Index (Paxtools 4.3.1 API)

A B C D E F G H I J K L M N O P Q 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
AbstractEdge - Class in org.biopax.paxtools.query.model: The base class for an edge in the traversed graph.
AbstractEdge(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.model.AbstractEdge: Edges should know their source and target nodes, and their graph.
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
AbstractGraph - Class in org.biopax.paxtools.query.model: Adapter class for a graph that is queried.
AbstractGraph() - Constructor for class org.biopax.paxtools.query.model.AbstractGraph: Empty constructor that initializes the object map.
AbstractNode - Class in org.biopax.paxtools.query.model
AbstractNode(Graph) - Constructor for class org.biopax.paxtools.query.model.AbstractNode: Constructor with the owner graph.
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.
AbstractSIFMiner - Class in org.biopax.paxtools.pattern.miner: Base class for SIF Miners.
AbstractSIFMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Constructor with interaction type.
AbstractSIFMiner(SIFType, String, String) - Constructor for class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs.
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(PathAccessor, Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).
access(E) - Method in class org.biopax.paxtools.util.AccessibleSet
access(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper
access1(Complex) - Method in class org.biopax.paxtools.examples.Tutorial
access2(Complex) - Method in class org.biopax.paxtools.examples.Tutorial
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
actChange(boolean, Map<EntityReference, Set<ModificationFeature>>, Map<EntityReference, Set<ModificationFeature>>) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for the activity of an EntityReference is changed through a Conversion.
actionPerformed(ActionEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog: Performs interactive operations.
ActivityConstraint - Class in org.biopax.paxtools.pattern.constraint: Checks if the PhysicalEntity controls anything.
ActivityConstraint(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.ActivityConstraint: Constructor with the desired activity.
ActivityModificationChangeConstraint - Class in org.biopax.paxtools.pattern.constraint: This is a very specialized constraint that checks if two PhysicalEntity of the same EntityReference have differential features, such that we can predict an activity change based on gain or loss of these features.
ActivityModificationChangeConstraint(boolean, Map<EntityReference, Set<ModificationFeature>>, Map<EntityReference, Set<ModificationFeature>>) - Constructor for class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Constructor with the desired change and maps to activating and inactivating features,
ActivityNetworkAnalyzer - Class in org.biopax.paxtools.io.sif.level3: Deprecated.
ActivityNetworkAnalyzer() - Constructor for class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.
add(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl
add(SimpleInteraction) - Method in class org.biopax.paxtools.io.sif.InteractionSet: If the interaction already exists, mediators are updated with merging.
add(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model: This method add the given onject to this model.
add(Constraint, String...) - Method in class org.biopax.paxtools.pattern.Pattern: Creates a mapped constraint with the given generative constraint and the indexes it applies.
add(Pattern) - Method in class org.biopax.paxtools.pattern.Pattern: Appends the constraints in the parameter pattern to the desired location.
add(E) - Method in class org.biopax.paxtools.util.BiopaxSafeSet
add(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper
addAccessor(PathAccessor, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Adds the given PathAccessor to the list of accessors to use to get field values of objects and their related objects.
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
addEntry(String, int, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Adds a new blacklisted ID.
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.
addMediator(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Adds a mediator to the interaction.
addMember(EntityReference) - Method in class org.biopax.paxtools.io.sif.level3.Group
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.
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
addPathwayAnnotations(Model, boolean, Class<? extends BioPAXElement>...) - Static method in class org.biopax.paxtools.controller.ModelUtils: Given BioPAX model, for each BioPAX object of the listed classes and their sub-classes, such as e.g.
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
addSubgroup(Group) - Method in class org.biopax.paxtools.io.sif.level3.Group
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
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Bind the wrapper of the given PhysicalEntity to the downstream.
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds the given PhysicalEntity to the downstream.
addToDownstream(PhysicalEntity, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Bind the wrapper of the given PhysicalEntity to the downstream.
addToDownstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds the given PhysicalEntity to the downstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Bind the wrapper of the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Bind the wrapper of the given element to the upstream.
addToUpstream(BioPAXElement, Graph) - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds the given element to the upstream.
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
addValidValue(String) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Adds the given valid value to the set of valid values.
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
AdjacencyMatrix - Class in org.biopax.paxtools.pattern.util: Adjacency matrix representation of a graph.
AdjacencyMatrix(boolean[][], List<String>) - Constructor for class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Constructor with contents.
AffectsRule - Class in org.biopax.paxtools.io.sif.level2: This is an experimental rule that mines ACTIVATES and INHIBITS relations between molecules.
AffectsRule() - Constructor for class org.biopax.paxtools.io.sif.level2.AffectsRule
analyzeStates(Model) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.

Given a model this method will analyze the states and populate the stateChangeMap and extendedControls maps.
AND - Class in org.biopax.paxtools.pattern.constraint: Used for getting logical AND of a set of constraints.
AND(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.AND: Constructor with the mapped constraints.
applies(BioPAXElement) - Method in class org.biopax.paxtools.controller.PathAccessor
assertIndLength(int[]) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Asserts the size of teh parameter array is equal to the variable size.
assignProcessAndLogicOpNodesToCompartment(Sbgn) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: This method finds process nodes and logical operator nodes in sbgn map and assigns them to a compartment by using majority rule.
atEquivalentLocation(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
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

BACKWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Backward traversal direction.
banned - Variable in class org.biopax.paxtools.query.model.AbstractNode: For saying: "If the algorithm traverses this node, it cannot traverse those others".
base - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
baseSet - Variable in class org.biopax.paxtools.util.AbstractFilterSet
BasicFilterFactory - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
BasicFilterFactory(String) - Constructor for class org.biopax.paxtools.util.BasicFilterFactory: Deprecated.
