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
setCOMMENT(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
setCOMPONENTS(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.impl.level2.complexImpl
 
setCOMPONENTS(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.complex
 
setCOMPONENTS(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
setCOMPONENTSof(complex) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
setCOMPONENTSof(complex) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
setCOMPONENTSof(complex) - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
setCONFIDENCE(Set<confidence>) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
setCONFIDENCE(Set<confidence>) - Method in interface org.biopax.paxtools.model.level2.evidence
 
setCONFIDENCE(Set<confidence>) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
setCONFIDENCE_VALUE(String) - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
setCONFIDENCE_VALUE(String) - Method in interface org.biopax.paxtools.model.level2.confidence
 
setCONFIDENCE_VALUE(String) - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
setConnect(HiRDBConnect) - Method in class org.biopax.paxtools.persistence.level2.HiRDB
 
setConnect(HiRDBConnect) - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
connect
setConnectionURL(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
connection URL (JDBC path)
setCONTROL_TYPE(ControlType) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
setCONTROL_TYPE(ControlType) - Method in interface org.biopax.paxtools.model.level2.control
 
setCONTROL_TYPE(ControlType) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
setCONTROLLED(Set<process>) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
setCONTROLLED(Set<process>) - Method in interface org.biopax.paxtools.model.level2.control
 
setCONTROLLED(Set<process>) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
setCONTROLLER(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
setCONTROLLER(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.control
 
setCONTROLLER(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.controlProxy
 
setDATA_SOURCE(Set<dataSource>) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setDATA_SOURCE(Set<dataSource>) - Method in interface org.biopax.paxtools.model.level2.entity
This method overrides existing set with the new set.
setDATA_SOURCE(Set<dataSource>) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setDB(String) - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
setDB(String) - Method in interface org.biopax.paxtools.model.level2.xref
 
setDB(String) - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
setDB_VERSION(String) - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
setDB_VERSION(String) - Method in interface org.biopax.paxtools.model.level2.xref
 
setDB_VERSION(String) - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
setDELTA_G(Set<deltaGprimeO>) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
setDELTA_G(Set<deltaGprimeO>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
setDELTA_G(Set<deltaGprimeO>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setDELTA_G_PRIME_O(float) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
setDELTA_G_PRIME_O(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
setDELTA_G_PRIME_O(float) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setDELTA_G_PRIME_O_x(String) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setDELTA_H(Set<Double>) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
setDELTA_H(Set<Double>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
setDELTA_H(Set<Double>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setDELTA_H_x(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setDELTA_S(Set<Double>) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
setDELTA_S(Set<Double>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
setDELTA_S(Set<Double>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setDELTA_S_x(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setDIRECTION(Direction) - Method in class org.biopax.paxtools.impl.level2.catalysisImpl
 
setDIRECTION(Direction) - Method in interface org.biopax.paxtools.model.level2.catalysis
 
setDIRECTION(Direction) - Method in class org.biopax.paxtools.proxy.level2.catalysisProxy
 
setEC_NUMBER(Set<String>) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
setEC_NUMBER(Set<String>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
setEC_NUMBER(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setEVIDENCE(Set<evidence>) - Method in class org.biopax.paxtools.impl.level2.processImpl
 
setEVIDENCE(Set<evidence>) - Method in interface org.biopax.paxtools.model.level2.process
 
setEVIDENCE(Set<evidence>) - Method in class org.biopax.paxtools.proxy.level2.processProxy
 
setEVIDENCE_CODE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
setEVIDENCE_CODE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.evidence
 
setEVIDENCE_CODE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
setEXPERIMENTAL_FORM(Set<experimentalForm>) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
setEXPERIMENTAL_FORM(Set<experimentalForm>) - Method in interface org.biopax.paxtools.model.level2.evidence
 
setEXPERIMENTAL_FORM(Set<experimentalForm>) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
setEXPERIMENTAL_FORM_TYPE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
setEXPERIMENTAL_FORM_TYPE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
setEXPERIMENTAL_FORM_TYPE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
setFactory(BioPAXFactory) - Method in class org.biopax.paxtools.impl.level2.ModelImpl
 
