Index (Paxtools Core (BioPAX object model, I/O API, implementation and extras) 5.0.0 API)

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

A

absoluteUris(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler: Sets the flag used when exporting a BioPAX model to RDF/XML: true - to always write full URI in rdf:resource and use rdf:about instead rdf:ID (does not matter xml:base is set or not).
AbstractAddRemoveCommand - Class in org.biopax.paxtools.command
AbstractAddRemoveCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.AbstractAddRemoveCommand
AbstractFilterSet<F,E> - Class in org.biopax.paxtools.util: Base class for implementing various filter sets.
AbstractFilterSet(Set<? extends F>) - Constructor for class org.biopax.paxtools.util.AbstractFilterSet
AbstractPropertyCommand<D extends BioPAXElement,R> - Class in org.biopax.paxtools.command
AbstractPropertyEditor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller: This is the base class for all property editors.
AbstractPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.AbstractPropertyEditor: Constructor.
AbstractTraverser - Class in org.biopax.paxtools.controller: This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required.
AbstractTraverser(EditorMap, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.AbstractTraverser
access(E) - Method in class org.biopax.paxtools.util.AccessibleSet
access(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper
AccessibleSet<E> - Class in org.biopax.paxtools.util: This is a decorator set for capturing a set member that is equal to the given parameter.
AccessibleSet() - Constructor for class org.biopax.paxtools.util.AccessibleSet
add(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl
add(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model: This method adds the given object to this model.
add(E) - Method in class org.biopax.paxtools.util.BiopaxSafeSet
add(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper
addAuthor(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
addAuthor(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
addAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
addAvailability(String) - Method in class org.biopax.paxtools.impl.level3.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 interface org.biopax.paxtools.model.level3.Entity: This method adds the given text to the avaialability set.
addCofactor(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
addCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis
addCofactor(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Catalysis: Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
AddCommand - Class in org.biopax.paxtools.command
AddCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.AddCommand
addComment(String) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl
addCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.Level2Element
addComment(String) - Method in interface org.biopax.paxtools.model.level3.Level3Element: A textual comment about this individual.
addComponent(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
addComponent(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Complex: Defines the PhysicalEntity subunits of this complex.
addCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex
addComponentStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
addComponentStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Complex: The stoichiometry of components in a complex.
addConfidence(Score) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: Confidence in the containing instance.
addCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence
addConfidence(Score) - Method in interface org.biopax.paxtools.model.level3.Evidence: Confidence in the containing instance.
addControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
addCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control
addControlled(Process) - Method in interface org.biopax.paxtools.model.level3.Control: The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
addController(Controller) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
addController(Controller) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
addCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control
addController(Controller) - Method in interface org.biopax.paxtools.model.level3.Control: The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
addDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity: This method adds the given value to the DATA_SOURCE set.
addDataSource(Provenance) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
addDataSource(Provenance) - Method in interface org.biopax.paxtools.model.level3.Entity: This method adds the given value to the DATA_SOURCE set.
addDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
addDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
addDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
addDeltaG(DeltaG) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
addDeltaG(DeltaG) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
addDeltaH(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
addDeltaH(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.
addDeltaS(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
addDeltaS(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.
addEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
addECNumber(String) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
addECNumber(String) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
addEntityFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
addEntityFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
addEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
addEntityReferenceType(EntityReferenceTypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Adds the given cv to the list of types
addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
addEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process: This method adds the given evidence to this process.
addEvidence(Evidence) - Method in interface org.biopax.paxtools.model.level3.Observable
addEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence
addEvidenceCode(EvidenceCodeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
addEvidenceCode(EvidenceCodeVocabulary) - Method in interface org.biopax.paxtools.model.level3.Evidence: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
addEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence
addEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
addExperimentalFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
addExperimentalFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: This method adds an experimental feature
addExperimentalForm(ExperimentalForm) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl
addExperimentalForm(ExperimentalForm) - Method in interface org.biopax.paxtools.model.level3.Evidence: Adds an experimental form.
addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: Adds an experimental form description.
addFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
addFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl
addFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
addFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
addINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
addInteractionType(InteractionVocabulary) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
addInteractionType(InteractionVocabulary) - Method in interface org.biopax.paxtools.model.level3.Interaction: Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
addKEQ(KPrime) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
addKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
addKEQ(KPrime) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: This quantity is dimensionless and is usually a single number.
addLeft(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
addLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
addLeft(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion: Adds a participant to the left side of the conversion interaction.
addMaxCardinalityRestriction(Class<? extends D>, int) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
addMaxCardinalityRestriction(Class<? extends D>, int) - Method in interface org.biopax.paxtools.controller.PropertyEditor: Sets a maximum cardinality for a domain.
addMemberEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
addMemberEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Adds the given entityReference to the member list
addMemberFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
addMemberFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature: An entity feature that belongs to this homology grouping.
addMemberPhysicalEntity(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
addMemberPhysicalEntity(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
addMethod - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor: This variable stores the method to invoke for adding the given value to the property managed by this commander.
addMissingEntityReference(Model, SimplePhysicalEntity) - Static method in class org.biopax.paxtools.controller.ModelUtils: For a non-generic simple physical entity (memberPhysicalEntity property is empty) that does not have entityReference property defined, this method generates and adds a new entity reference of proper type to both this entity and the model, and also copies names and xrefs from the source physical entity to the generated entity reference (UnificationXrefs are converted to RelationshipXref and then also deleted from the original entity.)
addName(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
addNAME(String) - Method in interface org.biopax.paxtools.model.level2.dataSource
addName(String) - Method in interface org.biopax.paxtools.model.level3.Named: This method adds the given value to the name set.
addNew(Class<T>, String) - Method in class org.biopax.paxtools.impl.ModelImpl
addNew(Class<T>, String) - Method in interface org.biopax.paxtools.model.Model: This method creates a new object using the model's factory, adds it to the model and returns it.
addNEXT_STEP(pathwayStep) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
addNextStep(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
addNextStep(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.PathwayStep
addNotFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
addNotFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl
addNotFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
addObjects(Set<BioPAXElement>) - Method in class org.biopax.paxtools.command.CommandManager
addParticipant(Entity) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
addParticipant(Entity) - Method in class org.biopax.paxtools.impl.level3.MolecularInteractionImpl
addParticipant(Entity) - Method in interface org.biopax.paxtools.model.level3.Interaction: The entities that participate in this interaction.
addPARTICIPANTS(InteractionParticipant) - Method in interface org.biopax.paxtools.model.level2.interaction
addParticipantStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
addParticipantStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Conversion: This method adds a stoichiometry for one of the participants of this conversion.
addPATHWAY_COMPONENTS(pathwayComponent) - Method in interface org.biopax.paxtools.model.level2.pathway
addPathwayComponent(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
addPathwayComponent(Process) - Method in interface org.biopax.paxtools.model.level3.Pathway
addPathwayOrder(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
addPathwayOrder(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.Pathway
addPHYSICAL_ENTITYof(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.physicalEntity
addProduct(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
addProduct(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
addProperty(BioPAXElement, PropertyEditor, Object) - Method in class org.biopax.paxtools.command.CommandManager
addRangeRestriction(Class<? extends BioPAXElement>, Set<Class<? extends BioPAXElement>>) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor: This method adds a range restriction to the property editor.
addRegionType(SequenceRegionVocabulary) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
addRegionType(SequenceRegionVocabulary) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
addRight(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
addRIGHT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
addRight(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion: Adds a participant to the right side of the conversion interaction.
addSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
addSource(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
addSOURCE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
addSource(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
addSTEP_INTERACTIONS(process) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
addStepProcess(Process) - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
addStepProcess(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
addStepProcess(Process) - Method in interface org.biopax.paxtools.model.level3.PathwayStep
addSTRUCTURE(chemicalStructure) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
addSubRegion(NucleicAcidRegionReference) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl
addSubRegion(NucleicAcidRegionReference) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference
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
addTerm(String) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
addTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
addTerm(String) - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary
addUrl(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
addURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
addUrl(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
addXref(Xref) - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl
addXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable
addXref(Xref) - Method in interface org.biopax.paxtools.model.level3.XReferrable
applies(BioPAXElement) - Method in class org.biopax.paxtools.controller.PathAccessor
atEquivalentLocation(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl: This method returns true if and only if two entity features are on the same known location on a known ER.
atEquivalentLocation(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature
AutoComplete - Annotation Type in org.biopax.paxtools.util: Interface for demarcating excise-able boundaries of the object graph.

B

base - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
baseSet - Variable in class org.biopax.paxtools.util.AbstractFilterSet
bindArrays(ObjectPropertyEditor, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory
bindArrays(String, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory
BindingFeature - Interface in org.biopax.paxtools.model.level3
BindingFeatureImpl - Class in org.biopax.paxtools.impl.level3
BindingFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.BindingFeatureImpl
bindInPairs(ObjectPropertyEditor, BioPAXElement...) - Method in class org.biopax.paxtools.impl.MockFactory
bindInPairs(String, BioPAXElement...) - Method in class org.biopax.paxtools.impl.MockFactory
bindValue(String, PropertyEditor, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method binds the value to the bpe.
BiochemicalPathwayStep - Interface in org.biopax.paxtools.model.level3: Definition: Imposes ordering on a step in a biochemical pathway.
BiochemicalPathwayStepImpl - Class in org.biopax.paxtools.impl.level3
BiochemicalPathwayStepImpl() - Constructor for class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
biochemicalReaction - Interface in org.biopax.paxtools.model.level2: A conversion interaction in which one or more entities (substrates) undergo ovalent changes to become one or more other entities (products).
BiochemicalReaction - Interface in org.biopax.paxtools.model.level3: Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
BiochemicalReactionImpl - Class in org.biopax.paxtools.impl.level3
BiochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
BioPAXElement - Interface in org.biopax.paxtools.model: This class represents a general BioPAXElement, regardless of Level.
BioPAXElementImpl - Class in org.biopax.paxtools.impl
BioPAXElementImpl() - Constructor for class org.biopax.paxtools.impl.BioPAXElementImpl
BioPAXFactory - Class in org.biopax.paxtools.model: Abstract factory class for instantiating BioPAX classes.
BioPAXFactory() - Constructor for class org.biopax.paxtools.model.BioPAXFactory: Protected Constructor without parameters.
BioPaxIOException - Exception in org.biopax.paxtools.util: This exception is thrown if a problem occurs during an input/output operation related to BioPAX Handlers.
BioPaxIOException(Throwable) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException
BioPaxIOException(String) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException
BioPaxIOException(String, Throwable) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException
BioPAXIOHandler - Interface in org.biopax.paxtools.io: This interface defines IO related operations that can be performed on BioPAX models.
BioPAXIOHandlerAdapter - Class in org.biopax.paxtools.io
BioPAXIOHandlerAdapter() - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
BioPAXIOHandlerAdapter(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
BioPAXIOHandlerAdapter(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
BioPAXLevel - Enum in org.biopax.paxtools.model: Enumeration type for BioPAX levels.
BiopaxSafeSet<E extends BioPAXElement> - Class in org.biopax.paxtools.util: A thread-safe set of BioPAX objects that also prevents adding several elements having the same URI.
BiopaxSafeSet() - Constructor for class org.biopax.paxtools.util.BiopaxSafeSet
bioSource - Interface in org.biopax.paxtools.model.level2: The biological source of an entity (e.g.
BioSource - Interface in org.biopax.paxtools.model.level3: Definition: The biological source of an entity (e.g.
BioSourceImpl - Class in org.biopax.paxtools.impl.level3
BioSourceImpl() - Constructor for class org.biopax.paxtools.impl.level3.BioSourceImpl
bp - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
BP_PREFIX - Static variable in enum org.biopax.paxtools.model.BioPAXLevel: This is the prefix used for all biopax releases.
BPCollections - Enum in org.biopax.paxtools.util
BPCollections.CollectionProvider - Interface in org.biopax.paxtools.util: This interface is responsible for setting the class and initialize and load factor for all sets and maps used in all model objects for performance purposes.
breakPathwayComponentCycle(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Removes cyclic pathway inclusions, non-trivial infinite loops, in 'pathwayComponent' biopax property.
buildCustomEditorMap(BioPAXLevel, InputStream) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