BFS - Class in org.biopax.paxtools.query.algorithm: Implements breadth-first search.
BFS(Set<Node>, Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.BFS: Constructor with all parameters.
BFS() - Constructor for class org.biopax.paxtools.query.algorithm.BFS: Empty constructor for other possible uses.
BinaryInteractionType - Enum in org.biopax.paxtools.io.sif: This class holds the description, tag (used in SIF file), the information if the interaction is directed for the relevant binary interaction types.
bindArrays(ObjectPropertyEditor, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory
bindArrays(String, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory
BINDING - Static variable in enum org.biopax.paxtools.io.sif.level3.ChangeType: Special static entity feature used as a 'hack' to capture complex membership.
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
bindsTo() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds two Protein that appear together in a Complex.
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
BiopaxValidatorClient - Class in org.biopax.paxtools.client: Simple (example) BioPAX Validator client to upload and check BioPAX OWL files.
BiopaxValidatorClient(String) - Constructor for class org.biopax.paxtools.client.BiopaxValidatorClient: Main Constructor It configures for the validator's URL (defined by DEFAULT_VALIDATOR_URL constant) and result format ().
BiopaxValidatorClient() - Constructor for class org.biopax.paxtools.client.BiopaxValidatorClient: Default Constructor It configures for the default validator URL.
BiopaxValidatorClient.RetFormat - Enum in org.biopax.paxtools.client
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
BLACK - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color black indicates that the node was processed.
blacklist - Variable in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Blacklist to detect ubiquitous small molecules.
blacklist - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Blacklist for identifying ubiquitous small molecules.
Blacklist - Class in org.biopax.paxtools.pattern.util: A blacklist is used for not using ubiquitous small molecules in patterns.
Blacklist() - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor for a blank blacklist.
Blacklist(String) - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor with resource file name.
Blacklist(InputStream) - Constructor for class org.biopax.paxtools.pattern.util.Blacklist: Constructor with resource input stream.
blacklist(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
BlacklistGenerator - Class in org.biopax.paxtools.pattern.miner: This class generates a blacklist for the given model.
BlacklistGenerator(BlacklistGenerator.Decider) - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Constructor with decider.
BlacklistGenerator() - Constructor for class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Default constructor.
Bound(float, float) - Constructor for class org.biopax.paxtools.io.sbgn.VNode.Bound
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.
breakCycles() - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Run the algorithm.
buildCustomEditorMap(BioPAXLevel, InputStream) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

C

calcReqWidthByStateAndInfos(List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.VNode: Calculates required width according to the given list state and info glyphs of this VNode.
canGenerate() - Method in interface org.biopax.paxtools.pattern.Constraint: Tells if this constraint is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Specifies if the constraint is generative.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ConversionSide: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.Empty: Cannot generate
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.OR: Can generate only if all of the wrapped constraints are generative.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.OtherSide: Deprecated.

This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.Participant: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.ParticipatingPE: Deprecated.

This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.RelatedControl: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: This is a generative constraint.
canGenerate() - Method in class org.biopax.paxtools.pattern.MappedConst: Can generate only if the wrapped constraint is generative.
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
catalysisPrecedes(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for detecting two EntityReferences are controlling consecutive reactions, where output of one reaction is input to the other.
CatalysisPrecedesMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the catalysis-precedes pattern.
CatalysisPrecedesMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner: Constructor that sets name and description.
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
changedFrom(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
changedInto(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
ChangeType - Enum in org.biopax.paxtools.io.sif.level3: This enum handles types of modifications and contains utility methods for extracting them.
checkActivityLabel() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if the chain has a member with an activity label.
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).
checkOntologyClassAndRegister(OntClass) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
checkOption(Object, Object, Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Checks if the options map has the given option with the given value.
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.
chemicalAffectsProteinThroughBinding(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: A small molecule is in a complex with a protein.
chemicalAffectsProteinThroughControl() - Static method in class org.biopax.paxtools.pattern.PatternBox: A small molecule controls an interaction of which the protein is a participant.
ChemicalAffectsThroughBindingMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the chemical-affects-protein pattern.
ChemicalAffectsThroughBindingMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner: Constructor that sets name and description.
ChemicalAffectsThroughControlMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the chemical-affects-protein pattern.
ChemicalAffectsThroughControlMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner: Constructor that sets name and description.
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
ChemicalNameNormalizer - Class in org.biopax.paxtools.pattern.util: This class is used for finding a standard name for a small molecule.
ChemicalNameNormalizer(Model) - Constructor for class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer: Constructor that also infers all the mapping.
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
children - Variable in class org.biopax.paxtools.io.sbgn.VCompound
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
clear() - Method in class org.biopax.paxtools.query.model.AbstractEdge: Does nothing yet.
clear() - Method in class org.biopax.paxtools.query.model.AbstractGraph: Clears memory of all wrapper in the object map.
clear() - Method in class org.biopax.paxtools.query.model.AbstractNode: Resets the path sign.
clear() - Method in interface org.biopax.paxtools.query.model.Graph: Should clear any analysis specific labeling on the graph.
clear() - Method in interface org.biopax.paxtools.query.model.GraphObject: This method should clear any analysis specific labels on the object.
clone(Model, 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.
clone() - Method in class org.biopax.paxtools.pattern.Match: Clones a match.