setFactory(BioPAXFactory) - Method in interface org.biopax.paxtools.model.level2.Model
 
setFEATURE_LOCATION(Set<sequenceLocation>) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setFEATURE_LOCATION(Set<sequenceLocation>) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
setFEATURE_LOCATION(Set<sequenceLocation>) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setFEATURE_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setFEATURE_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
setFEATURE_TYPE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setID(String) - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
setID(String) - Method in interface org.biopax.paxtools.model.level2.xref
 
setID(String) - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
setID_VERSION(String) - Method in class org.biopax.paxtools.impl.level2.xrefImpl
 
setID_VERSION(String) - Method in interface org.biopax.paxtools.model.level2.xref
 
setID_VERSION(String) - Method in class org.biopax.paxtools.proxy.level2.xrefProxy
 
setIndexBase(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
index base
setINTERACTION_TYPE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
setINTERACTION_TYPE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
 
setINTERACTION_TYPE(Set<openControlledVocabulary>) - Method in class org.biopax.paxtools.proxy.level2.physicalInteractionProxy
 
setIONIC_STRENGTH(float) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
setIONIC_STRENGTH(float) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
setIONIC_STRENGTH(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
setIONIC_STRENGTH(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
 
setIONIC_STRENGTH(float) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setIONIC_STRENGTH(float) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setIONIC_STRENGTH_x(String) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setIONIC_STRENGTH_x(String) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setK_PRIME(float) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
setK_PRIME(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
 
setK_PRIME(float) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setK_PRIME_x(String) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setKEQ(Set<kPrime>) - Method in class org.biopax.paxtools.impl.level2.biochemicalReactionImpl
 
setKEQ(Set<kPrime>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
 
setKEQ(Set<kPrime>) - Method in class org.biopax.paxtools.proxy.level2.biochemicalReactionProxy
 
setKeyName(String) - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
setLEFT(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
setLEFT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion
 
setLEFT(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
setLEFT_x(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
setMethod - Variable in class org.biopax.paxtools.controller.PropertyEditor
This variable stores the method to invoke for setting a property to the to the given value.
setMOLECULAR_WEIGHT(double) - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
setMOLECULAR_WEIGHT(double) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
setMOLECULAR_WEIGHT(double) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
setMOLECULAR_WEIGHT_x(String) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
setNAME(String) - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
setNAME(Set<String>) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
setNAME(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setNAME(String) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setNAME(String) - Method in interface org.biopax.paxtools.model.level2.bioSource
 
setNAME(Set<String>) - Method in interface org.biopax.paxtools.model.level2.dataSource
 
setNAME(String) - Method in interface org.biopax.paxtools.model.level2.entity
This method sets the preferred full name for this entity to the given value.
setNAME(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
setNAME(String) - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
setNAME(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
setNAME(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setNAME(String) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setNEXT_STEP(Set<pathwayStep>) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
setNEXT_STEP(Set<pathwayStep>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
setNEXT_STEP(Set<pathwayStep>) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
setOptions(String[]) - Method in class org.biopax.paxtools.persistence.level2.HiRDBTrial
 
setORGANISM(bioSource) - Method in class org.biopax.paxtools.impl.level2.complexImpl
ORGANISM of origin for this sequence entity
setORGANISM(bioSource) - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
setORGANISM(bioSource) - Method in interface org.biopax.paxtools.model.level2.complex
 
setORGANISM(bioSource) - Method in interface org.biopax.paxtools.model.level2.pathway
 
setORGANISM(bioSource) - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
 
setORGANISM(bioSource) - Method in class org.biopax.paxtools.proxy.level2.complexProxy
 
setORGANISM(bioSource) - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
setORGANISM(bioSource) - Method in class org.biopax.paxtools.proxy.level2.sequenceEntityProxy
 
setPARTICIPANT(physicalEntityParticipant) - Method in class org.biopax.paxtools.impl.level2.experimentalFormImpl
 
