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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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