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
clusterID - Variable in class org.biopax.paxtools.io.sbgn.VNode
collectChangedPhosphorylationSites(PhysicalEntity, PhysicalEntity, boolean) - Static method in class org.biopax.paxtools.pattern.util.DifferentialModificationUtil
collectEntities(Set<PhysicalEntity>, InteractionSetL3) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor
collectSimpleMembersRecursive(PhysicalEntity, Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
colors - Variable in class org.biopax.paxtools.query.algorithm.BFS: Color labels.
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
CommonFeatureStringGenerator - Class in org.biopax.paxtools.io.sbgn: Prepares displayable Stat class to generate labels like "pY@123" for modification features and like x[30 - 122] for fragment features.
CommonFeatureStringGenerator() - Constructor for class org.biopax.paxtools.io.sbgn.CommonFeatureStringGenerator
CommonIDFetcher - Class in org.biopax.paxtools.pattern.miner: Tries to get gene symbols or uniprot IDs for genes and display names for small molecules.
CommonIDFetcher() - Constructor for class org.biopax.paxtools.pattern.miner.CommonIDFetcher
CommonStreamQuery - Class in org.biopax.paxtools.query.algorithm: Searches common downstream or common upstream of a specified set of entities based on the given direction within the boundaries of a specified length limit.
CommonStreamQuery(Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Constructor for Common Stream with Selected Nodes.
CommonStreamQuery(Collection<Set<Node>>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Constructor for Common Stream with Entity States.
compareTo(Object) - Method in class org.biopax.paxtools.controller.ConversionScore
compareTo(Object) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
complete(Collection<BioPAXElement>, Model) - 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
complexes() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to its parent Complex recursively.
ComplexImpl - Class in org.biopax.paxtools.impl.level3
ComplexImpl() - Constructor for class org.biopax.paxtools.impl.level3.ComplexImpl
complexMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex to its members recursively (also getting member of the inner complexes).
ComponentRule - Class in org.biopax.paxtools.io.sif.level2: Component.InSame: A and B are components of same flattened complex structure, A and B are simple.
ComponentRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule: Constructor with default values.
ComponentRule(int) - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule: Constructor with threshold
ComponentRule(int, boolean) - Constructor for class org.biopax.paxtools.io.sif.level2.ComponentRule: Constructor with threshold and exception suppressing option.
ComponentRule - Class in org.biopax.paxtools.io.sif.level3: This rule class mines complex membership relations.
ComponentRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ComponentRule
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
compToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex or SimplePhysicalEntity to the related EntityReference.
con1 - Variable in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Generative constraint for first group of generated elements, to use on first mapped element.
con2 - Variable in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Generative constraint for second group of generated elements, to use on second mapped element.
ConBox - Class in org.biopax.paxtools.pattern.constraint: Some predefined constraints.
ConBox() - Constructor for class org.biopax.paxtools.pattern.constraint.ConBox
concat(Set<String>, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Converts the set of string to a single string.
confidence - Interface in org.biopax.paxtools.model.level2: Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure.
connectArcToPort(SbgnPDNode, Port) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: This method connects the existing arcs to the newly created ports which are created by ChiLay and SBGNPD Layout.
ConsecutiveCatalysisRule - Class in org.biopax.paxtools.io.sif.level2: This class creates an interaction between two entities if they are catalyzing consecutive conversions.
ConsecutiveCatalysisRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule
ConsecutiveCatalysisRule - Class in org.biopax.paxtools.io.sif.level3: This class creates an interaction between two entities if they are catalyzing consecutive conversions.
ConsecutiveCatalysisRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule
Constraint - Interface in org.biopax.paxtools.pattern: A constraint to check if a set of variables satisfy the requirements.
ConstraintAdapter - Class in org.biopax.paxtools.pattern.constraint: This is a base class for a Constraint.
ConstraintAdapter(int) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Constructor with size.
ConstraintAdapter(int, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Constructor with size.
ConstraintAdapter() - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Empty constructor.
ConstraintChain - Class in org.biopax.paxtools.pattern.constraint: Used for using several constraints as a chain.
ConstraintChain(Constraint...) - Constructor for class org.biopax.paxtools.pattern.constraint.ConstraintChain: Constructor with the chained constraints.
constraints - Variable in class org.biopax.paxtools.pattern.Pattern: List of mapped constraints.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsPhosphorylationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Constructs the pattern to use for mining.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Constructs the pattern.
constructPattern() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner: Constructs the pattern.
ConsumptionControlledByMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the consumption-controlled-by pattern.
ConsumptionControlledByMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructor that sets name and description.
ConsumptionControlledByMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner: Constructor for extension purposes.
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) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene
containsID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC
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.
containsSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene
containsSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC
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
controlled() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Process
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.
controllerPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controller PhysicalEntity
ControlRule - Class in org.biopax.paxtools.io.sif.level2: A controls a conversion which B is at left or right or both.
ControlRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ControlRule
ControlRule - Class in org.biopax.paxtools.io.sif.level3: A controls a conversion which B is at left or right or both.
ControlRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ControlRule
controlsConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the controlled Conversion, skipping the middle Control.
controlsDegradationIndirectly() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds cases where protein A changes state of B, and B is then degraded.
ControlsDegradationIndirectMiner - Class in org.biopax.paxtools.pattern.miner: Yet another miner for the controls-degradation pattern.
ControlsDegradationIndirectMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner: Constructor that sets name and description.
ControlsExpressionMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the transcriptional regulation pattern.
ControlsExpressionMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructor that sets name and description.