setPARTICIPANT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
 
setPARTICIPANT(physicalEntityParticipant) - Method in class org.biopax.paxtools.proxy.level2.experimentalFormProxy
 
setParticipantInverse(InteractionParticipant, boolean) - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.controlImpl
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.interactionImpl
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionAdapter
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.physicalInteractionImpl
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in interface org.biopax.paxtools.model.level2.interaction
 
setPARTICIPANTS(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
setPARTICIPANTS_x(Set<InteractionParticipant>) - Method in class org.biopax.paxtools.proxy.level2.interactionProxy
 
setPassword(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
database user password
setPATHWAY_COMPONENTS(Set<pathwayComponent>) - Method in class org.biopax.paxtools.impl.level2.pathwayImpl
 
setPATHWAY_COMPONENTS(Set<pathwayComponent>) - Method in interface org.biopax.paxtools.model.level2.pathway
 
setPATHWAY_COMPONENTS(Set<pathwayComponent>) - Method in class org.biopax.paxtools.proxy.level2.pathwayProxy
 
setPH(float) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
setPH(float) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
setPH(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
setPH(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
 
setPH(float) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setPH(float) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setPH_x(String) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setPH_x(String) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setPHYSICAL_ENTITY(physicalEntity) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
setPHYSICAL_ENTITY(physicalEntity) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
setPHYSICAL_ENTITY(physicalEntity) - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
setPMG(float) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
setPMG(float) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
setPMG(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
setPMG(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
 
setPMG(float) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setPMG(float) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setPMG_x(String) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setPMG_x(String) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setPOSITION_STATUS(PositionStatusType) - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
setPOSITION_STATUS(PositionStatusType) - Method in interface org.biopax.paxtools.model.level2.sequenceSite
 
setPOSITION_STATUS(PositionStatusType) - Method in class org.biopax.paxtools.proxy.level2.sequenceSiteProxy
 
setPropertyToBean(Object, Object) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
 
setPropertyToBean(Object, Object) - Method in class org.biopax.paxtools.controller.PropertyEditor
 
setProxyId(long) - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
setProxyId(long) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
setPUName(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
persistence unit name
setRDFId(String) - Method in class org.biopax.paxtools.impl.level2.bioPAXElementImpl
 
setRDFId(String) - Method in interface org.biopax.paxtools.model.level2.BioPAXElement
 
setRDFId(List<String>) - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
setRDFId(String) - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
setRDFId(String) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
setRELATIONSHIP_TYPE(String) - Method in class org.biopax.paxtools.impl.level2.relationshipXrefImpl
 
setRELATIONSHIP_TYPE(String) - Method in interface org.biopax.paxtools.model.level2.relationshipXref
 
setRELATIONSHIP_TYPE(String) - Method in class org.biopax.paxtools.proxy.level2.relationshipXrefProxy
 
setRIGHT(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
setRIGHT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion
 
setRIGHT(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
setRIGHT_x(Set<physicalEntityParticipant>) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
setSEQUENCE(String) - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
 
setSEQUENCE(String) - Method in class org.biopax.paxtools.proxy.level2.sequenceEntityProxy
 
setSEQUENCE_FEATURE_LIST(Set<sequenceFeature>) - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
setSEQUENCE_FEATURE_LIST(Set<sequenceFeature>) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
 
setSEQUENCE_FEATURE_LIST(Set<sequenceFeature>) - Method in class org.biopax.paxtools.proxy.level2.sequenceParticipantProxy
 
setSEQUENCE_INTERVAL_BEGIN(sequenceSite) - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
setSEQUENCE_INTERVAL_BEGIN(sequenceSite) - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
 
setSEQUENCE_INTERVAL_BEGIN(sequenceSite) - Method in class org.biopax.paxtools.proxy.level2.sequenceIntervalProxy
 
setSEQUENCE_INTERVAL_END(sequenceSite) - Method in class org.biopax.paxtools.impl.level2.sequenceIntervalImpl
 
setSEQUENCE_INTERVAL_END(sequenceSite) - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
 