C

canInstantiate(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.model.BioPAXFactory: Checks whether objects of a BioPAX model interface can be created (some types are not official BioPAX types, abstract classes).
canRedo() - Method in class org.biopax.paxtools.command.CommandManager
canRedo() - Method in class org.biopax.paxtools.command.PropertyAddCommand
canRedo() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
canUndo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand
canUndo() - Method in class org.biopax.paxtools.command.CommandManager
canUndo() - Method in class org.biopax.paxtools.command.PropertyAddCommand
canUndo() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
catalysis - Interface in org.biopax.paxtools.model.level2: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
Catalysis - Interface in org.biopax.paxtools.model.level3: Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
CatalysisDirectionType - Enum in org.biopax.paxtools.model.level3: This enum represents the direction of a catalysis under all physiological conditions if there is one.
CatalysisImpl - Class in org.biopax.paxtools.impl.level3
CatalysisImpl() - Constructor for class org.biopax.paxtools.impl.level3.CatalysisImpl
CellularLocationVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
CellularLocationVocabularyImpl - Class in org.biopax.paxtools.impl.level3
CellularLocationVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl
CellVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A reference to the Cell Type Ontology (CL).
CellVocabularyImpl - Class in org.biopax.paxtools.impl.level3
CellVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.CellVocabularyImpl
checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ModulationImpl
checkERFeatureSet(EntityReference, boolean) - Static method in class org.biopax.paxtools.controller.ModelUtils: Finds and adds all (missing) entity features to given entity reference from all its owner simple physical entities ('feature' and 'notFeature' properties).
checkRestrictions - Static variable in class org.biopax.paxtools.controller.AbstractPropertyEditor
checkRestrictions(R, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Checks if the bean and the value are consistent with the cardinality rules of the model.
checkRestrictions(R, D) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
checkRestrictions(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler: If set to true, property editors will check restrictions at the subclass level and throw an exception if violated.
chemDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.controller.IdFetcher: Set to prefer collecting chemical IDs of such Xrefs where the small molecules db starts with or equals given string, ignoring case.
ChemicalConstant - Interface in org.biopax.paxtools.model.level3
ChemicalConstantImpl - Class in org.biopax.paxtools.impl.level3
ChemicalConstantImpl() - Constructor for class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
chemicalStructure - Interface in org.biopax.paxtools.model.level2: Describes a small molecule structure.
ChemicalStructure - Interface in org.biopax.paxtools.model.level3: Definition: The chemical structure of a small molecule.
ChemicalStructureImpl - Class in org.biopax.paxtools.impl.level3
ChemicalStructureImpl() - Constructor for class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
ClassFilterSet<E,F extends E> - Class in org.biopax.paxtools.util: A FilterSet that filters based on the class.
ClassFilterSet(Set<? extends E>, Class<F>) - Constructor for class org.biopax.paxtools.util.ClassFilterSet
classToEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl: A map from classes to their registered editors.
classToEditorSet - Variable in class org.biopax.paxtools.controller.EditorMapImpl: Another map to keep editors as a set rather than a map.
classToInverseEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl: A map from classes to their registered inverse editors
clone(Model, Set<BioPAXElement>) - Method in class org.biopax.paxtools.controller.Cloner: Deprecated.
use Cloner.clone(Set) instead ('source' model was not used in previous versions)
clone(Set<BioPAXElement>) - Method in class org.biopax.paxtools.controller.Cloner: For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored.
Cloner - Class in org.biopax.paxtools.controller: Specifically "Clones" the BioPAX elements set (traverses to obtain dependent elements), puts them to the new model using the visitor and traverser framework; ignores elements that are not in the source list (compare to Fetcher).
Cloner(EditorMap, BioPAXFactory) - Constructor for class org.biopax.paxtools.controller.Cloner
collectSimpleMembersRecursive(PhysicalEntity, Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
Command - Interface in org.biopax.paxtools.command
CommandManager - Class in org.biopax.paxtools.command: This is a class for manipulating a BioPAX model via undoable commands
CommandManager(Model) - Constructor for class org.biopax.paxtools.command.CommandManager
compareTo(Object) - Method in class org.biopax.paxtools.controller.ConversionScore
complete(Collection<BioPAXElement>, Model) - Method in class org.biopax.paxtools.controller.Completer: Deprecated.
use Completer.complete(Collection) instead (- model is never explicitly used there)
complete(Collection<BioPAXElement>) - Method in class org.biopax.paxtools.controller.Completer
Completer - Class in org.biopax.paxtools.controller: This class is used for getting a valid subgraph from a set of BioPAX elements.
Completer(EditorMap) - Constructor for class org.biopax.paxtools.controller.Completer
complex - Interface in org.biopax.paxtools.model.level2: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
Complex - Interface in org.biopax.paxtools.model.level3: Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
complexAssembly - Interface in org.biopax.paxtools.model.level2: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
ComplexAssembly - Interface in org.biopax.paxtools.model.level3: Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
ComplexAssemblyImpl - Class in org.biopax.paxtools.impl.level3
ComplexAssemblyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl
ComplexImpl - Class in org.biopax.paxtools.impl.level3
ComplexImpl() - Constructor for class org.biopax.paxtools.impl.level3.ComplexImpl
CompositeIterator<T> - Class in org.biopax.paxtools.util: A composite iterator that iterates over multiple iterators.
CompositeIterator(Collection<? extends Collection<? extends T>>) - Constructor for class org.biopax.paxtools.util.CompositeIterator: This constructor creates an iterator instance from a set of collections
confidence - Interface in org.biopax.paxtools.model.level2: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure.
contains(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl: This method returns true if given element is the same object ("==") as the object stored in the model usually (for self-consistent models) but not necessarily under the element's ID.
contains(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model: This method returns true if the parameter is contained within this model.
contains(Object) - Method in class org.biopax.paxtools.util.AbstractFilterSet
contains(Object) - Method in class org.biopax.paxtools.util.BiopaxSafeSet
containsEquivalent(Set<? extends BioPAXElement>, BioPAXElement) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker
containsID(String) - Method in class org.biopax.paxtools.impl.ModelImpl
containsID(String) - Method in interface org.biopax.paxtools.model.Model: This method checks for the biopax element with the given id, returns true if the object with the given id exists.
control - Interface in org.biopax.paxtools.model.level2
Control - Interface in org.biopax.paxtools.model.level3: Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
ControlImpl - Class in org.biopax.paxtools.impl.level3
ControlImpl() - Constructor for class org.biopax.paxtools.impl.level3.ControlImpl
ControlledVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: This class represents a term from an external controlled vocabulary (CV).
ControlledVocabularyImpl - Class in org.biopax.paxtools.impl.level3
ControlledVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl: Constructor.
Controller - Interface in org.biopax.paxtools.model.level3: This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
ControlType - Enum in org.biopax.paxtools.model.level2: User: root Date: Aug 1, 2006 Time: 5:37:34 PM_DOT
ControlType - Enum in org.biopax.paxtools.model.level3: Defines the nature of the control relationship between the controller and the controlled entities.
conversion - Interface in org.biopax.paxtools.model.level2
Conversion - Interface in org.biopax.paxtools.model.level3: Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.
ConversionDirectionType - Enum in org.biopax.paxtools.model.level3: This enum is used for specifying the direction of a Conversion.
ConversionImpl - Class in org.biopax.paxtools.impl.level3
ConversionImpl() - Constructor for class org.biopax.paxtools.impl.level3.ConversionImpl
ConversionScore - Class in org.biopax.paxtools.controller: Encapsulation of scores of conversions, and related information
ConversionScore(conversion, conversion, Double, Map<physicalEntityParticipant, physicalEntityParticipant>, boolean) - Constructor for class org.biopax.paxtools.controller.ConversionScore
convertFromOWL(InputStream) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.
convertFromOWL(InputStream) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.
convertToOWL(Model, OutputStream) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This method will write the model to the output stream.
convertToOWL(Model, OutputStream, String...) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.
convertToOWL(Model, OutputStream, String...) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Similar to BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) (org.biopax.paxtools.model.Model, Object)}, but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.
convertToOWL(Model, OutputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler: Converts a model into BioPAX (OWL) format, and writes it into the outputStream.
convertToOwl(Model) - Static method in class org.biopax.paxtools.io.SimpleIOHandler: Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string.
copy(Model, T, String) - Method in class org.biopax.paxtools.controller.ShallowCopy: Creates a copy of the BioPAX object with all its properties are the same, and also adds it to a model.
copy(T, String) - Method in class org.biopax.paxtools.controller.ShallowCopy: Returns a copy of the BioPAX element (with all the property values are same)
copyPEPFields() - Method in class org.biopax.paxtools.controller.ReusedPEPHelper
CovalentBindingFeature - Interface in org.biopax.paxtools.model.level3: Definition: An entity feature that represent the covalently bound state of a physical entity.
CovalentBindingFeatureImpl - Class in org.biopax.paxtools.impl.level3
CovalentBindingFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
create(PropertyAccessor<D, R>, Class) - Static method in class org.biopax.paxtools.controller.FilteredPropertyAccessor: FactoryMethod that creates a filtered property accessor by decorating a given accessor with a class filter.
create(PropertyAccessor<D, R>) - Static method in class org.biopax.paxtools.controller.TransitivePropertyAccessor
create(Class<T>, String) - Method in class org.biopax.paxtools.impl.MockFactory
create(String, String) - Method in class org.biopax.paxtools.impl.MockFactory
create(Model, Class<T>, int, String) - Method in class org.biopax.paxtools.impl.MockFactory
create(Model, Class<T>, int) - Method in class org.biopax.paxtools.impl.MockFactory
create(String, String) - Method in class org.biopax.paxtools.model.BioPAXFactory
create(Class<T>, String) - Method in class org.biopax.paxtools.model.BioPAXFactory: Universal method that creates a new BioPAX object.
createAndAdd(Model, String, String) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method is called by the reader for each OWL instance in the OWL model.
createAndBind(Model) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.
createAndBind(Model) - Method in class org.biopax.paxtools.io.SimpleIOHandler
createAndRegisterBeanEditor(String, Class, Map<Class<? extends BioPAXElement>, Set<Class<? extends BioPAXElement>>>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
createMap() - Method in interface org.biopax.paxtools.util.BPCollections.CollectionProvider
createMap() - Method in enum org.biopax.paxtools.util.BPCollections
createModel() - Method in class org.biopax.paxtools.model.BioPAXFactory: Creates a new BioPAX model.
createPropertyEditor(Class<D>, String) - Static method in class org.biopax.paxtools.controller.AbstractPropertyEditor: This method creates a property reflecting on the domain and property.
createSafeSet() - Method in enum org.biopax.paxtools.util.BPCollections
createSet() - Method in interface org.biopax.paxtools.util.BPCollections.CollectionProvider
createSet() - Method in enum org.biopax.paxtools.util.BPCollections

D

DataPropertyEditor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller: Created by igor on 13/08/15.
dataSource - Interface in org.biopax.paxtools.model.level2: XREF Should be only unification and publication xrefs
DecoratingPropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller
DecoratingPropertyAccessor(PropertyAccessor<D, R>) - Constructor for class org.biopax.paxtools.controller.DecoratingPropertyAccessor
Degradation - Interface in org.biopax.paxtools.model.level3: Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
DegradationImpl - Class in org.biopax.paxtools.impl.level3
DegradationImpl() - Constructor for class org.biopax.paxtools.impl.level3.DegradationImpl
DeltaG - Interface in org.biopax.paxtools.model.level3: Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
DeltaGImpl - Class in org.biopax.paxtools.impl.level3
DeltaGImpl() - Constructor for class org.biopax.paxtools.impl.level3.DeltaGImpl
deltaGprimeO - Interface in org.biopax.paxtools.model.level2
detectRange(Method) - Static method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Given the multiple cardinality feature, the range of the get method is returned.
Direction - Enum in org.biopax.paxtools.model.level2: Catalysis direction controlled vocabulary
dna - Interface in org.biopax.paxtools.model.level2
Dna - Interface in org.biopax.paxtools.model.level3: Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
DnaImpl - Class in org.biopax.paxtools.impl.level3
DnaImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaImpl
DnaReference - Interface in org.biopax.paxtools.model.level3: A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
DnaReferenceImpl - Class in org.biopax.paxtools.impl.level3
DnaReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaReferenceImpl
DnaRegion - Interface in org.biopax.paxtools.model.level3: Definition: A region on a DNA molecule.
DnaRegionImpl - Class in org.biopax.paxtools.impl.level3
DnaRegionImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaRegionImpl
DnaRegionReference - Interface in org.biopax.paxtools.model.level3: Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
DnaRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3
DnaRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl
domain - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter: This is the Class representing the domain of the property.
domain - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple

E

editor(String, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.impl.MockFactory
EditorMap - Interface in org.biopax.paxtools.controller: This class contains methods that eases to use editors for specific or a set of property.
editorMap - Variable in class org.biopax.paxtools.controller.Traverser
editorMap - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
EditorMapImpl - Class in org.biopax.paxtools.controller: This is the base adapter for all editor maps.
EditorMapImpl(BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.EditorMapImpl
encodeBase62(String) - Static method in class org.biopax.paxtools.controller.ModelUtils
entity - Interface in org.biopax.paxtools.model.level2: This class represents a discrete biological unit used when describing pathways.
Entity - Interface in org.biopax.paxtools.model.level3: This class represents a discrete biological unit used when describing pathways.
EntityFeature - Interface in org.biopax.paxtools.model.level3: Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
EntityFeatureImpl - Class in org.biopax.paxtools.impl.level3
EntityFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityFeatureImpl
EntityImpl - Class in org.biopax.paxtools.impl.level3
EntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityImpl: Helper object for managing names
EntityReference - Interface in org.biopax.paxtools.model.level3: Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists.
EntityReferenceImpl - Class in org.biopax.paxtools.impl.level3
EntityReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityReferenceImpl: Constructor.
EntityReferenceTypeVocabulary - Interface in org.biopax.paxtools.model.level3: Definiiton: A reference to a term from an entity reference group ontology.
EntityReferenceTypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3
EntityReferenceTypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl
EnumeratedPropertyEditor<D extends BioPAXElement,R extends Enum> - Class in org.biopax.paxtools.controller: Provides an ENUM class compatible editor by extending the PropertyEditor.
EnumeratedPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.EnumeratedPropertyEditor
equals(Object) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl: true if and only if the other obj has the same biopax type (same BioPAXElement.getModelInterface(), not a subclass) and same URI.
equivalenceCode() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl
equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
equivalenceCode() - Method in interface org.biopax.paxtools.model.BioPAXElement: If two elements are equivalent, then their equivalence code should be the same.
EquivalenceGrouper<T extends BioPAXElement> - Class in org.biopax.paxtools.util: Utility class for equivalence based comparison of a set of BioPAXElements.
EquivalenceGrouper(Set<? extends T>) - Constructor for class org.biopax.paxtools.util.EquivalenceGrouper
EquivalenceGrouper() - Constructor for class org.biopax.paxtools.util.EquivalenceGrouper
evidence - Interface in org.biopax.paxtools.model.level2
Evidence - Interface in org.biopax.paxtools.model.level3: Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
EvidenceCodeVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
EvidenceCodeVocabularyImpl - Class in org.biopax.paxtools.impl.level3
EvidenceCodeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl
evidenceFilter - Static variable in class org.biopax.paxtools.controller.Fetcher: A property filter to ignore 'evidence' ('EVIDENCE' in L2) property (it can eventually lead to other organism, experimental entities)
EvidenceImpl - Class in org.biopax.paxtools.impl.level3
EvidenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.EvidenceImpl: Constructor.
experimentalForm - Interface in org.biopax.paxtools.model.level2
ExperimentalForm - Interface in org.biopax.paxtools.model.level3: Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
ExperimentalFormImpl - Class in org.biopax.paxtools.impl.level3
ExperimentalFormImpl() - Constructor for class org.biopax.paxtools.impl.level3.ExperimentalFormImpl: Constructor.
ExperimentalFormVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A term that describes the form of the physical entity in the context of the experiment.
ExperimentalFormVocabularyImpl - Class in org.biopax.paxtools.impl.level3
ExperimentalFormVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl
externalReferenceUtilityClass - Interface in org.biopax.paxtools.model.level2