ControlsExpressionMiner(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner: Constructor for extending this class.
controlsExpressionWithConversion() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds the cases where transcription relation is shown using a Conversion instead of a TemplateReaction.
ControlsExpressionWithConvMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the transcriptional regulation pattern, modeled using Conversion.
ControlsExpressionWithConvMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner: Constructor that sets name and description.
controlsExpressionWithTemplateReac() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds transcription factors that trans-activate or trans-inhibit an entity.
controlsInteraction() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the controlled Interaction, skipping the middle Control.
controlsMetabolicCatalysis(Blacklist, boolean) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a Protein controlling a reaction whose participant is a small molecule.
ControlsNotParticipant - Class in org.biopax.paxtools.pattern.constraint: Checks if a controller of this Control is also a participant of the controlled interactions.
ControlsNotParticipant() - Constructor for class org.biopax.paxtools.pattern.constraint.ControlsNotParticipant: Constructor.
controlsPhosphorylation() - Static method in class org.biopax.paxtools.pattern.PatternBox
ControlsPhosphorylationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-phosphorylation pattern.
ControlsPhosphorylationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsPhosphorylationMiner: Constructor that sets the type.
ControlsProductionOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-production-of pattern.
ControlsProductionOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner: Constructor that sets name, description and type.
controlsStateChange() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
controlsStateChangeBothControlAndPart() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
controlsStateChangeButIsParticipant() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
ControlsStateChangeDetailedMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change-detailed pattern.
ControlsStateChangeDetailedMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Constructor that sets name and description.
ControlsStateChangeOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
ControlsStateChangeOfMiner(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructor for extension purposes.
ControlsStateChangeOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Empty constructor.
ControlsStateChangeOfMiner(SIFType) - Constructor for class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner: Constructor for extension purposes.
controlsStateChangeThroughBindingSmallMolecule(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
controlsStateChangeThroughControllerSmallMolecule(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
controlsStateChangeThroughDegradation() - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds cases where proteins affect their degradation.
ControlsTogetherRule - Class in org.biopax.paxtools.io.sif.level2: Implements Co-Control rule, which means A and B have a control over the same interaction.
ControlsTogetherRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule
ControlsTogetherRule - Class in org.biopax.paxtools.io.sif.level3: Implements Co-Control rule, which means A and B have a control over the same interaction.
ControlsTogetherRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule
controlsTransport() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a ProteinReference has a member PhysicalEntity that is controlling a transportation of another ProteinReference.
ControlsTransportMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-transport pattern.
ControlsTransportMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsTransportMiner: Constructor that sets name and description.
controlsTransportOfChemical(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule.
ControlsTransportOfChemicalMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-transport-of-chemical pattern.
ControlsTransportOfChemicalMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner: Constructor that sets name and description.
controlToConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Conversion, traversing downstream Controls recursively.
controlToInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled Interaction, traversing downstream Controls recursively.
controlToTempReac() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
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.
ControlWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for the Control class.
ControlWrapper(Control, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Constructor with the Control and the owner graph.
ControlWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for the Control class.
ControlWrapper(Control, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Constructor with the Control and the owner graph.
conv - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Wrapped Conversion.
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
ConversionSide - Class in org.biopax.paxtools.pattern.constraint: Given Conversion and its one of the participants (at the left or right), traverses to either the participants at the other side or the same side.
ConversionSide(ConversionSide.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.ConversionSide: Constructor.
ConversionSide(ConversionSide.Type, Blacklist, RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.ConversionSide: Constructor.
ConversionSide.Type - Enum in org.biopax.paxtools.pattern.constraint: This enum tells if the user want to traverse towards other side of the conversion or stay at the same side.
ConversionWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for the Conversion class.
ConversionWrapper(Conversion, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Constructor with the Conversion to wrap and the owner graph.
convert(InputStream, OutputStream, boolean) - Method in class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter: Converts the PSI-MI inputStream into BioPAX outputStream.
convert(EntrySet, OutputStream, boolean) - Method in class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter: Converts the PSI interactions from the EntrySet and places into BioPAX output stream.
convert(Model) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter: Creates GSEA entries from the pathways contained in the model.
convert(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.CustomFormat: Prepares the line in the output file for the given interaction.
convert(SIFInteraction) - Method in interface org.biopax.paxtools.pattern.miner.SIFToText: Creates the textual data corresponding to the given binary interaction.
convertFromJsonld(InputStream, OutputStream) - Method in class org.biopax.paxtools.io.jsonld.JsonldBiopaxConverter
convertFromJsonld(InputStream, OutputStream) - Method in interface org.biopax.paxtools.io.jsonld.JsonldConverter: Convert inputstream in jsonld format to outputsream in owl/rdf format.
convertFromMultipleOwlFiles(String...) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This method will read multiple OWL document and will merge them into an in memory BioPAX model.
convertFromMultipleOwlFiles(String...) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Deprecated.
experimental and incomplete; e.g., files are to be ordered, i.e., a former file should not point to the latter. Use it at your own risk. Or, use #convertFromOWL to get independent models; then, try merging them...
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.
convertGroupsToInteractions() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3: Creates membership links between group nodes and members in the generated SIF graph.
convertStepDirection(StepDirection) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter
convertTab(InputStream, OutputStream, boolean) - Method in class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter: Converts the PSI-MITAB inputStream into BioPAX outputStream.
convertToAdjacencyMatrix(Collection<SIFInteraction>, SIFType...) - Static method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Converts the given collection of interactions into an adjacency matrix.
convertToJsonld(InputStream, OutputStream) - Method in class org.biopax.paxtools.io.jsonld.JsonldBiopaxConverter
convertToJsonld(InputStream, OutputStream) - Method in interface org.biopax.paxtools.io.jsonld.JsonldConverter: Convert inputstream in owl/rdf format to outputsream in jsonld format.