setSEQUENCE_INTERVAL_END(sequenceSite) - Method in class org.biopax.paxtools.proxy.level2.sequenceIntervalProxy
 
setSEQUENCE_POSITION(int) - Method in class org.biopax.paxtools.impl.level2.sequenceSiteImpl
 
setSEQUENCE_POSITION(int) - Method in interface org.biopax.paxtools.model.level2.sequenceSite
 
setSEQUENCE_POSITION(int) - Method in class org.biopax.paxtools.proxy.level2.sequenceSiteProxy
 
setSession(HiRDBSession) - Method in class org.biopax.paxtools.persistence.level2.HiRDB
 
setSHORT_NAME(String) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setSHORT_NAME(String) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setSHORT_NAME(String) - Method in interface org.biopax.paxtools.model.level2.entity
An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.
setSHORT_NAME(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
setSHORT_NAME(String) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setSHORT_NAME(String) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setSOURCE(Set<String>) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
setSOURCE(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
setSOURCE(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
setSPONTANEOUS(SpontaneousType) - Method in class org.biopax.paxtools.impl.level2.conversionImpl
 
setSPONTANEOUS(SpontaneousType) - Method in interface org.biopax.paxtools.model.level2.conversion
 
setSPONTANEOUS(SpontaneousType) - Method in class org.biopax.paxtools.proxy.level2.conversionProxy
 
setSTEP_INTERACTIONS(Set<process>) - Method in class org.biopax.paxtools.impl.level2.pathwayStepImpl
 
setSTEP_INTERACTIONS(Set<process>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
 
setSTEP_INTERACTIONS(Set<process>) - Method in class org.biopax.paxtools.proxy.level2.pathwayStepProxy
 
setSTOICHIOMETRIC_COEFFICIENT(double) - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
setSTOICHIOMETRIC_COEFFICIENT(double) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
 
setSTOICHIOMETRIC_COEFFICIENT(double) - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
setSTOICHIOMETRIC_COEFFICIENT_x(String) - Method in class org.biopax.paxtools.proxy.level2.physicalEntityParticipantProxy
 
setSTRUCTURE(Set<chemicalStructure>) - Method in class org.biopax.paxtools.impl.level2.smallMoleculeImpl
Setter for Structure.
setSTRUCTURE(Set<chemicalStructure>) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
 
setSTRUCTURE(Set<chemicalStructure>) - Method in class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
setSTRUCTURE_DATA(String) - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
setSTRUCTURE_DATA(String) - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
 
setSTRUCTURE_DATA(String) - Method in class org.biopax.paxtools.proxy.level2.chemicalStructureProxy
 
setSTRUCTURE_FORMAT(String) - Method in class org.biopax.paxtools.impl.level2.chemicalStructureImpl
 
setSTRUCTURE_FORMAT(String) - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
 
setSTRUCTURE_FORMAT(String) - Method in class org.biopax.paxtools.proxy.level2.chemicalStructureProxy
 
setSYNONYMS(Set<String>) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setSYNONYMS(Set<String>) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setSYNONYMS(Set<String>) - Method in interface org.biopax.paxtools.model.level2.entity
This method overrides existing set with the new set.
setSYNONYMS(Set<String>) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
 
setSYNONYMS(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setSYNONYMS(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setTAXON_XREF(unificationXref) - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
setTAXON_XREF(unificationXref) - Method in interface org.biopax.paxtools.model.level2.bioSource
 
setTAXON_XREF(unificationXref) - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
setTEMPERATURE(float) - Method in class org.biopax.paxtools.impl.level2.deltaGprimeOImpl
 
setTEMPERATURE(float) - Method in class org.biopax.paxtools.impl.level2.kPrimeImpl
 
setTEMPERATURE(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
 
setTEMPERATURE(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
 
setTEMPERATURE(float) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setTEMPERATURE(float) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setTEMPERATURE_x(String) - Method in class org.biopax.paxtools.proxy.level2.deltaGprimeOProxy
 
setTEMPERATURE_x(String) - Method in class org.biopax.paxtools.proxy.level2.kPrimeProxy
 
