Index

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV NEXT

FRAMES NO FRAMES

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

A

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

B

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

C

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