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.jena.JenaIOHandler: Writes a model in OWL format using the an output stream.
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.
convToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to the upstream Control (and its upstream Control recursively).
convToController() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to the controller of the upstream Control (and its upstream Control recursively).
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
copySimplePointers(Model, Named, Named) - Static method in class org.biopax.paxtools.controller.ModelUtils: Copies names and xrefs from source to target biopax object; it does not copy unification xrefs but instead adds relationship xrefs using the same db and id values as source's unification xrefs.
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.
createAndAdd(BioPAXElement, BioPAXElement, InteractionSetL3, BinaryInteractionType, BioPAXElement...) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Creates the binary interaction and adds to the inferred interaction list.
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.jena.JenaIOHandler
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
createAndRegisterBeanEditor(OntProperty, OntResource) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
createClique(InteractionSetL3, List<BioPAXElement>, BinaryInteractionType, BioPAXElement...) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Creates an interactions between every ordered pair of components.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.DataSourceFilter: Creates the accessor from Entity to its data source name.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.OrganismFilter: Creates the accessor from PhysicalEntity to the organism of related EntityReference.
createFieldAccessors() - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: The child class should populate the list of PathAccessor object using the addAccessor method.
createLayout(Sbgn) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Applies CoSE layout to the given SBGN model.
createLEdges(List<Arc>, Layout) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Creates LNodes from Arcs of Sbgn and adds it to the passed layout object.
createLNode(VNode, VNode, Layout) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Helper function for creating LNode objects from VNode objects and adds them to the given layout.
createMap() - Method in class org.biopax.paxtools.trove.TProvider
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
createSBGN(Model) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Creates an Sbgn object from the given model.
createSet() - Method in class org.biopax.paxtools.trove.TProvider
createSet() - Method in interface org.biopax.paxtools.util.BPCollections.CollectionProvider
createSet() - Method in enum org.biopax.paxtools.util.BPCollections
createSIFInteraction(Match, IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Creates a SIF interaction for the given match.
createSIFInteraction(Match, IDFetcher) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Creates SIF interactions for the given match.
createStateVar(EntityFeature, ObjectFactory) - Method in class org.biopax.paxtools.io.sbgn.CommonFeatureStringGenerator: Creates State to represent the entity feature.
createStateVar(EntityFeature, ObjectFactory) - Method in interface org.biopax.paxtools.io.sbgn.FeatureDecorator: Creates the State for the given EntityFeature.
createVNodes(VCompound, List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Recursively creates VNodes from Glyphs of Sbgn.
CSCOBothControllerAndParticipantMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOBothControllerAndParticipantMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner: Constructor that sets name and description.
CSCOButIsParticipantMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOButIsParticipantMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner: Constructor that sets name and description.
CSCOThroughBindingSmallMoleculeMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOThroughBindingSmallMoleculeMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner: Constructor that sets name and description.
CSCOThroughControllingSmallMoleculeMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the controls-state-change pattern.
CSCOThroughControllingSmallMoleculeMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner: Constructor that sets name and description.
CSCOThroughDegradationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the degradation pattern.
CSCOThroughDegradationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner: Constructor that sets name and description.
ctrl - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Wrapped control.
ctrl - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Wrapped control.
CustomFormat - Class in org.biopax.paxtools.pattern.miner: Used for customizing the columns in the SIF text output.
CustomFormat(String...) - Constructor for class org.biopax.paxtools.pattern.miner.CustomFormat
CycleBreaker - Class in org.biopax.paxtools.query.algorithm: When an algorithm searches for a paths between multiple source nodes, or from a source to a target node (source and targets may overlap), sometimes there comes paths from and to the same node, i.e cycles.
CycleBreaker(Set<GraphObject>, Set<Node>, int) - Constructor for class org.biopax.paxtools.query.algorithm.CycleBreaker: Constructor with the objects in the result, source and target nodes, and search limit.

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
DataSourceFieldBridge - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
DataSourceFieldBridge() - Constructor for class org.biopax.paxtools.util.DataSourceFieldBridge: Deprecated.
DataSourceFilter - Class in org.biopax.paxtools.query.wrapperL3: Filter by data source.
DataSourceFilter(String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.DataSourceFilter: Constructor.
DataSourceFilterFactory - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
DataSourceFilterFactory() - Constructor for class org.biopax.paxtools.util.DataSourceFilterFactory: Deprecated.
DecoratingPropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller
DecoratingPropertyAccessor(PropertyAccessor<D, R>) - Constructor for class org.biopax.paxtools.controller.DecoratingPropertyAccessor
DEFAULT_FIELDS - Static variable in class org.biopax.paxtools.search.SearchEngine
DEFAULT_MAX_HITS_PER_PAGE - Static variable in class org.biopax.paxtools.search.SearchEngine
DEFAULT_VALIDATOR_URL - Static variable in class org.biopax.paxtools.client.BiopaxValidatorClient: Default BioPAX Validator's URL
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
DeltaFeatureExtractor - Class in org.biopax.paxtools.pattern.example: This class goes over the state change pattern results and writes down the gained and lost modifications through these directed relations.
DeltaFeatureExtractor() - Constructor for class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
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
description - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Description of the miner.
detectRange(Method) - Static method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Given the multiple cardinality feature, the range of the get method is returned.