setTERM(Set<String>) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
setTERM(Set<String>) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
 
setTERM(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
setTISSUE(openControlledVocabulary) - Method in class org.biopax.paxtools.impl.level2.bioSourceImpl
 
setTISSUE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.bioSource
 
setTISSUE(openControlledVocabulary) - Method in class org.biopax.paxtools.proxy.level2.bioSourceProxy
 
setTITLE(String) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
setTITLE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
setTITLE(String) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
setup() - Method in class org.biopax.paxtools.persistence.level2.HiRDB
setup before upload / download
setup() - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
setup before upload / download
setup() - Method in class org.biopax.paxtools.persistence.level2.HiRDBSession
setup
setUploadDate(Date) - Method in class org.biopax.paxtools.persistence.level2.OwlFileInfo
 
setUploadDate(Date) - Method in class org.biopax.paxtools.persistence.level2.ProxyIdInfo
 
setURL(Set<String>) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
setURL(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
setURL(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
setUser(String) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
database user
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.confidenceImpl
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.dataSourceImpl
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.entityImpl
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.evidenceImpl
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.openControlledVocabularyImpl
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.impl.level2.sequenceFeatureImpl
 
setXREF(Set<xref>) - Method in interface org.biopax.paxtools.model.level2.XReferrable
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.confidenceProxy
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.dataSourceProxy
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.entityProxy
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.evidenceProxy
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.openControlledVocabularyProxy
 
setXREF(Set<xref>) - Method in class org.biopax.paxtools.proxy.level2.sequenceFeatureProxy
 
setYEAR(int) - Method in class org.biopax.paxtools.impl.level2.publicationXrefImpl
 
setYEAR(int) - Method in interface org.biopax.paxtools.model.level2.publicationXref
 
setYEAR(int) - Method in class org.biopax.paxtools.proxy.level2.publicationXrefProxy
 
size() - Method in class org.biopax.paxtools.util.AbstractFilterSet
 
size() - Method in class org.biopax.paxtools.util.AbstractSingleElementSet
 
smallMolecule - Interface in org.biopax.paxtools.model.level2
 
smallMoleculeImpl - Class in org.biopax.paxtools.impl.level2
 
smallMoleculeImpl() - Constructor for class org.biopax.paxtools.impl.level2.smallMoleculeImpl
 
smallMoleculeProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for smallMolecule
smallMoleculeProxy() - Constructor for class org.biopax.paxtools.proxy.level2.smallMoleculeProxy
 
SpontaneousType - Enum in org.biopax.paxtools.model.level2
 
stateCode() - Method in class org.biopax.paxtools.impl.level2.physicalEntityParticipantImpl
 
stateCode() - Method in class org.biopax.paxtools.impl.level2.sequenceParticipantImpl
 
StringPropertyEditor - Class in org.biopax.paxtools.controller
User: root Date: Aug 23, 2006 Time: 4:42:27 PM
StringPropertyEditor(String, Method, Class, Class, boolean) - Constructor for class org.biopax.paxtools.controller.StringPropertyEditor
 
StringSetBridge - Class in org.biopax.paxtools.proxy.level2
bridge of String Set for Hibernate-search
StringSetBridge() - Constructor for class org.biopax.paxtools.proxy.level2.StringSetBridge
Creates a new instance of StringSetBridge
stringSetToDoubleSet(Set<String>) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
stringToDouble(String) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
stringToFloat(String) - Method in class org.biopax.paxtools.proxy.level2.BioPAXElementProxy
 
subMain(String[]) - Method in class org.biopax.paxtools.persistence.level2.HiRDBTrial
submain