F

factory - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
fetch(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.Fetcher: Adds the element and all its children (found via traversing into object properties that pass all the filters defined in the Constructor, and also taking #isSkipSubPathways into account) to the target model.
fetch(BioPAXElement) - Method in class org.biopax.paxtools.controller.Fetcher: Recursively finds and collects all child objects, while escaping possible infinite loops.
fetch(BioPAXElement, int) - Method in class org.biopax.paxtools.controller.Fetcher: Recursively collects unique child objects from BioPAX object type properties that pass all the filters (as set via Constructor).
fetch(BioPAXElement, Class<T>) - Method in class org.biopax.paxtools.controller.Fetcher: Goes over object type biopax properties to collect nested objects (using only properties that pass all the filters set in Constructor, and taking #isSkipSubPathways into account) of the given biopax element, its children, etc.
Fetcher - Class in org.biopax.paxtools.controller: This class is used to fetch an element (traverse it to obtain its dependent elements) and to add this element into a model using the visitor and traverse functions.
Fetcher(EditorMap, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.Fetcher: Constructor.
fetchID(BioPAXElement) - Method in class org.biopax.paxtools.controller.IdFetcher
filter(Model) - Method in interface org.biopax.paxtools.controller.ModelFilter
filter(PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.Traverser
filter(Model) - Method in class org.biopax.paxtools.converter.LevelUpgrader: Converts a BioPAX Model, Level 1 or 2, to the Level 3.
filter(E) - Method in class org.biopax.paxtools.util.ClassFilterSet: This filter method implementation filters based on isInstance function.
Filter<T> - Interface in org.biopax.paxtools.util: Generic interface for defining filter decorators.
filter(T) - Method in interface org.biopax.paxtools.util.Filter: Can e.g., analyze, modify or convert the given object (or model) to another format.
filterClass - Variable in class org.biopax.paxtools.util.ClassFilterSet
FilteredPropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller: This class is a decorating property accessor that filters values with a given class.
filterInverse(PropertyEditor) - Method in interface org.biopax.paxtools.controller.PropertyFilterBilinked
filterInverse(PropertyEditor) - Method in class org.biopax.paxtools.controller.TraverserBilinked
filters - Variable in class org.biopax.paxtools.controller.Traverser
findCommonPublications(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable
findCommonRelationships(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable
findCommonUnifications(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable
findEquivalentIntersection(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker
findFeaturesAddedToSecond(PhysicalEntity, PhysicalEntity, boolean) - Static method in class org.biopax.paxtools.controller.ModelUtils
findInverseGetMethod() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
fixDanglingInverseProperties(BioPAXElement, Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Unlinks inverse properties of the BioPAX object from values the model does not have.
fixDanglingObjectProperties(BioPAXElement, Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Unlinks object properties of the BioPAX object from values the model does not have.
fixReusedPEP(physicalEntityParticipant, BioPAXElement) - Method in class org.biopax.paxtools.controller.ReusedPEPHelper
fixReusedPEPs(boolean) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This option is only applicable two level 2 models.
fixReusedPEPs(boolean) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Enables (true) or disables (false) the fixing of reused peps.
FragmentFeature - Interface in org.biopax.paxtools.model.level3: Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
FragmentFeatureImpl - Class in org.biopax.paxtools.impl.level3
FragmentFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

