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.