Dialog - Class in org.biopax.paxtools.pattern.miner: This is the user interface with GUI for selecting a model, a pattern miner, and an output file.
Dialog(Miner...) - Constructor for class org.biopax.paxtools.pattern.miner.Dialog: Constructor for the dialog.
differentialActivity(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an activity.
DifferentialModificationUtil - Class in org.biopax.paxtools.pattern.util: THis class is used for comparing modification features of two PhysicalEntity objects of same EntityReference.
DifferentialModificationUtil() - Constructor for class org.biopax.paxtools.pattern.util.DifferentialModificationUtil
DirectedRelationMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the directed relations between proteins.
DirectedRelationMiner() - Constructor for class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Constructor that sets name and description.
Direction - Enum in org.biopax.paxtools.model.level2: Catalysis direction controlled vocabulary
direction - Variable in class org.biopax.paxtools.query.algorithm.BFS: Whether the direction is FORWARD, it is REVERSE otherwise.
Direction - Enum in org.biopax.paxtools.query.algorithm: Direction is used for specifying upstream, downstream or both.
direction - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: The direction that the Conversion is wrapped.
dist - Variable in class org.biopax.paxtools.query.algorithm.BFS: Distance labels.
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
doLayout - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Flag to run a layout before writing down the sbgn.
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
downstream - Variable in class org.biopax.paxtools.query.model.AbstractNode: Set of downstream edges.
downstreamInited - Variable in class org.biopax.paxtools.query.model.AbstractNode: Flag to remember if downstream links were created.
DOWNWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Backward traversal direction.

E

Edge - Interface in org.biopax.paxtools.query.model: Wrapper interface for edges in a graph to be queried.
EdgeL3 - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for links between L3 objects.
EdgeL3(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3.EdgeL3: Constructor with source and target nodes, and the owner graph.
EdgeL3 - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for links between L3 objects.
EdgeL3(Node, Node, Graph) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3: Constructor with source and target nodes, and the owner graph.
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
Empty - Class in org.biopax.paxtools.pattern.constraint: Checks if the parameter constraint cannot generate any candidate.
Empty(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.Empty: Constructor with the generative Constraint.
EMPTY - Static variable in class org.biopax.paxtools.pattern.constraint.Field: Possible parameter value indicating user desire the field to be empty.
emptyOK - Variable in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Option to accept objects if the field is empty or null.
enrichWithCM(Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets parent complexes or complex members recursively according to the type of the linkage.
enrichWithGenerics(Set<BioPAXElement>, Set<BioPAXElement>) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets the linked homologies and then switches to complex-relationship mode.
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
entityHasAChange(BioPAXElement, Conversion, GroupMap, Set<PEStateChange>, Map<Conversion, Set<EntityReference>>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify
entityHasAChange(BioPAXElement, Conversion, GroupMap, Set<PEStateChange>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify
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
EntrezGene - Class in org.biopax.paxtools.io.sbgn.idmapping: This class provides a mapping Entrez Gene IDs and gene symbols.
EntrezGene() - Constructor for class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene
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
equal(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
Equality - Class in org.biopax.paxtools.pattern.constraint: Checks identity of two elements.
Equality(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Equality: Constructor with the desired output.
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.
equals(Object) - Method in class org.biopax.paxtools.io.sif.level3.Group
equals(Object) - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
equals(Object) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: This method checks for source, target and type equality.
equals(Object) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
equals(Object) - Method in class org.biopax.paxtools.query.model.AbstractEdge
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 class org.biopax.paxtools.io.sif.level3.Group
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
erToPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From EntityReference to the member PhysicalEntity
EventWrapper - Class in org.biopax.paxtools.query.wrapperL3: This is the parent wrapper class for both Conversion and TemplateReaction objects.
EventWrapper(GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.EventWrapper: Constructor with the owner graph.
EventWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: This is the parent wrapper class for both Conversion and TemplateReaction objects.
EventWrapper(GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Constructor with the owner graph.
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.
EXISTENCE - Static variable in enum org.biopax.paxtools.io.sif.level3.ChangeType: Special static entity feature used for representing changes that effect existence of protein -i.e.
expandGroups() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3: This method iteratively replaces groups with BioPAX elements
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
ExpressionRule - Class in org.biopax.paxtools.io.sif.level3: This rule mines the transctivation and transinhibition relations between entities.
ExpressionRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ExpressionRule
externalReferenceUtilityClass - Interface in org.biopax.paxtools.model.level2
extractClass(Resource) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
extractModifNames(Map) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Extracts the modification terms from the moficiation features.
extractModifNames(Set) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Extracts terms of the modification features.

F

factory - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
featStrGen - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: This class is used for generating short printable strings (text in info boxes) from recognized entity features.
FeatureDecorator - Interface in org.biopax.paxtools.io.sbgn: Generates a State class representing an entity feature.
featureSubstring - Variable in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Partial names of the features to be considered.
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.
fetch(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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.pattern.miner.CommonIDFetcher
fetchID(BioPAXElement) - Method in interface org.biopax.paxtools.pattern.miner.IDFetcher: Finds a String ID for the given element.
fetchIDs(BioPAXElement, IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
Field - Class in org.biopax.paxtools.pattern.constraint: Checks if an element has or has not a specific value for a field, or the field value of another element.
Field(String, Field.Operation, Object) - Constructor for class org.biopax.paxtools.pattern.constraint.Field: Constructor with accessor string for the field value of the element and the desired value.
Field(String, String, Field.Operation) - Constructor for class org.biopax.paxtools.pattern.constraint.Field: Constructor with accessor strings for the field value of the element and the desired value that will be reached from the second element.