G

Gene - Interface in org.biopax.paxtools.model.level3: Definition: A continuant that encodes information that can be inherited through replication.
GeneImpl - Class in org.biopax.paxtools.impl.level3
GeneImpl() - Constructor for class org.biopax.paxtools.impl.level3.GeneImpl
generateClassMetrics(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Generates simple counts of different elements in the model.
GeneticInteraction - Interface in org.biopax.paxtools.model.level3: Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
GeneticInteractionImpl - Class in org.biopax.paxtools.impl.level3
GeneticInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
get(BioPAXLevel) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap: To obtain a copy of the editor map for the corresponding level, use the
get(String) - Method in class org.biopax.paxtools.util.BiopaxSafeSet: Gets a BioPAX element by URI.
getAbsoluteRegion() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
getAbsoluteRegion() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
getAddedElements() - Method in class org.biopax.paxtools.controller.Merger: After a merge is accomplished, this set will contain the newly added elements.
getAddMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getAddMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor
getAllChildren(BioPAXElement, Filter<PropertyEditor>...) - Static method in class org.biopax.paxtools.controller.ModelUtils: Gets all the child BioPAX elements of a given BioPAX element (using the "tuned" Fetcher) and adds them to a new model.
getAllInteractions() - Method in interface org.biopax.paxtools.model.level2.physicalEntity
getAllInteractions(Class<T>) - Method in interface org.biopax.paxtools.model.level2.physicalEntity
getAnnotations() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
getAnnotations() - Method in interface org.biopax.paxtools.model.BioPAXElement: A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
getAuthor() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getAuthor() - Method in interface org.biopax.paxtools.model.level3.PublicationXref
getAUTHORS() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getAvailability() - Method in class org.biopax.paxtools.impl.level3.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 interface org.biopax.paxtools.model.level3.Entity: The contents of this set can be modified but semantic consistency is not guaranteed.
getBindsTo() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl
getBindsTo() - Method in interface org.biopax.paxtools.model.level3.BindingFeature: A binding feature represents a "half" of the bond between two entities.
getBuckets() - Method in class org.biopax.paxtools.util.EquivalenceGrouper
getByID(String) - Method in class org.biopax.paxtools.impl.ModelImpl
getByID(String) - Method in interface org.biopax.paxtools.model.Model: This method returns the biopax element with the given id, returns null if the object with the given id does not exist in this model.
getCatalysisDirection() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
getCatalysisDirection() - Method in interface org.biopax.paxtools.model.level3.Catalysis: This property represents the direction of this catalysis under all physiological conditions if there is one.
getCellType() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
getCELLTYPE() - Method in interface org.biopax.paxtools.model.level2.bioSource
getCellType() - Method in interface org.biopax.paxtools.model.level3.BioSource: A cell type, e.g.
getCELLULAR_LOCATION() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
getCellularLocation() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getCellularLocation() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity: A cellular location, e.g.
getChemDbStartsWithOrEquals() - Method in class org.biopax.paxtools.controller.IdFetcher
getCHEMICAL_FORMULA() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
getChemicalFormula() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
getChemicalFormula() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
getCofactor() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
getCOFACTOR() - Method in interface org.biopax.paxtools.model.level2.catalysis
getCofactor() - Method in interface org.biopax.paxtools.model.level3.Catalysis: Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
getComment() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl
getCOMMENT() - Method in interface org.biopax.paxtools.model.level2.Level2Element
getComment() - Method in interface org.biopax.paxtools.model.level3.Level3Element: A textual comment about this individual.
getComponent() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getComponent() - Method in interface org.biopax.paxtools.model.level3.Complex: Defines the PhysicalEntity subunits of this complex.
getComponentOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getComponentOf() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
getCOMPONENTS() - Method in interface org.biopax.paxtools.model.level2.complex
getComponentStoichiometry() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getComponentStoichiometry() - Method in interface org.biopax.paxtools.model.level3.Complex: The stoichiometry of components in a complex.
getConfidence() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: Confidence in the containing instance.
getCONFIDENCE() - Method in interface org.biopax.paxtools.model.level2.evidence
getConfidence() - Method in interface org.biopax.paxtools.model.level3.Evidence: Confidence in the containing instance.
getCONFIDENCE_VALUE() - Method in interface org.biopax.paxtools.model.level2.confidence: The value of the confidence measure.
getCONTROL_TYPE() - Method in interface org.biopax.paxtools.model.level2.control
getControlled() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getCONTROLLED() - Method in interface org.biopax.paxtools.model.level2.control
getControlled() - Method in interface org.biopax.paxtools.model.level3.Control: The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
getControlledOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
getControlledOf() - Method in interface org.biopax.paxtools.model.level3.Process
getController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getCONTROLLER() - Method in interface org.biopax.paxtools.model.level2.control
getController() - Method in interface org.biopax.paxtools.model.level3.Control: The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
getControllerOf() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
getControllerOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getControllerOf() - Method in interface org.biopax.paxtools.model.level3.Controller: This method returns the list of Control interactions that this entity controls.
getControlType() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getControlType() - Method in interface org.biopax.paxtools.model.level3.Control: Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.
getConversion1() - Method in class org.biopax.paxtools.controller.ConversionScore
getConversion2() - Method in class org.biopax.paxtools.controller.ConversionScore
getConversionDirection() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getConversionDirection() - Method in interface org.biopax.paxtools.model.level3.Conversion: This property represents the direction of the reaction.
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.
getDataSource() - Method in class org.biopax.paxtools.impl.level3.EntityImpl
getDataSource() - Method in interface org.biopax.paxtools.model.level3.Entity: This method returns a set of free text descriptions of the source of this data, e.g.
getDatasources(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils: Collects all Provenance objects associated with this one as follows: - if the element is Entity (has 'dataSource' property) or is Provenence itself, get the values and quit; - if the biopax element is PathwayStep or EntityReference, traverse into some of its object/inverse properties to collect dataSource values from associated entities.
getDb() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getDB() - Method in interface org.biopax.paxtools.model.level2.xref
getDb() - Method in interface org.biopax.paxtools.model.level3.Xref
getDB_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref
getDbVersion() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getDbVersion() - Method in interface org.biopax.paxtools.model.level3.Xref
getDefaultFactory() - Method in enum org.biopax.paxtools.model.BioPAXLevel: This method returns the default factory for this level
getDELTA_G() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
getDELTA_G_PRIME_O() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
getDELTA_H() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
getDELTA_S() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
getDeltaG() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getDeltaG() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
getDeltaGPrime0() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl
getDeltaGPrime0() - Method in interface org.biopax.paxtools.model.level3.DeltaG: For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
getDeltaH() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getDeltaH() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.
getDeltaS() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getDeltaS() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.
getDirectChildren(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils: Gets direct children of a given BioPAX element and adds them to a new model.
getDirectChildrenAsSet(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils: Collects direct children of a given BioPAX element.
getDIRECTION() - Method in interface org.biopax.paxtools.model.level2.catalysis
getDisplayName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl
getDisplayName() - Method in interface org.biopax.paxtools.model.level3.Named: 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.
getDomain() - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Returns the domain of the property.
getDomain() - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter: Returns the domain of the property.
getEC_NUMBER() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
getECNumber() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getECNumber() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
getEditorForProperty(String, Class<D>) - Method in interface org.biopax.paxtools.controller.EditorMap: This method returns the editor intended to handle property named property of a class (javaClass).
getEditorForProperty(String, Class<D>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getEditorForProperty(String, Class<D>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getEditorMap() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
getEditorMap() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
getEditorsForProperty(String) - Method in interface org.biopax.paxtools.controller.EditorMap: This method returns the set of editors intended to handle property named property.
getEditorsForProperty(String) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getEditorsForProperty(String) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getEditorsOf(BioPAXElement) - Method in interface org.biopax.paxtools.controller.EditorMap: This method returns the set of editors whose domain subsumes the class of given BioPAX element.
getEditorsOf(Class<? extends BioPAXElement>) - Method in interface org.biopax.paxtools.controller.EditorMap: This method returns the set of editors whose domain subsumes the given class
getEditorsOf(BioPAXElement) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getEditorsOf(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getEditorsOf(BioPAXElement) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getEditorsOf(Class<? extends BioPAXElement>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getEntityFeature() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getEntityFeature() - Method in interface org.biopax.paxtools.model.level3.EntityReference: Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
getEntityFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getEntityFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Inverse of EntityReference.getEntityFeature()
getEntityReference() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
getEntityReference() - Method in interface org.biopax.paxtools.model.level3.SimplePhysicalEntity: Reference entity for this physical entity.
getEntityReferenceOf() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getEntityReferenceOf() - Method in interface org.biopax.paxtools.model.level3.EntityReference: Inverse of SimplePhysicalEntity.getEntityReference()
getEntityReferenceType() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getEntityReferenceType() - Method in interface org.biopax.paxtools.model.level3.EntityReference
getEvidence() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getEvidence() - Method in class org.biopax.paxtools.impl.level3.EntityImpl
getEvidence() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getEvidence() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getEVIDENCE() - Method in interface org.biopax.paxtools.model.level2.process: Gets all evidence objects.
getEvidence() - Method in interface org.biopax.paxtools.model.level3.Observable
getEVIDENCE_CODE() - Method in interface org.biopax.paxtools.model.level2.evidence
getEvidenceCode() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
getEvidenceCode() - Method in interface org.biopax.paxtools.model.level3.Evidence: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
getEXPERIMENTAL_FORM() - Method in interface org.biopax.paxtools.model.level2.evidence
getEXPERIMENTAL_FORM_TYPE() - Method in interface org.biopax.paxtools.model.level2.experimentalForm
getExperimentalFeature() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
getExperimentalFeature() - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: Contents of this set should not be modified.
getExperimentalForm() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl
getExperimentalForm() - Method in interface org.biopax.paxtools.model.level3.Evidence: Contents of this set should not be modified.
getExperimentalFormDescription() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
getExperimentalFormDescription() - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: Descriptor of this experimental form from a controlled vocabulary.
getExperimentalFormEntity() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
getExperimentalFormEntity() - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm
getFactory() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
getFactory() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
getFeature() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getFeature() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
getFEATURE_LOCATION() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
getFEATURE_TYPE() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
getFeatureIntersection(PhysicalEntity, ModelUtils.FeatureType, PhysicalEntity, ModelUtils.FeatureType) - Static method in class org.biopax.paxtools.controller.ModelUtils
getFeatureLocation() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getFeatureLocation() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Location of the feature on the sequence of the interactor.
getFeatureLocationType() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getFeatureLocationType() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
getFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Inverse of PhysicalEntity.getFeature() Contents of this set is generated automatically and should not be modified.
getFeatureSetByType(PhysicalEntity, ModelUtils.FeatureType) - Static method in class org.biopax.paxtools.controller.ModelUtils
getFilename() - Method in enum org.biopax.paxtools.model.BioPAXLevel: This method returns the filename of the owl file
getGenericEntityReferences() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
getGenericEntityReferences() - Method in interface org.biopax.paxtools.model.level3.SimplePhysicalEntity: This method returns: The entity reference of this PhysicalEntity plus If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively
getGetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getGetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor
getId() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getId() - Method in class org.biopax.paxtools.io.SimpleIOHandler
getID() - Method in interface org.biopax.paxtools.model.level2.xref
getId() - Method in interface org.biopax.paxtools.model.level3.Xref
getID_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref
getIdVersion() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getIdVersion() - Method in interface org.biopax.paxtools.model.level3.Xref
getImplClass(Class<T>) - Method in class org.biopax.paxtools.model.BioPAXFactory: Get a concrete or abstract BioPAX type (not interface), from org.biopax.paxtools.impl..*, i.e., one that has persistence/search annotations, etc.
getINTERACTION_TYPE() - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
getInteractionScore() - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
getInteractionScore() - Method in interface org.biopax.paxtools.model.level3.GeneticInteraction
getInteractionType() - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
getInteractionType() - Method in interface org.biopax.paxtools.model.level3.Interaction: Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
getInterfaceForName(String) - Method in enum org.biopax.paxtools.model.BioPAXLevel: Gets the BioPAX type (java interface) by name.
getIntraMolecular() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl
getIntraMolecular() - Method in interface org.biopax.paxtools.model.level3.BindingFeature: IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule.
getInverseAccessor() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
getInverseEditorsOf(BioPAXElement) - Method in interface org.biopax.paxtools.controller.EditorMap: Properties in BioPAX specification is unidirectional.
getInverseEditorsOf(Class<? extends BioPAXElement>) - Method in interface org.biopax.paxtools.controller.EditorMap: Properties in BioPAX specification is unidirectional.
getInverseEditorsOf(BioPAXElement) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getInverseEditorsOf(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getInverseEditorsOf(BioPAXElement) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getInverseEditorsOf(Class<? extends BioPAXElement>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getInverseGetMethod() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
getIONIC_STRENGTH() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
getIONIC_STRENGTH() - Method in interface org.biopax.paxtools.model.level2.kPrime
getIonicStrength() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
getIonicStrength() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant: The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi).
getK_PRIME() - Method in interface org.biopax.paxtools.model.level2.kPrime
getKEQ() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getKEQ() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
getKEQ() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: This quantity is dimensionless and is usually a single number.
getKeywords(BioPAXElement, int, Filter<DataPropertyEditor>...) - Static method in class org.biopax.paxtools.controller.ModelUtils: Collects data type (not object) property values (can be then used for full-text indexing).
getKnownSubClassesOf(Class<E>) - Method in interface org.biopax.paxtools.controller.EditorMap: Returns a set of sub classes of a given class.
getKnownSubClassesOf(Class<E>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getKnownSubClassesOf(Class<E>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getKPrime() - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl
getKPrime() - Method in interface org.biopax.paxtools.model.level3.KPrime: The apparent equilibrium constant K'.
getLeft() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getLEFT() - Method in interface org.biopax.paxtools.model.level2.conversion
getLeft() - Method in interface org.biopax.paxtools.model.level3.Conversion: The participants on the left side of the conversion interaction.
getLevel() - Method in interface org.biopax.paxtools.controller.EditorMap: Returns the BioPAX level for which editor map is created.
getLevel() - Method in class org.biopax.paxtools.controller.EditorMapImpl
getLevel() - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getLevel() - Method in class org.biopax.paxtools.impl.MockFactory
getLevel() - Method in class org.biopax.paxtools.impl.ModelImpl
getLevel() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
getLevel() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
getLevel() - Method in class org.biopax.paxtools.model.BioPAXFactory: Gets the level.
getLevel() - Method in interface org.biopax.paxtools.model.Model: This method returns the level of the objects that are contained within this model.
getLevelFileAsStream() - Method in enum org.biopax.paxtools.model.BioPAXLevel: This method loads the level file as resource and returns it as an input stream
getLevelFromNameSpace(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel
getLocalId(BioPAXElement) - Static method in class org.biopax.paxtools.converter.LevelUpgrader: Gets the local part of the BioPAX element ID.
getMatch(physicalEntityParticipant) - Method in class org.biopax.paxtools.controller.ConversionScore
getMatchedPEPs() - Method in class org.biopax.paxtools.controller.ConversionScore
getMatchingEnum(Object) - Method in class org.biopax.paxtools.converter.LevelUpgrader
getMaxCardinality(Class<? extends D>) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getMaxCardinality(Class<? extends D>) - Method in interface org.biopax.paxtools.controller.PropertyEditor: Return the maximum cardinality that is defined for the property to which editor is belong.
getMemberEntityReference() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getMemberEntityReference() - Method in interface org.biopax.paxtools.model.level3.EntityReference
getMemberEntityReferenceOf() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getMemberEntityReferenceOf() - Method in interface org.biopax.paxtools.model.level3.EntityReference: Reverse of EntityReference.getMemberEntityReference()
getMemberFeature() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getMemberFeature() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: An entity feature that belongs to this homology grouping.
getMemberFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getMemberFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Reverse of EntityFeature.getMemberFeature()
getMemberPhysicalEntity() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getMemberPhysicalEntity() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity: Please avoid using this property in your BioPAX L3 models unless absolutely sure/required, for there is an alternative way (using PhysicalEntity/entityReference/memberEntityReference), and this will probably be deprecated in the future BioPAX releases.
getMemberPhysicalEntityOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getMemberPhysicalEntityOf() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
getMemberReferences() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getMemberReferences() - Method in interface org.biopax.paxtools.model.level3.Complex: Gets the EntityReferences of the member simple physical entities.
getMergedElements() - Method in class org.biopax.paxtools.controller.Merger: After a merge is accomplished, this set will contain the merged elements.
getMethod - Variable in class org.biopax.paxtools.controller.SimplePropertyAccessor: 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.level3.BindingFeatureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CellVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DegradationImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaRegionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.GeneImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ModulationImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.MolecularInteractionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProteinImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProteinReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProvenanceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaRegionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceLocationImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TissueVocabularyImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TransportImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl
getModelInterface() - Method in class org.biopax.paxtools.impl.level3.UnificationXrefImpl
getModelInterface() - Method in interface org.biopax.paxtools.model.BioPAXElement: This method returns the actual model interface that a class implements.
getModelInterface() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity: Overridden to provide better downcasting
getModificationType() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
getModificationType() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
getModificationType() - Method in interface org.biopax.paxtools.model.level3.ModificationFeature
getMOLECULAR_WEIGHT() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
getMolecularWeight() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
getMolecularWeight() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
getName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl
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 interface org.biopax.paxtools.model.level3.Named: Names for this entity, including standardName and shortName if defined.
getNameSpace() - Method in enum org.biopax.paxtools.model.BioPAXLevel: This method returns the namespace defined for this level.
getNameSpacePrefixMap() - Method in class org.biopax.paxtools.impl.ModelImpl
getNameSpacePrefixMap() - Method in interface org.biopax.paxtools.model.Model: This method returns a map of name space prefixes.
getNEXT_STEP() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
getNextStep() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getNextStep() - Method in interface org.biopax.paxtools.model.level3.PathwayStep
getNextStepOf() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getNextStepOf() - Method in interface org.biopax.paxtools.model.level3.PathwayStep
getNotFeature() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
getNotFeature() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
getNotFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
getNotFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Inverse of PhysicalEntity.getNotFeature() Contents of this set is generated automatically and should not be modified.
getObject(Model, String, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils: A more strict, type-safe way to ask for a biopax object from the model, unlike Model.getByID(String).
getObjects() - Method in class org.biopax.paxtools.impl.ModelImpl
getObjects(Class<T>) - Method in class org.biopax.paxtools.impl.ModelImpl
getObjects() - Method in interface org.biopax.paxtools.model.Model: This method returns a set of objects in the model.
getObjects(Class<T>) - Method in interface org.biopax.paxtools.model.Model: This method returns a set of objects in the model of the given class.
getOrganism() - Method in class org.biopax.paxtools.impl.level3.GeneImpl
getOrganism() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
getOrganism() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
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 interface org.biopax.paxtools.model.level3.Gene: An organism, e.g.
getOrganism() - Method in interface org.biopax.paxtools.model.level3.Pathway: An organism, e.g.
getOrganism() - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference: An organism, e.g.
getOrganisms(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils: Collects BioSource objects from this or related elements (where it makes sense; though the biopax element might have no or empty 'organism' property at all.
getPackageName() - Method in enum org.biopax.paxtools.model.BioPAXLevel
getParentPathways(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils: Collects all parent Pathway objects recursively traversing the inverse object properties of the biopax element.
getParticipant() - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
getPARTICIPANT() - Method in interface org.biopax.paxtools.model.level2.experimentalForm
getParticipant() - Method in interface org.biopax.paxtools.model.level3.Interaction: The entities that participate in this interaction.
getParticipantOf() - Method in class org.biopax.paxtools.impl.level3.EntityImpl
getParticipantOf() - Method in interface org.biopax.paxtools.model.level3.Entity: This method returns the interaction that this entity/pep takes part in.
getPARTICIPANTS() - Method in interface org.biopax.paxtools.model.level2.interaction
getParticipantStoichiometry() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getParticipantStoichiometry() - Method in interface org.biopax.paxtools.model.level3.Conversion: Stoichiometry of the left (Conversion.getLeft()) and right(Conversion.getRight()) participants.
getPATHWAY_COMPONENTS() - Method in interface org.biopax.paxtools.model.level2.pathway
getPathwayComponent() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
getPathwayComponent() - Method in interface org.biopax.paxtools.model.level3.Pathway
getPathwayComponentOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
getPathwayComponentOf() - Method in interface org.biopax.paxtools.model.level3.Process
getPathwayController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getPathwayOrder() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
getPathwayOrder() - Method in interface org.biopax.paxtools.model.level3.Pathway
getPathwayOrderOf() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getPathwayOrderOf() - Method in interface org.biopax.paxtools.model.level3.PathwayStep
getPatoData() - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl
getPatoData() - Method in interface org.biopax.paxtools.model.level3.PhenotypeVocabulary
getPeController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl
getPh() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
getPH() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
getPH() - Method in interface org.biopax.paxtools.model.level2.kPrime
getPh() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant: A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.
getPhenotype() - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
getPhenotype() - Method in interface org.biopax.paxtools.model.level3.GeneticInteraction
getPHYSICAL_ENTITY() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
getPhysicalEntity() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
getPhysicalEntity() - Method in interface org.biopax.paxtools.model.level3.Stoichiometry
getPMg() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
getPMG() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
getPMG() - Method in interface org.biopax.paxtools.model.level2.kPrime
getPMg() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant
getPOSITION_STATUS() - Method in interface org.biopax.paxtools.model.level2.sequenceSite
getPositionStatus() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
getPositionStatus() - Method in interface org.biopax.paxtools.model.level3.SequenceSite
getPresentationName() - Method in class org.biopax.paxtools.command.AddCommand
getPresentationName() - Method in class org.biopax.paxtools.command.PropertyAddCommand
getPresentationName() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
getPresentationName() - Method in class org.biopax.paxtools.command.PropertySetCommand
getPresentationName() - Method in class org.biopax.paxtools.command.RemoveCommand
getPrimarySetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getPrimarySetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor: Returns the primary set method of the editor.
getProduct() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
getProduct() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
getProperty() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getProperty() - Method in interface org.biopax.paxtools.controller.PropertyEditor
getRange() - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Returns the range of the editor.
getRange() - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter: Returns the range of the editor.
getRDFCommentEditor(BioPAXElement) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Paxtools maps BioPAX:comment (L3) and BioPAX:COMMENT (L2) to rdf:comment.
getRedoPresentationName() - Method in class org.biopax.paxtools.command.AddCommand
getRedoPresentationName() - Method in class org.biopax.paxtools.command.PropertyAddCommand
getRedoPresentationName() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
getRedoPresentationName() - Method in class org.biopax.paxtools.command.PropertySetCommand
getRedoPresentationName() - Method in class org.biopax.paxtools.command.RemoveCommand
getRegionType() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
getRegionType() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
getRELATIONSHIP_TYPE() - Method in interface org.biopax.paxtools.model.level2.relationshipXref
getRelationshipType() - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl
getRelationshipType() - Method in interface org.biopax.paxtools.model.level3.RelationshipXref: Definition:A controlled vocabulary term that defines the type of relationship that this xref defines.
getRemoveMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getRemoveMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor
getRestrictedRanges() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
getRestrictedRangesFor(Class<? extends D>) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
getReusedPEPHelper() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This is a helper class initialized only if fixReusedPEPs is true.
getRight() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getRIGHT() - Method in interface org.biopax.paxtools.model.level2.conversion
getRight() - Method in interface org.biopax.paxtools.model.level3.Conversion: The participants on the right side of the conversion interaction.
getRootElements(Model, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils: Finds "root" BioPAX objects that belong to a particular class (incl.
getScore() - Method in class org.biopax.paxtools.controller.ConversionScore
getScoreSource() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl
getScoreSource() - Method in interface org.biopax.paxtools.model.level3.Score: This property defines the source of the scoring methodology.
getSeqDbStartsWithOrEquals() - Method in class org.biopax.paxtools.controller.IdFetcher
getSequence() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
getSEQUENCE() - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
getSequence() - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference: Polymer sequence in uppercase letters.
getSEQUENCE_FEATURE_LIST() - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
getSEQUENCE_INTERVAL_BEGIN() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
getSEQUENCE_INTERVAL_END() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
getSEQUENCE_POSITION() - Method in interface org.biopax.paxtools.model.level2.sequenceSite
getSequenceIntervalBegin() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
getSequenceIntervalBegin() - Method in interface org.biopax.paxtools.model.level3.SequenceInterval
getSequenceIntervalEnd() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
getSequenceIntervalEnd() - Method in interface org.biopax.paxtools.model.level3.SequenceInterval
getSequencePosition() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
getSequencePosition() - Method in interface org.biopax.paxtools.model.level3.SequenceSite
getSetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getSetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor
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
getSimpleMembers() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getSimpleMembers(Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getSimpleMembers() - Method in interface org.biopax.paxtools.model.level3.Complex: Gets the member physical entities which are not complex.
getSource() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getSOURCE() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getSource() - Method in interface org.biopax.paxtools.model.level3.PublicationXref
getSpontaneous() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getSPONTANEOUS() - Method in interface org.biopax.paxtools.model.level2.conversion
getSpontaneous() - Method in interface org.biopax.paxtools.model.level3.Conversion: Specifies whether a conversion occurs spontaneously or not.
getStandardName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl
getStandardName() - Method in interface org.biopax.paxtools.model.level3.Named: The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
getSTEP_INTERACTIONS() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
getStepConversion() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
getStepConversion() - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep: This method returns the central conversion of this BiochemicalPathwayStep.
getStepDirection() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
getStepDirection() - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep: This property can be used for annotating direction of enzymatic activity.
getStepProcess() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
getStepProcess() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
getStepProcess() - Method in interface org.biopax.paxtools.model.level3.PathwayStep
getStepProcessOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
getStepProcessOf() - Method in interface org.biopax.paxtools.model.level3.Process
getSTOICHIOMETRIC_COEFFICIENT() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
getStoichiometricCoefficient() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
getStoichiometricCoefficient() - Method in interface org.biopax.paxtools.model.level3.Stoichiometry: Stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.
getStructure() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
getSTRUCTURE() - Method in interface org.biopax.paxtools.model.level2.smallMolecule
getStructure() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
getSTRUCTURE_DATA() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
getSTRUCTURE_FORMAT() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
getStructureData() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
getStructureData() - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure: This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI.
getStructureFormat() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
getStructureFormat() - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure: This property specifies which format is used to define chemical structure.
getSubclassEditorsForProperty(String, Class<D>) - Method in interface org.biopax.paxtools.controller.EditorMap: This method returns the set of editors intended to handle property named property.
getSubclassEditorsForProperty(String, Class<D>) - Method in class org.biopax.paxtools.controller.EditorMapImpl
getSubclassEditorsForProperty(String, Class<D>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
getSubRegion() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl
getSubRegion() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference
getSubRegionOf() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
getSubRegionOf() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
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
getTAXON_XREF() - Method in interface org.biopax.paxtools.model.level2.bioSource
getTemperature() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.kPrime
getTemperature() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant
getTemplate() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
getTemplate() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
getTemplateDirection() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
getTemplateDirection() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
getTerm() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
getTERM() - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
getTerm() - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary
getThreshold() - Method in class org.biopax.paxtools.controller.Integrator: Returns the threshold value (the smallest score for integrating two conversions)
getTissue() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
getTISSUE() - Method in interface org.biopax.paxtools.model.level2.bioSource
getTissue() - Method in interface org.biopax.paxtools.model.level3.BioSource: An external controlled vocabulary of tissue types.
getTitle() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getTITLE() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getTitle() - Method in interface org.biopax.paxtools.model.level3.PublicationXref
getUndoPresentationName() - Method in class org.biopax.paxtools.command.AddCommand
getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertyAddCommand
getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertySetCommand
getUndoPresentationName() - Method in class org.biopax.paxtools.command.RemoveCommand
getUnknown() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getUnknown() - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor
getUnknown() - Method in interface org.biopax.paxtools.controller.PropertyEditor: Gets the unknown value.
getUri() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
getUri() - Method in interface org.biopax.paxtools.model.BioPAXElement: This method returns the absolute URI of the element.
getUrl() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getURL() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getUrl() - Method in interface org.biopax.paxtools.model.level3.PublicationXref
getValue() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl
getValue() - Method in interface org.biopax.paxtools.model.level3.Score: This property defines the value of the score.
getValueFromBean(D) - Method in class org.biopax.paxtools.controller.FilteredPropertyAccessor
getValueFromBean(BioPAXElement) - Method in class org.biopax.paxtools.controller.PathAccessor
getValueFromBean(D) - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Returns the value of the bean using the default getMethod.
getValueFromBean(D) - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor: Returns the value of the bean using the default SimplePropertyAccessor.getMethod.
getValueFromBean(D) - Method in class org.biopax.paxtools.controller.TransitivePropertyAccessor
getValueFromBean(D) - Method in class org.biopax.paxtools.controller.UnionPropertyAccessor
getValueFromBeans(Collection<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.PathAccessor
getValueFromBeans(Collection<? extends D>) - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Returns the values for a collection of beans using the default getMethod.
getValueFromBeans(Collection<? extends D>) - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter
getValueFromModel(Model) - Method in class org.biopax.paxtools.controller.PathAccessor: This method runs the path query on all the elements within the model.
getVisitor() - Method in class org.biopax.paxtools.controller.Traverser
getXmlBase() - Method in class org.biopax.paxtools.impl.ModelImpl
getXmlBase() - Method in interface org.biopax.paxtools.model.Model: Gets the model's xml:base (URI prefix/namespace), which normally the majority of the BioPAX object's absolute URIs in the model begin with.
getXmlStreamInfo() - Method in class org.biopax.paxtools.io.SimpleIOHandler: This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.
getXref() - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl
getXREF() - Method in interface org.biopax.paxtools.model.level2.XReferrable
getXref() - Method in interface org.biopax.paxtools.model.level3.XReferrable
getXrefOf() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getXrefOf() - Method in interface org.biopax.paxtools.model.level3.Xref
getYear() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getYEAR() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getYear() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

