All Classes
AbstractAddRemoveCommand
AbstractEdge
AbstractFilterSet
AbstractGraph
AbstractNode
AbstractPropertyCommand
AbstractPropertyEditor
AbstractSIFMiner
AbstractTraverser
AccessibleSet
ActivityConstraint
ActivityModificationChangeConstraint
ActivityNetworkAnalyzer
AddCommand
AdjacencyMatrix
AffectsRule
AND
AutoComplete
BasicFilterFactory
BFS
BinaryInteractionType
BindingFeature
BindingFeatureImpl
BiochemicalPathwayStep
BiochemicalPathwayStepImpl
biochemicalReaction
BiochemicalReaction
BiochemicalReactionImpl
BioPAXElement
BioPAXElementImpl
BioPAXFactory
BioPaxIOException
BioPAXIOHandler
BioPAXIOHandlerAdapter
BioPAXLevel
BiopaxSafeSet
BiopaxValidatorClient
BiopaxValidatorClient.RetFormat
bioSource
BioSource
BioSourceImpl
Blacklist
BlacklistGenerator
BPCollections
BPCollections.CollectionProvider
catalysis
Catalysis
CatalysisDirectionType
CatalysisImpl
CatalysisPrecedesMiner
CellularLocationVocabulary
CellularLocationVocabularyImpl
CellVocabulary
CellVocabularyImpl
ChangeType
ChemicalAffectsThroughBindingMiner
ChemicalAffectsThroughControlMiner
ChemicalConstant
ChemicalConstantImpl
ChemicalNameNormalizer
chemicalStructure
ChemicalStructure
ChemicalStructureImpl
ClassFilterSet
Cloner
Command
CommandManager
CommonFeatureStringGenerator
CommonIDFetcher
CommonStreamQuery
Completer
complex
Complex
complexAssembly
ComplexAssembly
ComplexAssemblyImpl
ComplexImpl
ComponentRule
ComponentRule
CompositeIterator
ConBox
confidence
ConsecutiveCatalysisRule
ConsecutiveCatalysisRule
Constraint
ConstraintAdapter
ConstraintChain
ConsumptionControlledByMiner
control
Control
ControlImpl
ControlledVocabulary
ControlledVocabularyImpl
Controller
ControlRule
ControlRule
ControlsDegradationIndirectMiner
ControlsExpressionMiner
ControlsExpressionWithConvMiner
ControlsNotParticipant
ControlsPhosphorylationMiner
ControlsProductionOfMiner
ControlsStateChangeDetailedMiner
ControlsStateChangeOfMiner
ControlsTogetherRule
ControlsTogetherRule
ControlsTransportMiner
ControlsTransportOfChemicalMiner
ControlType
ControlType
ControlWrapper
ControlWrapper
conversion
Conversion
ConversionDirectionType
ConversionImpl
ConversionScore
ConversionSide
ConversionSide.Type
ConversionWrapper
CovalentBindingFeature
CovalentBindingFeatureImpl
CSCOBothControllerAndParticipantMiner
CSCOButIsParticipantMiner
CSCOThroughBindingSmallMoleculeMiner
CSCOThroughControllingSmallMoleculeMiner
CSCOThroughDegradationMiner
CustomFormat
CycleBreaker
DataPropertyEditor
dataSource
DataSourceFieldBridge
DataSourceFilter
DataSourceFilterFactory
DecoratingPropertyAccessor
Degradation
DegradationImpl
DeltaFeatureExtractor
DeltaG
DeltaGImpl
deltaGprimeO
Dialog
DifferentialModificationUtil
DirectedRelationMiner
Direction
Direction
dna
Dna
DnaImpl
DnaReference
DnaReferenceImpl
DnaRegion
DnaRegionImpl
DnaRegionReference
DnaRegionReferenceImpl
Edge
EdgeL3
EdgeL3
EditorMap
EditorMapImpl
Empty
entity
Entity
EntityFeature
EntityFeatureImpl
EntityImpl
EntityReference
EntityReferenceImpl
EntityReferenceTypeVocabulary
EntityReferenceTypeVocabularyImpl
EntrezGene
EnumeratedPropertyEditor
Equality
EquivalenceGrouper
EventWrapper
EventWrapper
evidence
Evidence
EvidenceCodeVocabulary
EvidenceCodeVocabularyImpl
EvidenceImpl
experimentalForm
ExperimentalForm
ExperimentalFormImpl
ExperimentalFormVocabulary
ExperimentalFormVocabularyImpl
ExpressionRule
externalReferenceUtilityClass
FeatureDecorator
Fetcher
Field
Field.Operation
FieldOfMultiple
Filter
Filter
FilteredPropertyAccessor
FragmentFeature
FragmentFeatureImpl
Gene
GeneImpl
GeneticInteraction
GeneticInteractionImpl
GOUnificationXREFtoRelationshipXREFConverter
Graph
GraphL3
GraphL3Undirected
GraphObject
Group
Grouper
GroupMap
GSEAConverter
HasAnID
HGNC
HGNC
IDConstraint
IDFetcher
IllegalBioPAXArgumentException
InComplexWithMiner
Indexer
Integrator
interaction
Interaction
InteractionImpl
InteractionParticipant
InteractionRule
InteractionRuleL2
InteractionRuleL2Adaptor
InteractionRuleL3
InteractionRuleL3Adaptor
InteractionSet
InteractionSetL3
InteractionVocabulary
InteractionVocabularyImpl
InteractionWrapper
InteractsWithMiner
InterToPartER
InterToPartER.Direction
JenaEditorMap