Field.Operation - Enum in org.biopax.paxtools.pattern.constraint
FIELD_AVAILABILITY - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_COMMENT - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_DATASOURCE - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_DATASOURCE - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_ECNUMBER - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_KEYWORD - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_KEYWORD - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_NAME - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_NAME - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_ORGANISM - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_ORGANISM - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_PATHWAY - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_PATHWAY - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_SEQUENCE - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_SIZE - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_TERM - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_TYPE - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_URI - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_XREFDB - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_XREFDB - Static variable in class org.biopax.paxtools.search.SearchEngine
FIELD_XREFID - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FIELD_XREFID - Static variable in class org.biopax.paxtools.search.SearchEngine
FieldOfMultiple - Class in org.biopax.paxtools.pattern.constraint: Checks if generated elements has or has not a specific value for a field, or the field value of another set of generated elements.
FieldOfMultiple(MappedConst, String, Field.Operation, Object) - Constructor for class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Constructor with accessor string for the field value of the element and the desired value.
FieldOfMultiple(MappedConst, String, MappedConst, String, Field.Operation) - Constructor for class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Constructor with accessor strings for the field value of the element and the desired value that will be reached from the second element.
fillArray(PhysicalEntity, PhysicalEntity, int, int) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Creates the chain that links the given endpoints.
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 - Class in org.biopax.paxtools.query.wrapperL3: This is the base filter class that can be applied to any level 3 element.
Filter() - Constructor for class org.biopax.paxtools.query.wrapperL3.Filter
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.
FILTER_BY_DATASOURCE - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
FILTER_BY_ORGANISM - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl
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
filters - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3
filters - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected
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
findDirectionInCatalysis(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Searches the controlling catalysis for possible direction of the conversion.
findDirectionInPathways(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Searches pathways that contains this conversion for the possible directions.
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 other 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.
fixReactome(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix
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.
flattenComplexContent - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Option to flatten nested complexes.
FORWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Forward traversal direction.
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
general - Static variable in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Some general modification sub-strings to use if exact terms are not conclusive.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.AND: Gets intersection of the generated elements by the member constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: This method has to be overridden by generative constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintChain: Chains the member constraints and returns the output of the last constraint.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConversionSide: Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.
generate(Match, int...) - Method in interface org.biopax.paxtools.pattern.Constraint: Generates candidate values for the variable to be generated.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Iterated over non-taboo participants and collectes related ER.
generate(Interaction, Set<Entity>) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Gets the related entity references of the given interaction.
generate(Conversion, InterToPartER.Direction, Set<Entity>) - Method in class org.biopax.paxtools.pattern.constraint.InterToPartER: Gets the related entity references of the given interaction,
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE: Gets to the linked PhysicalEntity.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.OR: Gets the intersection of the generated values of wrapped constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.OtherSide: Deprecated.

Checks which side is the first PhysicalEntity, and gathers participants on the other side.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Participant: Identifies the conversion direction and gets the related participants.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Identifies the conversion direction and gets the related participants.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ParticipatingPE: Deprecated.

First evaluates the direction that the Control is affecting the Conversion, then gets the related participants.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: Uses the encapsulated PAthAccessor to generate satisfying elements.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.RelatedControl: According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Gets the first mapped element along with the generated elements of wrapped constraint.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.XOR: Gets xor of the generated elements by the member constraints.
generate(Match, int...) - Method in class org.biopax.paxtools.pattern.MappedConst: Calls generate method of the constraint with index translation.
generateBlacklist(Model) - Method in class org.biopax.paxtools.pattern.miner.BlacklistGenerator: Generates the blacklist.
generateClassMetrics(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: Generates simple counts of different elements in the model.
genericEquiv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to its generic equivalents, i.e.
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(int) - Method in class org.biopax.paxtools.pattern.Match: Gets element at the index.
get(String, Pattern) - Method in class org.biopax.paxtools.pattern.Match: Gets element corresponding to the given label in the pattern.
get(String[], Pattern) - Method in class org.biopax.paxtools.pattern.Match: Gets elements corresponding to the given labels in the pattern.
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
getAllSimpleMembers() - Method in class org.biopax.paxtools.io.sif.level3.Group
getAllStates(EntityReference) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.
getAName(BioPAXElement) - Method in class org.biopax.paxtools.pattern.Match: Finds a name for the variable.
getANameForSIF(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: This method is used when we want to use readable names in the simple SIF format instead of IDs.
getAnnotations() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
getAnnotations() - Method in class org.biopax.paxtools.io.sif.level3.Group
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.
getBanned() - Method in class org.biopax.paxtools.query.model.AbstractNode
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.
getBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 2.
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.
getCatalysisDirection(Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control, if exists.
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.
getCellularLocations(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets cellular locations of the given elements in a string set.
getCellularLocations() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Retrieves the cellular location of the PhysicalEntity.
getCellularLocationsOfSource() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects cellular location terms of source objects.
getCellularLocationsOfTarget() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects cellular location terms of target objects.
getChain(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
getChangedModifications(PhysicalEntity, PhysicalEntity) - Static method in class org.biopax.paxtools.pattern.util.DifferentialModificationUtil: Gets the differential features.
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
getChildren() - Method in class org.biopax.paxtools.io.sbgn.VCompound: Returns the child list of this VCompound
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.
getColor(Node) - Method in class org.biopax.paxtools.query.algorithm.BFS: Gets color tag of the node
getColumnValue(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.OutputColumn: Get the string to write in the output file.