H

hasElement(BioPAXElement) - Method in enum org.biopax.paxtools.model.BioPAXLevel
hasEquivalentCellularLocation(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
hasEquivalentCellularLocation(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
hasEquivalentFeatures(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
hasEquivalentFeatures(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
hasEquivalentIntersection(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker
hashCode() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl: This method is consistent with the overridden BioPAXElementImpl.equals(Object) method (biopax type and URI are what matters)
hasInverseLink() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
hasNext() - Method in class org.biopax.paxtools.util.CompositeIterator

I

IdFetcher - Class in org.biopax.paxtools.controller: Tries to get preferred type IDs of an entity reference.
IdFetcher() - Constructor for class org.biopax.paxtools.controller.IdFetcher: Constructor.
idMap - Variable in class org.biopax.paxtools.impl.ModelImpl
IllegalBioPAXArgumentException - Exception in org.biopax.paxtools.util: This exception is thrown typically when BioPAX domain or cardinality restrictions are violated.
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
impl - Variable in class org.biopax.paxtools.controller.DecoratingPropertyAccessor
init(InputStream) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.
init(InputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler
integrate() - Method in class org.biopax.paxtools.controller.Integrator: Integrates target and source(s) and returns a sorted (desc) list of conversion scores.
integrate(List<ConversionScore>) - Method in class org.biopax.paxtools.controller.Integrator: Does the integration using user-provided scores list.
Integrator - Class in org.biopax.paxtools.controller: This class is intended to merge and to integrate BioPAX Level2 models not necessarily from the same resource - if models allow such a thing.
Integrator(EditorMap, Model, Model...) - Constructor for class org.biopax.paxtools.controller.Integrator
interaction - Interface in org.biopax.paxtools.model.level2
Interaction - Interface in org.biopax.paxtools.model.level3: Definition: A biological relationship between two or more entities.
InteractionImpl - Class in org.biopax.paxtools.impl.level3
InteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.InteractionImpl
InteractionParticipant - Interface in org.biopax.paxtools.model.level2: marker interface for entities and PEPs
InteractionVocabulary - Interface in org.biopax.paxtools.model.level3: A reference to the PSI Molecular Interaction ontology (MI) interaction type.
InteractionVocabularyImpl - Class in org.biopax.paxtools.impl.level3
InteractionVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl
invokeMethod(Method, D, R) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Calls the method onto bean with the value as its parameter.
isAbsoluteUris() - Method in class org.biopax.paxtools.io.SimpleIOHandler
isAddDependencies() - Method in class org.biopax.paxtools.impl.ModelImpl
isAddDependencies() - Method in interface org.biopax.paxtools.model.Model: When addDependencies is false, the model will not check for the dependent objects of a newly added object.
isCompleteBackward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
isCompleteForward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
isCOMPONENTof() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
isCONTROLLEDOf() - Method in interface org.biopax.paxtools.model.level2.process
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
isEquivalent(BioPAXElement) - Method in interface org.biopax.paxtools.model.BioPAXElement: This method compares the given element for equivalency.
isEquivalent(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker
isFixReusedPEPs() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This option is only applicable two level 2 models.
isFixReusedPEPs() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Workaround for a very common Level 2 issue.
isInBioPAXNameSpace(String) - Method in class org.biopax.paxtools.controller.EditorMapImpl
isInBioPAXNameSpace(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel: This method returns true if the given string starts with the BP_PREFIX
isInEquivalentState(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
isInstanceOfAtLeastOne(Set<Class<? extends BioPAXElement>>, Object) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Checks if value is an instance of one of the classes given in a set.
isInverseMultipleCardinality() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
isInverseOnly() - Method in class org.biopax.paxtools.controller.TraverserBilinked
isMergeDuplicates() - Method in class org.biopax.paxtools.io.SimpleIOHandler
isMultipleCardinality() - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Checks if the property to which editor is assigned has multiple cardinality.
isMultipleCardinality() - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter: Checks if the property to which editor is assigned has multiple cardinality.
isMultipleCardinality(Method) - Static method in class org.biopax.paxtools.controller.SimplePropertyAccessor
isNEXT_STEPof() - Method in interface org.biopax.paxtools.model.level2.pathwayStep
isNormalizeNameSpaces() - Method in class org.biopax.paxtools.io.SimpleIOHandler
isPARTICIPANTSof() - Method in interface org.biopax.paxtools.model.level2.InteractionParticipant: This method returns the interaction that this entity/pep takes part in.
isPATHWAY_COMPONENTSof() - Method in interface org.biopax.paxtools.model.level2.pathwayComponent
isPATHWAY_COMPONENTSof() - Method in interface org.biopax.paxtools.model.level2.process
isPHYSICAL_ENTITYof() - Method in interface org.biopax.paxtools.model.level2.physicalEntity
isReverseMatch() - Method in class org.biopax.paxtools.controller.ConversionScore
isSignificant() - Method in class org.biopax.paxtools.command.PropertyAddCommand
isSignificant() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
isSkipSubPathways() - Method in class org.biopax.paxtools.controller.Completer
isSkipSubPathways() - Method in class org.biopax.paxtools.controller.Fetcher
isSTEP_INTERACTIONSOf() - Method in interface org.biopax.paxtools.model.level2.process
isUnknown(Object) - Method in class org.biopax.paxtools.controller.DecoratingPropertyAccessor
isUnknown(Object) - Method in class org.biopax.paxtools.controller.PathAccessor
isUnknown(Object) - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor: According the editor type, this methods checks if value equals to one of the unknown values defined under BioPAXElement or is an empty set or set of "unknown" values.
isUnknown(Object) - Method in interface org.biopax.paxtools.controller.PropertyAccessor: Checks if the value is unkown.
isUnknown(Object) - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor: Checks if the value is unkown.
isUnknown(Object) - Method in class org.biopax.paxtools.controller.UnionPropertyAccessor
isXREFof() - Method in interface org.biopax.paxtools.model.level2.xref
iterator() - Method in interface org.biopax.paxtools.controller.EditorMap
iterator() - Method in class org.biopax.paxtools.controller.EditorMapImpl
iterator() - Method in enum org.biopax.paxtools.controller.SimpleEditorMap
iterator() - Method in class org.biopax.paxtools.util.AbstractFilterSet
iterator() - Method in class org.biopax.paxtools.util.BiopaxSafeSet

K

kPrime - Interface in org.biopax.paxtools.model.level2
KPrime - Interface in org.biopax.paxtools.model.level3: The apparent equilibrium constant, K', and associated values.
KPrimeImpl - Class in org.biopax.paxtools.impl.level3
KPrimeImpl() - Constructor for class org.biopax.paxtools.impl.level3.KPrimeImpl

L

L3ElementImpl - Class in org.biopax.paxtools.impl.level3: Base BioPAX Level3 element.
L3ElementImpl() - Constructor for class org.biopax.paxtools.impl.level3.L3ElementImpl
level - Variable in class org.biopax.paxtools.controller.EditorMapImpl
level - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
Level2Element - Interface in org.biopax.paxtools.model.level2: Created by IntelliJ IDEA.
Level3Element - Interface in org.biopax.paxtools.model.level3: A Level 3 specific element.
LevelUpgrader - Class in org.biopax.paxtools.converter: Upgrades BioPAX L1 and L2 to Level 3.
LevelUpgrader() - Constructor for class org.biopax.paxtools.converter.LevelUpgrader: Default Constructor that also loads 'classesmap' and 'propsmap' from the properties files.
LevelUpgrader(BioPAXFactory) - Constructor for class org.biopax.paxtools.converter.LevelUpgrader: Constructor
locationAndFeatureCode() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
locationCode() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
log - Static variable in class org.biopax.paxtools.controller.AbstractPropertyEditor
log - Static variable in class org.biopax.paxtools.controller.PathAccessor

M

mapClassName(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.impl.MockFactory
mapClassName(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.model.BioPAXFactory: Maps a BioPAX type (model interface) to the full-qualified class name of an implementing class.
md5hex(String) - Static method in class org.biopax.paxtools.controller.ModelUtils: Calculates MD5 hash code (as 32-byte hex.
merge(Model, Model...) - Method in class org.biopax.paxtools.controller.Merger: Merges the source models into target model.
merge(Model, Model...) - Method in class org.biopax.paxtools.controller.SimpleMerger: Merges the source models into target model, one after another (in the order they are listed).
merge(Model, Collection<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.SimpleMerger: Merges the elements and all their child biopax objects into the target model.
merge(Model, BioPAXElement) - Method in class org.biopax.paxtools.controller.SimpleMerger: Merges the source element (and its "downstream" dependents) into target model.
merge(Model) - Method in class org.biopax.paxtools.impl.ModelImpl: This is default implementation that uses the id-based merging (SimpleMerger.merge(Model, Model...)) NOTE: some applications, such as those dealing with persistence/transactions or advanced BioPAX alignment/comparison algorithms (like the Patch), may have to implement and use a more specific method instead.
merge(Model) - Method in interface org.biopax.paxtools.model.Model: Merges the source model into this one.
mergeDuplicates(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler: If set to true, the reader will merge duplicate individuals, i.e.
mergeEquivalentInteractions(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Merges equivalent interactions (currently - Conversions only).
mergeEquivalentPhysicalEntities(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Merges equivalent physical entities.
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
MockFactory - Class in org.biopax.paxtools.impl: This factory returns decorated objects for testing.
MockFactory(BioPAXLevel) - Constructor for class org.biopax.paxtools.impl.MockFactory
Model - Interface in org.biopax.paxtools.model: A model acts as a container for BioPAX elements.
ModelFilter - Interface in org.biopax.paxtools.controller: A generic filter interface for Models.
ModelImpl - Class in org.biopax.paxtools.impl: This is the default implementation of the Model.
ModelImpl() - Constructor for class org.biopax.paxtools.impl.ModelImpl
ModelImpl(BioPAXLevel) - Constructor for class org.biopax.paxtools.impl.ModelImpl
ModelImpl(BioPAXFactory) - Constructor for class org.biopax.paxtools.impl.ModelImpl
ModelUtils - Class in org.biopax.paxtools.controller: Several useful algorithms and examples, e.g., to extract root or child BioPAX L3 elements, remove dangling, replace elements or URIs, fix/infer property values, etc.
ModificationFeature - Interface in org.biopax.paxtools.model.level3: Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
ModificationFeatureImpl - Class in org.biopax.paxtools.impl.level3
ModificationFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
modulation - Interface in org.biopax.paxtools.model.level2: get controlled should be catalysis
Modulation - Interface in org.biopax.paxtools.model.level3: Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
ModulationImpl - Class in org.biopax.paxtools.impl.level3
ModulationImpl() - Constructor for class org.biopax.paxtools.impl.level3.ModulationImpl
MolecularInteraction - Interface in org.biopax.paxtools.model.level3: Definition: An interaction in which at least one participant is a physical entity, e.g.
MolecularInteractionImpl - Class in org.biopax.paxtools.impl.level3
MolecularInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.MolecularInteractionImpl
multipleCardinality - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter: This is false if there is a cardinality restriction of one on the property.