JenaIOHandler
JsonldBiopaxConverter
JsonldConverter
kPrime
KPrime
KPrimeImpl
L3ElementImpl
L3ToSBGNPDConverter
Level2Element
Level3Element
LevelUpgrader
LimitType
LinkedPE
LinkedPE.Type
ListUbiqueDetector
Macros
Main
MappedConst
Match
MaximumInteractionThresholdExceedException
Merger
Miner
MinerAdapter
MockFactory
Model
ModelFilter
ModelImpl
ModelUtils
ModificationChangeConstraint
ModificationChangeConstraint.Type
ModificationFeature
ModificationFeatureImpl
modulation
Modulation
ModulationImpl
MolecularInteraction
MolecularInteractionImpl
MultiPathConstraint
Named
NamedImpl
NeighborhoodQuery
NeighborOfMiner
Node
NonUbique
NOT
NucleicAcid
NucleicAcidImpl
NucleicAcidReference
NucleicAcidReferenceImpl
NucleicAcidRegionReference
NucleicAcidRegionReferenceImpl
ObjectPropertyEditor
Observable
OldFormatWriter
openControlledVocabulary
OR
OrganismFieldBridge
OrganismFilter
OrganismFilterFactory
OtherSide
OutputColumn
OutputColumn.Type
ParentPathwayFieldBridge
Participant
ParticipatesInConv
ParticipatesRule
ParticipatesRule
ParticipatingPE
PathAccessor
PathConstraint
PathsBetweenQuery
PathsFromToQuery
pathway
Pathway
pathwayComponent
PathwayComponentLister
PathwayGenesExtractor
PathwayImpl
pathwayStep
PathwayStep
PathwayStepImpl
Pattern
PatternBox
PaxtoolsMain
PEChainsIntersect
PEStateChange
PhenotypeVocabulary
PhenotypeVocabularyImpl
physicalEntity
PhysicalEntity
PhysicalEntityChain
PhysicalEntityChain.Activity
PhysicalEntityImpl
physicalEntityParticipant
PhysicalEntityWrapper
PhysicalEntityWrapper
physicalInteraction
PositionStatusType
PositionStatusType
PrimitivePropertyEditor
process
Process
ProcessImpl
ProgressWatcher
PropertyAccessor
PropertyAccessorAdapter
PropertyAddCommand
PropertyEditor
PropertyFilterBilinked
PropertyRemoveCommand
PropertySetCommand
protein
Protein
ProteinImpl
ProteinNameLister
ProteinReference
ProteinReferenceImpl
Provenance
ProvenanceImpl
Prune
PsiToBiopax3Converter
PublicationStatisticsAnalyzer
publicationXref
PublicationXref
PublicationXrefImpl
QueryExecuter
ReactomeEntitySetUnificationXrefFix
ReactsWithMiner
RelatedControl
RelatedGenesOfInteractionsMiner
RelationshipTypeVocabulary
RelationshipTypeVocabularyImpl
relationshipXref
RelationshipXref
RelationshipXrefImpl
RelType
RemoveCommand
ReusedPEPHelper
rna
Rna
RnaImpl
RnaReference
RnaReferenceImpl
RnaRegion
RnaRegionImpl
RnaRegionReference
RnaRegionReferenceImpl
SBGNLayoutManager
Score
ScoreImpl
SearchEngine
SearchEngine.HitAnnotation
Searcher
Searcher
SearchResult
SelfOrThis
sequenceEntity
SequenceEntity
SequenceEntityReference
SequenceEntityReferenceImpl
sequenceFeature
sequenceInterval
SequenceInterval
SequenceIntervalImpl
sequenceLocation
SequenceLocation
SequenceLocationImpl
SequenceModificationVocabulary
SequenceModificationVocabularyImpl
sequenceParticipant
SequenceRegionVocabulary
SequenceRegionVocabularyImpl
sequenceSite
SequenceSite
SequenceSiteImpl
SetEquivalenceChecker
SetStringBridge
ShallowCopy
SIFEnum
SIFInteraction
SIFMiner
SifnxExportExample
SIFSearcher
SIFToText
SIFType
SimpleEditorMap
SimpleInteraction
SimpleInteractionConverter
SimpleIOExample
SimpleIOHandler
SimpleMerger
SimplePhysicalEntity
SimplePhysicalEntityImpl
SimplePropertyAccessor
Simplify
Size
Size.Type
smallMolecule
SmallMolecule
SmallMoleculeImpl
SmallMoleculeReference
SmallMoleculeReferenceImpl
SpontaneousType
StepDirection
Stoichiometry
StoichiometryImpl
StringFieldFilter
StringPropertyEditor
StructureFormatType
TemplateDirectionType
TemplateReaction
TemplateReactionImpl
TemplateReactionRegulation
TemplateReactionRegulationImpl
TemplateReactionWrapper
TissueVocabulary
TissueVocabularyImpl
TProvider
TransitivePropertyAccessor
transport
Transport
TransportImpl
transportWithBiochemicalReaction
TransportWithBiochemicalReaction
TransportWithBiochemicalReactionImpl
Traverser
TraverserBilinked
Tutorial
Type
UbiqueDetector
UbiqueFilter
UbiquitousIDMiner
UnificationIDtoRDFIDLister
unificationXref
UnificationXref
UnificationXrefImpl
UnionPropertyAccessor
UsedToProduceMiner
UseOfReflection
utilityClass
UtilityClass
VCompound
Visitor
VNode
XOR
xref
Xref
XReferrable
XReferrable
XReferrableImpl
XrefFieldBridge
XrefImpl