T

tokenStream(String, Reader) - Method in class org.biopax.paxtools.persistence.PaxtoolsTextAnalyzer
 
transport - Interface in org.biopax.paxtools.model.level2
 
transportImpl - Class in org.biopax.paxtools.impl.level2
 
transportImpl() - Constructor for class org.biopax.paxtools.impl.level2.transportImpl
 
transportProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for transport
transportProxy() - Constructor for class org.biopax.paxtools.proxy.level2.transportProxy
 
transportWithBiochemicalReaction - Interface in org.biopax.paxtools.model.level2
 
transportWithBiochemicalReactionImpl - Class in org.biopax.paxtools.impl.level2
 
transportWithBiochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level2.transportWithBiochemicalReactionImpl
 
transportWithBiochemicalReactionProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for transportWithBiochemicalReaction
transportWithBiochemicalReactionProxy() - Constructor for class org.biopax.paxtools.proxy.level2.transportWithBiochemicalReactionProxy
 
traverse(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.Traverser
 
Traverser - Class in org.biopax.paxtools.controller
This is a utility class for traversing over the dependent objects of a biopax element, based on property editors
Traverser(EditorMap, Visitor) - Constructor for class org.biopax.paxtools.controller.Traverser
 

U

UnificationIDtoRDFIDLister - Class in org.biopax.paxtools.examples
User: root Date: Jan 18, 2007 Time: 4:56:53 PM
UnificationIDtoRDFIDLister() - Constructor for class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
 
unificationXref - Interface in org.biopax.paxtools.model.level2
 
unificationXrefImpl - Class in org.biopax.paxtools.impl.level2
User: root Date: Apr 26, 2006 Time: 3:12:15 PM_DOT
unificationXrefImpl() - Constructor for class org.biopax.paxtools.impl.level2.unificationXrefImpl
 
unificationXrefProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for unificationXref
unificationXrefProxy() - Constructor for class org.biopax.paxtools.proxy.level2.unificationXrefProxy
 
UnifiedCluster - Class in org.biopax.paxtools.controller
Utility class for unifying based on unification xrefs.
UnifiedCluster() - Constructor for class org.biopax.paxtools.controller.UnifiedCluster
 
Unknown - Enum in org.biopax.paxtools.model
User: demir Date: Aug 16, 2007 Time: 8:13:23 PM
UNKNOWN_DOUBLE - Static variable in interface org.biopax.paxtools.model.level2.BioPAXElement
 
UNKNOWN_FLOAT - Static variable in interface org.biopax.paxtools.model.level2.BioPAXElement
 
UNKNOWN_INT - Static variable in interface org.biopax.paxtools.model.level2.BioPAXElement
 
updatePARTICIPANTS(Set<? extends InteractionParticipant>, Set<? extends InteractionParticipant>) - Method in class org.biopax.paxtools.impl.level2.interactionAdapter
 
uploadOWL(String, InputStream) - Method in class org.biopax.paxtools.persistence.level2.HiRDBConnect
upload owl data
utilityClass - Interface in org.biopax.paxtools.model.level2
 
utilityClassProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for utilityClass
utilityClassProxy() - Constructor for class org.biopax.paxtools.proxy.level2.utilityClassProxy
 

V

valueOf(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.ControlType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.PositionStatusType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.SpontaneousType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.Unknown
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biopax.paxtools.model.BioPAXLevel
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biopax.paxtools.model.level2.ControlType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biopax.paxtools.model.level2.Direction
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biopax.paxtools.model.level2.PositionStatusType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biopax.paxtools.model.level2.SpontaneousType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum org.biopax.paxtools.model.Unknown
Returns an array containing the constants of this enum type, in the order they're declared.
visit(BioPAXElement, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Fetcher
 
visit(BioPAXElement, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Merger
 
visit(BioPAXElement, Model, PropertyEditor) - Method in interface org.biopax.paxtools.controller.Visitor
 
Visitor - Interface in org.biopax.paxtools.controller
Basic visitor interface for classes using Traverser.

X

xref - Interface in org.biopax.paxtools.model.level2
 
XReferrable - Interface in org.biopax.paxtools.model.level2
 
xrefImpl - Class in org.biopax.paxtools.impl.level2
 
xrefImpl() - Constructor for class org.biopax.paxtools.impl.level2.xrefImpl
 
xrefProxy - Class in org.biopax.paxtools.proxy.level2
Proxy for xref
xrefProxy() - Constructor for class org.biopax.paxtools.proxy.level2.xrefProxy
 

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