N

Named - Interface in org.biopax.paxtools.model.level3: Interface for all classes that can have names in BioPAX.
NamedImpl - Class in org.biopax.paxtools.impl.level3
NamedImpl() - Constructor for class org.biopax.paxtools.impl.level3.NamedImpl
namespaces - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
next() - Method in class org.biopax.paxtools.util.CompositeIterator
nextStepFilter - Static variable in class org.biopax.paxtools.controller.Fetcher: This property filter can be used to ignore 'nextStep' ('NEXT-STEP' in L2) property when fetching a sub-graph of child biopax elements, because using this property can eventually lead outside current pathway context into peer pathways, etc.
normalizeGenerics(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Converts generic simple physical entities, i.e., physical entities except Complexes that have not empty memberPhysicalEntity property, into equivalent physical entities with generic entity references (which have members); this is a better and less error prone way to model generic molecules in BioPAX L3.
normalizeNameSpaces(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler: Sets the flag used when exporting a BioPAX model to RDF/XML: true - to clean up current namespaces (e.g., those read from a file) and use defaults instead (prefixes: 'rdf', 'rdfs', 'owl', 'xsd')
NucleicAcid - Interface in org.biopax.paxtools.model.level3: Tagger interface for DNA and RNA
NucleicAcidImpl - Class in org.biopax.paxtools.impl.level3
NucleicAcidImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidImpl
NucleicAcidReference - Interface in org.biopax.paxtools.model.level3: Role interface for NucleicAcidReferences, namely DNA and RNA.
NucleicAcidReferenceImpl - Class in org.biopax.paxtools.impl.level3
NucleicAcidReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl
NucleicAcidRegionReference - Interface in org.biopax.paxtools.model.level3
NucleicAcidRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3
NucleicAcidRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

O

objectPropertiesOnlyFilter - Static variable in class org.biopax.paxtools.controller.Fetcher: A property filter to visit only biopax object type properties.
ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement> - Class in org.biopax.paxtools.controller: Provides an editor for all object value types, e.g.
ObjectPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.ObjectPropertyEditor: Full constructor.
Observable - Interface in org.biopax.paxtools.model.level3: User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
openControlledVocabulary - Interface in org.biopax.paxtools.model.level2
org.biopax.paxtools.command - package org.biopax.paxtools.command: This package contains classes for implementing undoable editing the model.
org.biopax.paxtools.controller - package org.biopax.paxtools.controller: This package contains various methods and algorithms for traversing and manipulating the model.
org.biopax.paxtools.converter - package org.biopax.paxtools.converter: This package contains a tools for upgrading BioPAX L1 and L2 to L3.
org.biopax.paxtools.impl - package org.biopax.paxtools.impl: This package contains the default BioPAX Model implementations.
org.biopax.paxtools.impl.level2 - package org.biopax.paxtools.impl.level2: This package contains the default implementation for BioPAX Level 2.
org.biopax.paxtools.impl.level3 - package org.biopax.paxtools.impl.level3: This package contains the default implementation for BioPAX Level 3.
org.biopax.paxtools.io - package org.biopax.paxtools.io: This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
org.biopax.paxtools.model - package org.biopax.paxtools.model: This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.
org.biopax.paxtools.model.level2 - package org.biopax.paxtools.model.level2: This package contains the interfaces that maps to the BioPAX level 2 specification.
org.biopax.paxtools.model.level3 - package org.biopax.paxtools.model.level3: This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
org.biopax.paxtools.util - package org.biopax.paxtools.util: This package contains various collections and utilities that is used by the other packages and modules of paxtools.
owl - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

P

parseValueFromString(String) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
parseValueFromString(String) - Method in class org.biopax.paxtools.controller.EnumeratedPropertyEditor
parseValueFromString(String) - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor
parseValueFromString(String) - Method in class org.biopax.paxtools.controller.StringPropertyEditor
PathAccessor - Class in org.biopax.paxtools.controller: This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.
PathAccessor(List<PropertyAccessor<? extends BioPAXElement, ?>>, BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.PathAccessor: Constructor for defining the access path with a list of accessors.
PathAccessor(String, BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.PathAccessor: Constructor for defining the access path via a XPath like string.
PathAccessor(String) - Constructor for class org.biopax.paxtools.controller.PathAccessor: This constructor defaults to BioPAX Level 3.
pathway - Interface in org.biopax.paxtools.model.level2
Pathway - Interface in org.biopax.paxtools.model.level3
pathwayComponent - Interface in org.biopax.paxtools.model.level2: Interface for pathway steps and processes
PathwayImpl - Class in org.biopax.paxtools.impl.level3
PathwayImpl() - Constructor for class org.biopax.paxtools.impl.level3.PathwayImpl
pathwayStep - Interface in org.biopax.paxtools.model.level2: This represents a set of pathway events.
PathwayStep - Interface in org.biopax.paxtools.model.level3: This represents a set of pathway events.
PathwayStepImpl - Class in org.biopax.paxtools.impl.level3
PathwayStepImpl() - Constructor for class org.biopax.paxtools.impl.level3.PathwayStepImpl: Constructor.
PhenotypeVocabulary - Interface in org.biopax.paxtools.model.level3
PhenotypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3
PhenotypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl
physicalEntity - Interface in org.biopax.paxtools.model.level2
PhysicalEntity - Interface in org.biopax.paxtools.model.level3
PhysicalEntityImpl - Class in org.biopax.paxtools.impl.level3
PhysicalEntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
physicalEntityParticipant - Interface in org.biopax.paxtools.model.level2
physicalInteraction - Interface in org.biopax.paxtools.model.level2
PositionStatusType - Enum in org.biopax.paxtools.model.level2
PositionStatusType - Enum in org.biopax.paxtools.model.level3
preparePep2PEIDMap(Model) - Method in class org.biopax.paxtools.converter.LevelUpgrader
PrimitivePropertyEditor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller: Provides a primitive (int, float, double) class compatible editor by extending the PropertyEditor.
PrimitivePropertyEditor(String, Method, Class<D>, Class<R>, 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
Process - Interface in org.biopax.paxtools.model.level3: Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
ProcessImpl - Class in org.biopax.paxtools.impl.level3
ProcessImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProcessImpl
property - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor: Local OWL name of the property
property - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple
PropertyAccessor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller: Allows generic access to the properties or a path of properties from a bean.
PropertyAccessorAdapter<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller: Adapter class for all property accessors.
PropertyAccessorAdapter(Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.PropertyAccessorAdapter
PropertyAddCommand - Class in org.biopax.paxtools.command
PropertyEditor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller
PropertyFilterBilinked - Interface in org.biopax.paxtools.controller: A generic interface for bidirectional property filter
PropertyRemoveCommand - Class in org.biopax.paxtools.command
PropertySetCommand<D extends BioPAXElement,R> - Class in org.biopax.paxtools.command
propertyToEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl: A map from property names to actual property editors.
protein - Interface in org.biopax.paxtools.model.level2
Protein - Interface in org.biopax.paxtools.model.level3
ProteinImpl - Class in org.biopax.paxtools.impl.level3
ProteinImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProteinImpl
ProteinReference - Interface in org.biopax.paxtools.model.level3: Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
ProteinReferenceImpl - Class in org.biopax.paxtools.impl.level3
ProteinReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProteinReferenceImpl
Provenance - Interface in org.biopax.paxtools.model.level3: Definition: The direct source of a pathway data or score.
ProvenanceImpl - Class in org.biopax.paxtools.impl.level3
ProvenanceImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProvenanceImpl
publicationXref - Interface in org.biopax.paxtools.model.level2
PublicationXref - Interface in org.biopax.paxtools.model.level3
PublicationXrefImpl - Class in org.biopax.paxtools.impl.level3
PublicationXrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.PublicationXrefImpl: Constructor.

R

range - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter: This is the Class representing the range of the property.
range - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple
rdf - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
rdfs - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
readNameSpaces() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method provides a hook for the implementers of this abstract class to set the namespaces of the model.
readNameSpaces() - Method in class org.biopax.paxtools.io.SimpleIOHandler
redo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand
redo() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand
redo() - Method in interface org.biopax.paxtools.command.Command
redo() - Method in class org.biopax.paxtools.command.CommandManager
redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand
redoAction() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand
redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AddCommand
redoAction() - Method in class org.biopax.paxtools.command.PropertyAddCommand
redoAction() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
redoAction() - Method in class org.biopax.paxtools.command.PropertySetCommand
redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.RemoveCommand
registerEditorsWithSubClasses(PropertyEditor, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.EditorMapImpl: This method registers an editor with sub classes - i.e.
registerModelClass(String) - Method in class org.biopax.paxtools.controller.EditorMapImpl: This method inserts the class into internal hashmaps and initializes the value collections.
RelationshipTypeVocabulary - Interface in org.biopax.paxtools.model.level3: Vocabulary for defining relationship Xref types.
RelationshipTypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3
RelationshipTypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl
relationshipXref - Interface in org.biopax.paxtools.model.level2
RelationshipXref - Interface in org.biopax.paxtools.model.level3: Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
RelationshipXrefImpl - Class in org.biopax.paxtools.impl.level3
RelationshipXrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.RelationshipXrefImpl
remove(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl
remove(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model: This method removes the given BioPAX Element from the model.
remove() - Method in class org.biopax.paxtools.util.CompositeIterator
removeAuthor(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
removeAuthor(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
removeAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
removeAvailability(String) - Method in class org.biopax.paxtools.impl.level3.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 interface org.biopax.paxtools.model.level3.Entity: This method removes the given text from the avaialability set.
removeCofactor(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
removeCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis
removeCofactor(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Catalysis: Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
RemoveCommand - Class in org.biopax.paxtools.command
RemoveCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.RemoveCommand
removeComment(String) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl
removeCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.Level2Element
removeComment(String) - Method in interface org.biopax.paxtools.model.level3.Level3Element: A textual comment about this individual.
removeComponent(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
removeComponent(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Complex: Defines the PhysicalEntity subunits of this complex.
removeCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex
removeComponentStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
removeComponentStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Complex: The stoichiometry of components in a complex.
removeConfidence(Score) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: Confidence in the containing instance.
removeCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence
removeConfidence(Score) - Method in interface org.biopax.paxtools.model.level3.Evidence: Confidence in the containing instance.
removeControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
removeCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control
removeControlled(Process) - Method in interface org.biopax.paxtools.model.level3.Control: The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
removeController(Controller) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
removeCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control
removeController(Controller) - Method in interface org.biopax.paxtools.model.level3.Control: The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
removeDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity: This method removes the given value from the DATA_SOURCE set.
removeDataSource(Provenance) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
removeDataSource(Provenance) - Method in interface org.biopax.paxtools.model.level3.Entity: This method removes the given value from the DATA_SOURCE set.
removeDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
removeDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
removeDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
removeDeltaG(DeltaG) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
removeDeltaG(DeltaG) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
removeDeltaH(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
removeDeltaH(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.
removeDeltaS(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
removeDeltaS(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.
removeEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
removeECNumber(String) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
removeECNumber(String) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
removeEntityFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
removeEntityFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.
removeEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
removeEntityReferenceType(EntityReferenceTypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Removes the given cv from the list of types
removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
removeEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process: This method remmoves the given evidence from this process.
removeEvidence(Evidence) - Method in interface org.biopax.paxtools.model.level3.Observable
removeEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence
removeEvidenceCode(EvidenceCodeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
removeEvidenceCode(EvidenceCodeVocabulary) - Method in interface org.biopax.paxtools.model.level3.Evidence: A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
removeEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence
removeEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
removeExperimentalFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
removeExperimentalFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: This method removes an experimental feature
removeExperimentalForm(ExperimentalForm) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl
removeExperimentalForm(ExperimentalForm) - Method in interface org.biopax.paxtools.model.level3.Evidence: Removes an experimental form.
removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm: Removes an experimental form description.
removeFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
removeFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
removeFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
removeINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
removeInteractionType(InteractionVocabulary) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
removeInteractionType(InteractionVocabulary) - Method in interface org.biopax.paxtools.model.level3.Interaction: Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".
removeKEQ(KPrime) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
removeKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
removeKEQ(KPrime) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction: This quantity is dimensionless and is usually a single number.
removeLeft(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
removeLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
removeLeft(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion: Removes a participant from the left side of the conversion interaction.
removeMemberEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
removeMemberEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.EntityReference: Removes the given entityReference from the member list
removeMemberFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
removeMemberFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature: An entity feature that belongs to this homology grouping.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
removeMemberPhysicalEntity(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
removeMethod - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor: 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.level3.NamedImpl
removeNAME(String) - Method in interface org.biopax.paxtools.model.level2.dataSource
removeName(String) - Method in interface org.biopax.paxtools.model.level3.Named: This method removes the given value from the name set.
removeNEXT_STEP(pathwayStep) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
removeNextStep(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
removeNextStep(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.PathwayStep
removeNotFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
removeNotFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity
removeObjects(Set<BioPAXElement>) - Method in class org.biopax.paxtools.command.CommandManager
removeObjectsIfDangling(Model, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils: Iteratively removes "dangling" elements of given type and its sub-types, e.g.
removeParticipant(Entity) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
removeParticipant(Entity) - Method in interface org.biopax.paxtools.model.level3.Interaction: The entities that participate in this interaction.
removePARTICIPANTS(InteractionParticipant) - Method in interface org.biopax.paxtools.model.level2.interaction
removeParticipantStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
removeParticipantStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Conversion: This method removes a stoichiometry for one of the participants of this conversion.
removePATHWAY_COMPONENTS(pathwayComponent) - Method in interface org.biopax.paxtools.model.level2.pathway
removePathwayComponent(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
removePathwayComponent(Process) - Method in interface org.biopax.paxtools.model.level3.Pathway
removePathwayOrder(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
removePathwayOrder(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.Pathway
removePHYSICAL_ENTITYof(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.physicalEntity
removeProduct(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
removeProduct(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
removeProperty(BioPAXElement, PropertyEditor, Object) - Method in class org.biopax.paxtools.command.CommandManager
removeRegionType(SequenceRegionVocabulary) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
removeRegionType(SequenceRegionVocabulary) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
removeRight(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
removeRIGHT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion
removeRight(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion: Removes a participant from the right side of the conversion interaction.
removeSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
removeSource(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
removeSOURCE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
removeSource(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
removeSTEP_INTERACTIONS(process) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
removeStepProcess(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
removeStepProcess(Process) - Method in interface org.biopax.paxtools.model.level3.PathwayStep
removeSTRUCTURE(chemicalStructure) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
removeSubRegion(NucleicAcidRegionReference) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl
removeSubRegion(NucleicAcidRegionReference) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference
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
removeTerm(String) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
removeTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
removeTerm(String) - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary
removeUrl(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
removeURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
removeUrl(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
removeValueFromBean(R, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
removeValueFromBean(Set<R>, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
removeValueFromBean(R, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor: Removes the value from the bean using the default removeMethod, if such method is defined (i.e., it's a multiple cardinality property), otherwise sets unknown value using PropertyEditor.setValueToBean(Object, org.biopax.paxtools.model.BioPAXElement) (but only if )
removeValueFromBean(Set<R>, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor: Removes the values from the bean using the PropertyEditor.removeValueFromBean(Object, org.biopax.paxtools.model.BioPAXElement) for each value in the set.
removeXref(Xref) - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl
removeXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable
removeXref(Xref) - Method in interface org.biopax.paxtools.model.level3.XReferrable
repair() - Method in class org.biopax.paxtools.impl.ModelImpl: This implementation "repairs" the model without unnecessarily copying objects: - recursively adds lost "children" (not null object property values for which Model.contains(BioPAXElement) returns False) - updates object properties (should refer to model's elements)
repair() - Method in interface org.biopax.paxtools.model.Model: Attempts to repair the model, i.e., make it self-consistent, integral.
replace(Model, Map<? extends BioPAXElement, ? extends BioPAXElement>) - Static method in class org.biopax.paxtools.controller.ModelUtils: Replaces BioPAX elements in the model with ones from the map, updates corresponding BioPAX object references.
replace(BioPAXElement, BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl: It does not automatically replace or clean up the old element's object properties, therefore, some child elements may become "dangling" if they were used by the replaced element only.
replace(BioPAXElement, BioPAXElement) - Method in interface org.biopax.paxtools.model.Model: Replaces existing BioPAX element with another one, of the same or possibly equivalent type, and updates all the affected references to it (object properties).
replaceEquivalentFeatures(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: This method iterates over the features in a model and tries to find equivalent objects and merges them.
reset() - Method in class org.biopax.paxtools.controller.AbstractTraverser: Clears the internal set of traversed biopax objects.
reset(InputStream) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
reset(InputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler
resetEditorMap() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g.
resetEditorMap() - Method in class org.biopax.paxtools.io.SimpleIOHandler: This method resets the editor map.
resetLevel(BioPAXLevel, BioPAXFactory) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Updates the level and factory for this I/O (final - because used in the constructor)
resourceFixes(BioPAXElement, Object) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: This method currently only fixes reusedPEPs if the option is set.
ReusedPEPHelper - Class in org.biopax.paxtools.controller: This class contains methods for handling reused PEPs - a historically common problem in BioPAX L2 exports.
ReusedPEPHelper(Model) - Constructor for class org.biopax.paxtools.controller.ReusedPEPHelper
rna - Interface in org.biopax.paxtools.model.level2
Rna - Interface in org.biopax.paxtools.model.level3
RnaImpl - Class in org.biopax.paxtools.impl.level3
RnaImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaImpl
RnaReference - Interface in org.biopax.paxtools.model.level3
RnaReferenceImpl - Class in org.biopax.paxtools.impl.level3
RnaReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaReferenceImpl
RnaRegion - Interface in org.biopax.paxtools.model.level3: Definition: A region on a RNA molecule.
RnaRegionImpl - Class in org.biopax.paxtools.impl.level3
RnaRegionImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaRegionImpl
RnaRegionReference - Interface in org.biopax.paxtools.model.level3: A RNA region reference
RnaRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3
RnaRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl

S

Score - Interface in org.biopax.paxtools.model.level3: Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method.
ScoreImpl - Class in org.biopax.paxtools.impl.level3
ScoreImpl() - Constructor for class org.biopax.paxtools.impl.level3.ScoreImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: Answers whether two Evidence objects are semantically equivalent.
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.UnificationXrefImpl
semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
seqDbStartsWithOrEquals(String) - Method in class org.biopax.paxtools.controller.IdFetcher: Set to prefer collecting gene/sequence IDs of such Xrefs where the db starts with or equals given string, ignoring case.
sequenceEntity - Interface in org.biopax.paxtools.model.level2: User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
SequenceEntity - Interface in org.biopax.paxtools.model.level3: Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
SequenceEntityReference - Interface in org.biopax.paxtools.model.level3: Tagger interface for protein, dna and rna entities
SequenceEntityReferenceImpl - Class in org.biopax.paxtools.impl.level3
SequenceEntityReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
sequenceFeature - Interface in org.biopax.paxtools.model.level2
sequenceInterval - Interface in org.biopax.paxtools.model.level2
SequenceInterval - Interface in org.biopax.paxtools.model.level3
SequenceIntervalImpl - Class in org.biopax.paxtools.impl.level3
SequenceIntervalImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
sequenceLocation - Interface in org.biopax.paxtools.model.level2
SequenceLocation - Interface in org.biopax.paxtools.model.level3: Definition: A location on a nucleotide or amino acid sequence.
SequenceLocationImpl - Class in org.biopax.paxtools.impl.level3
SequenceLocationImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceLocationImpl: Constructor.
SequenceModificationVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
SequenceModificationVocabularyImpl - Class in org.biopax.paxtools.impl.level3
SequenceModificationVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl
sequenceParticipant - Interface in org.biopax.paxtools.model.level2
SequenceRegionVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
SequenceRegionVocabularyImpl - Class in org.biopax.paxtools.impl.level3
SequenceRegionVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl
sequenceSite - Interface in org.biopax.paxtools.model.level2
SequenceSite - Interface in org.biopax.paxtools.model.level3
SequenceSiteImpl - Class in org.biopax.paxtools.impl.level3
SequenceSiteImpl() - Constructor for class org.biopax.paxtools.impl.level3.SequenceSiteImpl
setAbsoluteRegion(SequenceLocation) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
setAbsoluteRegion(SequenceLocation) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference
setAddDependencies(boolean) - Method in class org.biopax.paxtools.impl.ModelImpl
setAddDependencies(boolean) - Method in interface org.biopax.paxtools.model.Model: When set to false, the model will not check for the dependent objects of a newly added object.
setAUTHORS(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setAVAILABILITY(Set<String>) - Method in interface org.biopax.paxtools.model.level2.entity: This method overrides existing set with the new set.
setBindsTo(BindingFeature) - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl: This method will set the paired binding feature that binds to this feature.
setBindsTo(BindingFeature) - Method in interface org.biopax.paxtools.model.level3.BindingFeature: A binding feature represents a "half" of the bond between two entities.
setCatalysisDirection(CatalysisDirectionType) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
setCatalysisDirection(CatalysisDirectionType) - Method in interface org.biopax.paxtools.model.level3.Catalysis: This property represents the direction of this catalysis under all physiological conditions if there is one.
setCellType(CellVocabulary) - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
setCELLTYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.bioSource
setCellType(CellVocabulary) - Method in interface org.biopax.paxtools.model.level3.BioSource: A cell type, e.g.
setCELLULAR_LOCATION(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
setCellularLocation(CellularLocationVocabulary) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
setCellularLocation(CellularLocationVocabulary) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity: A cellular location, e.g.
setCHEMICAL_FORMULA(String) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
setChemicalFormula(String) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
setChemicalFormula(String) - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
setCOFACTOR(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.catalysis
setComment(Set<String>) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl
setCOMMENT(Set<String>) - Method in interface org.biopax.paxtools.model.level2.Level2Element
setComponent(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
setCOMPONENTS(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.complex
setCOMPONENTSof(complex) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
setComponentStoichiometry(Set<Stoichiometry>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
setCONFIDENCE(Set<confidence>) - Method in interface org.biopax.paxtools.model.level2.evidence
setCONFIDENCE_VALUE(String) - Method in interface org.biopax.paxtools.model.level2.confidence: The value of the confidence measure.
setCONTROL_TYPE(ControlType) - Method in interface org.biopax.paxtools.model.level2.control
setCONTROLLED(Set<process>) - Method in interface org.biopax.paxtools.model.level2.control
setCONTROLLER(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.control
setControlType(ControlType) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
setControlType(ControlType) - Method in interface org.biopax.paxtools.model.level3.Control: Sets the controlType BioPAX property value, which fefines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.
setConversionDirection(ConversionDirectionType) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
setConversionDirection(ConversionDirectionType) - Method in interface org.biopax.paxtools.model.level3.Conversion: This property represents the direction of the reaction.
setDATA_SOURCE(Set<dataSource>) - Method in interface org.biopax.paxtools.model.level2.entity: This method overrides existing set with the new set.
setDataSource(Set<Provenance>) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
setDb(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
setDB(String) - Method in interface org.biopax.paxtools.model.level2.xref
setDb(String) - Method in interface org.biopax.paxtools.model.level3.Xref
setDB_VERSION(String) - Method in interface org.biopax.paxtools.model.level2.xref
setDbVersion(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
setDbVersion(String) - Method in interface org.biopax.paxtools.model.level3.Xref
setDELTA_G(Set<deltaGprimeO>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setDELTA_G_PRIME_O(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
setDELTA_H(Set<Double>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setDELTA_S(Set<Double>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setDeltaG(Set<DeltaG>) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
setDeltaGPrime0(float) - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl
setDeltaGPrime0(float) - Method in interface org.biopax.paxtools.model.level3.DeltaG: For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.
setDIRECTION(Direction) - Method in interface org.biopax.paxtools.model.level2.catalysis
setDisplayName(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
setDisplayName(String) - Method in interface org.biopax.paxtools.model.level3.Named: 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.
setEC_NUMBER(Set<String>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setEditorMap(EditorMap) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
setEditorMap(EditorMap) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
setEntityFeatureOf(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.DnaImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.DnaRegionImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.ProteinImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.RnaImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.RnaRegionImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl
setEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.SimplePhysicalEntity: Reference entity for this physical entity.
SetEquivalenceChecker - Class in org.biopax.paxtools.util: This class performs set operations based on equivalence.
SetEquivalenceChecker() - Constructor for class org.biopax.paxtools.util.SetEquivalenceChecker
setEVIDENCE(Set<evidence>) - Method in interface org.biopax.paxtools.model.level2.process
setEVIDENCE_CODE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.evidence
setEXPERIMENTAL_FORM(Set<experimentalForm>) - Method in interface org.biopax.paxtools.model.level2.evidence
setEXPERIMENTAL_FORM_TYPE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
setExperimentalFormEntity(Entity) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
setExperimentalFormEntity(Entity) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm
setFactory(BioPAXFactory) - Method in class org.biopax.paxtools.impl.ModelImpl
setFactory(BioPAXFactory) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
setFactory(BioPAXFactory) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
setFactory(BioPAXFactory) - Method in interface org.biopax.paxtools.model.Model: This method sets the factory this model will use for creating BioPAX objects.
setFEATURE_LOCATION(Set<sequenceLocation>) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
setFEATURE_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature
setFeatureLocation(SequenceLocation) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setFeatureLocation(SequenceLocation) - Method in interface org.biopax.paxtools.model.level3.EntityFeature: Location of the feature on the sequence of the interactor.
setFeatureLocationType(SequenceRegionVocabulary) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setFeatureLocationType(SequenceRegionVocabulary) - Method in interface org.biopax.paxtools.model.level3.EntityFeature: A controlled vocabulary term describing the type of the sequence location such as C-Terminal or SH2 Domain.
setId(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
setID(String) - Method in interface org.biopax.paxtools.model.level2.xref
setId(String) - Method in interface org.biopax.paxtools.model.level3.Xref
setID_VERSION(String) - Method in interface org.biopax.paxtools.model.level2.xref
setIdVersion(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
setIdVersion(String) - Method in interface org.biopax.paxtools.model.level3.Xref
setINTERACTION_TYPE(Set<openControlledVocabulary>) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction
setInteractionScore(Score) - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
setInteractionScore(Score) - Method in interface org.biopax.paxtools.model.level3.GeneticInteraction
setIntraMolecular(Boolean) - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl
setIntraMolecular(Boolean) - Method in interface org.biopax.paxtools.model.level3.BindingFeature: IntraMolecular flag is true iff this binding feature represents a bond within the same molecule, for example a disulfide bond within the same molecule.
setInverseOnly(boolean) - Method in class org.biopax.paxtools.controller.TraverserBilinked
setIONIC_STRENGTH(float) - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO
setIONIC_STRENGTH(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
setIonicStrength(float) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
setIonicStrength(float) - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant: The ionic strength is defined as half of the total sum of the concentration (ci) of every ionic species (i) in the solution times the square of its charge (zi).
setK_PRIME(float) - Method in interface org.biopax.paxtools.model.level2.kPrime
setKEQ(Set<kPrime>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setKPrime(float) - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl
setKPrime(float) - Method in interface org.biopax.paxtools.model.level3.KPrime: The apparent equilibrium constant K'.
setLEFT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion
setMethod - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor: This variable stores the method to invoke for setting a property to the to the given value.
setModificationType(SequenceModificationVocabulary) - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl
setModificationType(SequenceModificationVocabulary) - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
setModificationType(SequenceModificationVocabulary) - Method in interface org.biopax.paxtools.model.level3.ModificationFeature
setMOLECULAR_WEIGHT(double) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
setMolecularWeight(float) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
setMolecularWeight(float) - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
setName(Set<String>) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
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(Set<String>) - Method in interface org.biopax.paxtools.model.level3.Named: This method is reserved for batch operations and should not be used for normal use.
setNEXT_STEP(Set<pathwayStep>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
setNormalizeModels(boolean) - Method in class org.biopax.paxtools.controller.Integrator: Fixes some of the known Open Controlled Vocabullary issues in the models.
setOnlyMapping(boolean) - Method in class org.biopax.paxtools.controller.Integrator: Enables/disables integration.
setOrganism(BioSource) - Method in class org.biopax.paxtools.impl.level3.GeneImpl
setOrganism(BioSource) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
setOrganism(BioSource) - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
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 interface org.biopax.paxtools.model.level3.Gene: An organism, e.g.
setOrganism(BioSource) - Method in interface org.biopax.paxtools.model.level3.Pathway: An organism, e.g.
setOrganism(BioSource) - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference: An organism, e.g.
setParticipant(Set<Entity>) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
setPARTICIPANT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
setPARTICIPANTS(Set<InteractionParticipant>) - Method in interface org.biopax.paxtools.model.level2.interaction
setPATHWAY_COMPONENTS(Set<pathwayComponent>) - Method in interface org.biopax.paxtools.model.level2.pathway
setPathwayOrderOf(Pathway) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
setPatoData(String) - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl
setPatoData(String) - Method in interface org.biopax.paxtools.model.level3.PhenotypeVocabulary
setPh(float) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
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 interface org.biopax.paxtools.model.level3.ChemicalConstant: A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.
setPhenotype(PhenotypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl
setPhenotype(PhenotypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.GeneticInteraction
setPHYSICAL_ENTITY(physicalEntity) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
setPhysicalEntity(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
setPhysicalEntity(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Stoichiometry
setPMg(float) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
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 interface org.biopax.paxtools.model.level3.ChemicalConstant
setPOSITION_STATUS(PositionStatusType) - Method in interface org.biopax.paxtools.model.level2.sequenceSite
setPositionStatus(PositionStatusType) - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
setPositionStatus(PositionStatusType) - Method in interface org.biopax.paxtools.model.level3.SequenceSite
setProduct(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
setProvider(BPCollections.CollectionProvider) - Method in enum org.biopax.paxtools.util.BPCollections: Sets a specific BPCollections.CollectionProvider (for multiple-cardinality BioPAX properties)
setRangeRestriction(Map<Class<? extends BioPAXElement>, Set<Class<? extends BioPAXElement>>>) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor: This method sets all range restrictions.
setRELATIONSHIP_TYPE(String) - Method in interface org.biopax.paxtools.model.level2.relationshipXref
setRelationshipType(RelationshipTypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl
setRelationshipType(RelationshipTypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.RelationshipXref: Definition:A controlled vocabulary term that defines the type of relationship that this xref defines.
setRIGHT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion
setScoreSource(Provenance) - Method in class org.biopax.paxtools.impl.level3.ScoreImpl
setScoreSource(Provenance) - Method in interface org.biopax.paxtools.model.level3.Score: This property defines the source of the scoring methodology.
setScoresOver(double) - Method in class org.biopax.paxtools.controller.Integrator: A score between two conversions is in the interval (0, 1].
setSelfRemove(boolean) - Method in class org.biopax.paxtools.controller.Integrator: Enables removal of elements from the target if they are contained both in source and target, and have a match with another conversion.
setSequence(String) - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl
setSEQUENCE(String) - Method in interface org.biopax.paxtools.model.level2.sequenceEntity
setSequence(String) - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference: Polymer sequence in uppercase letters.
setSEQUENCE_FEATURE_LIST(Set<sequenceFeature>) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant
setSEQUENCE_INTERVAL_BEGIN(sequenceSite) - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
setSEQUENCE_INTERVAL_END(sequenceSite) - Method in interface org.biopax.paxtools.model.level2.sequenceInterval
setSEQUENCE_POSITION(int) - Method in interface org.biopax.paxtools.model.level2.sequenceSite
setSequenceIntervalBegin(SequenceSite) - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
setSequenceIntervalBegin(SequenceSite) - Method in interface org.biopax.paxtools.model.level3.SequenceInterval
setSequenceIntervalEnd(SequenceSite) - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
setSequenceIntervalEnd(SequenceSite) - Method in interface org.biopax.paxtools.model.level3.SequenceInterval
setSequencePosition(int) - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
setSequencePosition(int) - Method in interface org.biopax.paxtools.model.level3.SequenceSite
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
setSkipSubPathways(boolean) - Method in class org.biopax.paxtools.controller.Completer: Use this property to optionally skip (if true) traversing into sub-pathways; i.e., when the value of BioPAX property 'pathwayComponent' or 'controlled' is a pathway.
setSkipSubPathways(boolean) - Method in class org.biopax.paxtools.controller.Fetcher: Use this property to optionally skip (if true) traversing into sub-pathways; i.e., when a biopax property, such as pathwayComponent or controlled, value is a Pathway.
setSOURCE(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setSpontaneous(Boolean) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
setSPONTANEOUS(SpontaneousType) - Method in interface org.biopax.paxtools.model.level2.conversion
setSpontaneous(Boolean) - Method in interface org.biopax.paxtools.model.level3.Conversion: Specifies whether a conversion occurs spontaneously or not.
setStandardName(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
setStandardName(String) - Method in interface org.biopax.paxtools.model.level3.Named: The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.
setSTEP_INTERACTIONS(Set<process>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
setStepConversion(Conversion) - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
setStepConversion(Conversion) - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep: This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion.
setStepDirection(StepDirection) - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl
setStepDirection(StepDirection) - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep: This property can be used for annotating direction of enzymatic activity.
setSTOICHIOMETRIC_COEFFICIENT(double) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
setStoichiometricCoefficient(float) - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl
setStoichiometricCoefficient(float) - Method in interface org.biopax.paxtools.model.level3.Stoichiometry: Sets the stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.
setStructure(ChemicalStructure) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
setSTRUCTURE(Set<chemicalStructure>) - Method in interface org.biopax.paxtools.model.level2.smallMolecule
setStructure(ChemicalStructure) - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference
setSTRUCTURE_DATA(String) - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
setSTRUCTURE_FORMAT(String) - Method in interface org.biopax.paxtools.model.level2.chemicalStructure
setStructureData(String) - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
setStructureData(String) - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure: This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI.
setStructureFormat(StructureFormatType) - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl
setStructureFormat(StructureFormatType) - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure: This property specifies which format is used to define chemical structure.
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
setTAXON_XREF(unificationXref) - Method in interface org.biopax.paxtools.model.level2.bioSource
setTemperature(float) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl
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 interface org.biopax.paxtools.model.level3.ChemicalConstant
setTemplate(NucleicAcid) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
setTemplate(NucleicAcid) - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
setTemplateDirection(TemplateDirectionType) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
setTemplateDirection(TemplateDirectionType) - Method in interface org.biopax.paxtools.model.level3.TemplateReaction
setTerm(Set<String>) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
setTERM(Set<String>) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary
setThreshold(Double) - Method in class org.biopax.paxtools.controller.Integrator: Sets the threshold value (the smallest score for integrating two conversions)
setTissue(TissueVocabulary) - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
setTISSUE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.bioSource
setTissue(TissueVocabulary) - Method in interface org.biopax.paxtools.model.level3.BioSource: An external controlled vocabulary of tissue types.
setTitle(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
setTITLE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setTitle(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
setURL(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setValue(String) - Method in class org.biopax.paxtools.impl.level3.ScoreImpl
setValue(String) - Method in interface org.biopax.paxtools.model.level3.Score: This property defines the value of the score.
setValueToBean(R, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
setValueToBean(Set<R>, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
setValueToBean(R, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor: Sets the value to the bean using the default setMethod if value is not null.
setValueToBean(Set<R>, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor
setVisitor(Visitor) - Method in class org.biopax.paxtools.controller.Traverser
setXmlBase(String) - Method in class org.biopax.paxtools.impl.ModelImpl
setXmlBase(String) - Method in interface org.biopax.paxtools.model.Model: Sets the xml:base to use when exporting a BioPAX model.
setXref(Set<Xref>) - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl
setXREF(Set<xref>) - Method in interface org.biopax.paxtools.model.level2.XReferrable
setYear(int) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
setYEAR(int) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setYear(int) - Method in interface org.biopax.paxtools.model.level3.PublicationXref
ShallowCopy - Class in org.biopax.paxtools.controller: "Clones" a BioPAX element - using direct properties and dependent children only.
ShallowCopy(EditorMap) - Constructor for class org.biopax.paxtools.controller.ShallowCopy: Deprecated.
use Level based constructor instead.
ShallowCopy(BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.ShallowCopy: BioPAXLevel based constructor
ShallowCopy() - Constructor for class org.biopax.paxtools.controller.ShallowCopy: Empty constructos that defaults to BioPAX L3.
shortenUri(String, String) - Static method in class org.biopax.paxtools.controller.ModelUtils: Creates a short URI from the URI, given the xml:base.
SimpleEditorMap - Enum in org.biopax.paxtools.controller: Provides a simple editor map for a level with a given factory.
SimpleIOHandler - Class in org.biopax.paxtools.io: Simple BioPAX reader/writer.
SimpleIOHandler() - Constructor for class org.biopax.paxtools.io.SimpleIOHandler: Basic constructor, defaults to Level 3 and default BioPAXFactory
SimpleIOHandler(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.SimpleIOHandler: Basic constructor, defaults to level.defaultFactory
SimpleIOHandler(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.SimpleIOHandler: Full constructor
SimpleIOHandler.Triple - Class in org.biopax.paxtools.io
SimpleMerger - Class in org.biopax.paxtools.controller: A "simple" BioPAX merger, a utility class to merge 'source' BioPAX models or a set of elements into the target model, using (URI) identity only.
SimpleMerger(EditorMap) - Constructor for class org.biopax.paxtools.controller.SimpleMerger
SimpleMerger(EditorMap, Filter<BioPAXElement>) - Constructor for class org.biopax.paxtools.controller.SimpleMerger
SimplePhysicalEntity - Interface in org.biopax.paxtools.model.level3: Tagger interface for non-complex physical entities
SimplePhysicalEntityImpl - Class in org.biopax.paxtools.impl.level3
SimplePhysicalEntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
SimplePropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller
SimplePropertyAccessor(Class<D>, Class<R>, boolean, Method) - Constructor for class org.biopax.paxtools.controller.SimplePropertyAccessor
size() - Method in class org.biopax.paxtools.util.AbstractFilterSet: This size operation runs on O(n) and should be avoided for large sets.
size() - Method in class org.biopax.paxtools.util.BiopaxSafeSet
smallMolecule - Interface in org.biopax.paxtools.model.level2
SmallMolecule - Interface in org.biopax.paxtools.model.level3
SmallMoleculeImpl - Class in org.biopax.paxtools.impl.level3
SmallMoleculeImpl() - Constructor for class org.biopax.paxtools.impl.level3.SmallMoleculeImpl
SmallMoleculeReference - Interface in org.biopax.paxtools.model.level3
SmallMoleculeReferenceImpl - Class in org.biopax.paxtools.impl.level3
SmallMoleculeReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl
SpontaneousType - Enum in org.biopax.paxtools.model.level2
stateCode() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
StepDirection - Enum in org.biopax.paxtools.model.level3: Catalysis direction controlled vocabulary
Stoichiometry - Interface in org.biopax.paxtools.model.level3: Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
StoichiometryImpl - Class in org.biopax.paxtools.impl.level3
StoichiometryImpl() - Constructor for class org.biopax.paxtools.impl.level3.StoichiometryImpl
StringPropertyEditor<D extends BioPAXElement> - Class in org.biopax.paxtools.controller: Provides an String class compatible editor by extending the PropertyEditor.
StringPropertyEditor(String, Method, Class<D>, boolean) - Constructor for class org.biopax.paxtools.controller.StringPropertyEditor
StructureFormatType - Enum in org.biopax.paxtools.model.level3
subgraphContains(BioPAXElement, String, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.Fetcher: Iterates over child objects of the given biopax element, using BioPAX object-type properties, until the element with specified URI and class (including its sub-classes).

T

TemplateDirectionType - Enum in org.biopax.paxtools.model.level3: TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
TemplateReaction - Interface in org.biopax.paxtools.model.level3
TemplateReactionImpl - Class in org.biopax.paxtools.impl.level3
TemplateReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.TemplateReactionImpl
TemplateReactionRegulation - Interface in org.biopax.paxtools.model.level3
TemplateReactionRegulationImpl - Class in org.biopax.paxtools.impl.level3
TemplateReactionRegulationImpl() - Constructor for class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl
TissueVocabulary - Interface in org.biopax.paxtools.model.level3: Definition: A reference to the BRENDA
TissueVocabularyImpl - Class in org.biopax.paxtools.impl.level3
TissueVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.TissueVocabularyImpl
toString() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
toString() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
toString() - Method in interface org.biopax.paxtools.controller.PropertyEditor
toString() - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor
toString() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
toString() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl
toString() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl
toString() - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl
toString() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl
toString() - Method in class org.biopax.paxtools.impl.level3.ProvenanceImpl
toString() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl
toString() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
toString() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
toString() - Method in class org.biopax.paxtools.io.SimpleIOHandler.Triple
toString() - Method in enum org.biopax.paxtools.model.level2.Direction
TransitivePropertyAccessor<R extends BioPAXElement,D extends R> - Class in org.biopax.paxtools.controller: This class is a transitive decorator for PropertyAccessors.
transport - Interface in org.biopax.paxtools.model.level2
Transport - Interface in org.biopax.paxtools.model.level3
TransportImpl - Class in org.biopax.paxtools.impl.level3
TransportImpl() - Constructor for class org.biopax.paxtools.impl.level3.TransportImpl
transportWithBiochemicalReaction - Interface in org.biopax.paxtools.model.level2
TransportWithBiochemicalReaction - Interface in org.biopax.paxtools.model.level3
TransportWithBiochemicalReactionImpl - Class in org.biopax.paxtools.impl.level3
TransportWithBiochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl
traverse(D, Model) - Method in class org.biopax.paxtools.controller.AbstractTraverser
traverse(D, Model) - Method in class org.biopax.paxtools.controller.Traverser: Traverse and visit Visitor all properties of the element.
traverse(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.TraverserBilinked
traverseElements(BioPAXElement, Model, PropertyEditor<?, ?>, Set<?>) - Method in class org.biopax.paxtools.controller.Traverser
traverser - Variable in class org.biopax.paxtools.controller.Completer
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, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.Traverser: The full constructor.
TraverserBilinked - Class in org.biopax.paxtools.controller: A bi-directional BioPAX properties traverser.
TraverserBilinked(EditorMap, Visitor, PropertyFilterBilinked...) - Constructor for class org.biopax.paxtools.controller.TraverserBilinked: Constructor.

U

undo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand
undo() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand
undo() - Method in interface org.biopax.paxtools.command.Command
undo() - Method in class org.biopax.paxtools.command.CommandManager
undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand
undoAction() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand
undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AddCommand
undoAction() - Method in class org.biopax.paxtools.command.PropertyAddCommand
undoAction() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand
undoAction() - Method in class org.biopax.paxtools.command.PropertySetCommand
undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.RemoveCommand
unificationXref - Interface in org.biopax.paxtools.model.level2
UnificationXref - Interface in org.biopax.paxtools.model.level3: Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity.
UnificationXrefImpl - Class in org.biopax.paxtools.impl.level3
UnificationXrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.UnificationXrefImpl
UnionPropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller: In OWL a single property can have multiple domains.
UnionPropertyAccessor(Set<PropertyAccessor<? extends D, ? extends R>>, Class<D>) - Constructor for class org.biopax.paxtools.controller.UnionPropertyAccessor
UNKNOWN_DOUBLE - Static variable in interface org.biopax.paxtools.model.BioPAXElement: Constant for representing unknown doubles.
UNKNOWN_FLOAT - Static variable in interface org.biopax.paxtools.model.BioPAXElement: Constant for representing unknown floats.
UNKNOWN_INT - Static variable in interface org.biopax.paxtools.model.BioPAXElement: Constant for representing unknown integers.
updateUri(Model, BioPAXElement, String) - Static method in class org.biopax.paxtools.controller.ModelUtils: Replaces the URI of a BioPAX object in the Model using java reflection.
useNameWhenNoDbMatch(boolean) - Method in class org.biopax.paxtools.controller.IdFetcher: Set the flag to use the entity reference's names when no desired ID type can be found (none of xref.db matched before, or there're no xrefs at all).
utilityClass - Interface in org.biopax.paxtools.model.level2
UtilityClass - Interface in org.biopax.paxtools.model.level3

V

valueOf(String) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap: Returns the enum constant of this type with the specified name.
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.level3.CatalysisDirectionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.ControlType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.ConversionDirectionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.PositionStatusType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.StepDirection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.StructureFormatType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.TemplateDirectionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.util.BPCollections: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.BioPAXLevel: Returns an array containing the constants of this enum type, in the order they are 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 are 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 are 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 are 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 are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.CatalysisDirectionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.ControlType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.ConversionDirectionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.PositionStatusType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.StepDirection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.StructureFormatType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.model.level3.TemplateDirectionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.util.BPCollections: Returns an array containing the constants of this enum type, in the order they are declared.
visit(Object, BioPAXElement, Model, PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.AbstractTraverser: This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.
visit(BioPAXElement, Object, Model, PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.AbstractTraverser: Calls the protected abstract method visit that is to be implemented in subclasses of this abstract class.
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Cloner
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Completer
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Merger: Checks whether model contains bpe element, and if it does, then it updates the value of the equivalent element for bpe by using the specific editor.
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.ShallowCopy: An implementation of this method should perform a BioPAX element and editor dependent operation on the model.
visit(BioPAXElement, Object, Model, PropertyEditor<?, ?>) - Method in interface org.biopax.paxtools.controller.Visitor: An implementation of this method should perform a BioPAX element and editor dependent operation on the model.
visit(Object, BioPAXElement, Model, PropertyEditor) - Method in class org.biopax.paxtools.converter.LevelUpgrader
visited - Variable in class org.biopax.paxtools.controller.AbstractTraverser
visitor - Variable in class org.biopax.paxtools.controller.Traverser
Visitor - Interface in org.biopax.paxtools.controller: Basic visitor interface for classes using Traverser.

W

writeObject(Writer, BioPAXElement) - Method in class org.biopax.paxtools.io.SimpleIOHandler: Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete).
writeRead(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Cuts the BioPAX model off other models and BioPAX objects by essentially performing write/read to/from OWL.

X

xref - Interface in org.biopax.paxtools.model.level2
Xref - Interface in org.biopax.paxtools.model.level3
XReferrable - Interface in org.biopax.paxtools.model.level2
XReferrable - Interface in org.biopax.paxtools.model.level3
XReferrableImpl - Class in org.biopax.paxtools.impl.level3: This class helps with managing the bidirectional xref links.
XReferrableImpl() - Constructor for class org.biopax.paxtools.impl.level3.XReferrableImpl: Default constructor.
XrefImpl - Class in org.biopax.paxtools.impl.level3
XrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.XrefImpl: Constructor.
xsd - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

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