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.
getCompoundName(SmallMoleculeReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the name of the small molecule to use in SIF.
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.
getConstr() - Method in class org.biopax.paxtools.pattern.MappedConst: Getter for the constraint.
getConstraints() - Method in class org.biopax.paxtools.pattern.Pattern: Getter for the constraint list.
getContext(String) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the context of the ubiquity of the ID.
getControl() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Gets the wrapped Control.
getControl() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Gets the wrapped Control.
getCONTROL_TYPE() - Method in interface org.biopax.paxtools.model.level2.control
getControlChain(Control, Interaction) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the chain of Control, staring from the given Control, leading to the given Interaction.
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.
getControllersAsString() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
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.
getConv() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
getConversion() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
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.
getConvParticipants(Conversion, RelType) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets input ot output participants of the Conversion.
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.
getDatasources() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl: Deprecated.
use getAnnotations() instead
getDataSources() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects data source names (Provenance display names) of mediators.
getDataTypeFor(PropertyEditor) - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
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
getDeltaCompartments(Match, String, String, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets delta compartments of the given two PE chains.
getDeltaControls() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
getDeltaFeatures(PhysicalEntity, PhysicalEntity, PhysicalEntity, PhysicalEntity) - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType: This method returns the features that are "changed" between the left and right physical entities.
getDeltaFeatures() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
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.
getDeltaModifications(Match, String, String, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets delta modifications of the given elements in string sets.
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.
getDescription() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType: Returns the description of the binary interaction as a string.
getDescription() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets description of the miner.
getDescription() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the description of the miner.
getDescription() - Method in enum org.biopax.paxtools.pattern.miner.SIFEnum: Gets the description of the SIF type.
getDescription() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Gets the description of the SIF type.
getDescription() - Method in enum org.biopax.paxtools.query.algorithm.Direction: Gets the description.
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
getDirection(Conversion, Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getDirection(Conversion, Pathway, Control) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getDirection(Conversion, Pathway) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the direction of the Control chain the the Interaction.
getDirection(Conversion) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter
getDirection() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
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.
getDisplayNameX() - Method in class org.biopax.paxtools.impl.level3.NamedImpl
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.
getDownstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Gets the downstream edges.
getDownstream() - Method in interface org.biopax.paxtools.query.model.Node
getDownstreamInteractions(Collection<Interaction>) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Gets the downstream interactions among the given set.
getDownstreamNoInit() - Method in class org.biopax.paxtools.query.model.AbstractNode: This class gets the downstream links but does not initialize.
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: The contents of this set should NOT be modified.
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()
getEntityReferenceOrGroup(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.level3.GroupMap
getEntityReferenceType() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
getEntityReferenceType() - Method in interface org.biopax.paxtools.model.level3.EntityReference
getEntityReferenceX() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
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
getFilter() - Method in class org.biopax.paxtools.util.BasicFilterFactory: Deprecated.
getFirst() - Method in class org.biopax.paxtools.pattern.Match: Gets first element of the match
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
getGeneSymbol(ProteinReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the gene symbol of the given EntityReference.
getGeneSymbol(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the gene symbol of the given EntityReference.
getGetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor
getGetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor
getGraph() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getGraph() - Method in class org.biopax.paxtools.query.model.AbstractNode
getGraph() - Method in interface org.biopax.paxtools.query.model.GraphObject: Every graph object should have an owner graph.
getGraphObject(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Gets the related wrapper for the given object, creates the wrapper if not created before.
getGraphObject(String) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Gets the wrapper object with its id (key).
getGraphObject(Object) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the wrapper of the related object.
getGroupMap() - Method in class org.biopax.paxtools.io.sif.level3.InteractionSetL3: Getter for the groupMap
getHeader() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Gets the header of the result file.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Sets header of the output.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the first line of the result file.
getHeader() - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Gets header of the result file.
getHeight() - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound
getHits() - Method in class org.biopax.paxtools.search.SearchResult
getId() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene: Provides Entrez Gene ID of the given gene symbol.
getID(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC: Provides HGNC ID of the given approved gene symbol.
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
getIdentifiers(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Uses uniprot name or gene symbol as identifier.
getIdMap() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
getIdVersion() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
getIdVersion() - Method in interface org.biopax.paxtools.model.level3.Xref
getIdx() - Method in class org.biopax.paxtools.impl.level3.XrefImpl
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.
getInds() - Method in class org.biopax.paxtools.pattern.MappedConst: Getter for the mapped indices.
getInteraction() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Gets the wrapped TemplateReaction
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.
getKey() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getKey(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph
getKey() - Method in interface org.biopax.paxtools.query.model.GraphObject: This method is used for storing the object in a Map.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: RDF ID of the Control is its key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: RDF ID of the Conversion and the direction is used for the key.
getKey(Object) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: RDF IDs of elements is used as key in the object map.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: RDF ID of the PhysicalEntity is used as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Uses RDF ID of TemplateReaction as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: RDF ID of the Control is its key.
getKey(Object) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: RDF IDs of elements is used as key in the object map.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Uses RDF ID of TemplateReaction as key.
getKey() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: RDF ID of the PhysicalEntity is used as key.
getKey() - Method in class org.biopax.paxtools.util.BasicFilterFactory: Deprecated.
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).
getKeywords() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl: Deprecated.
use getAnnotations() instead
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'.
getLabel(GraphObject) - Method in class org.biopax.paxtools.query.algorithm.BFS: Gets the distance label of the object.
getLast() - Method in class org.biopax.paxtools.pattern.Match: Gets last element of the match.
getLeft() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getLeft() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
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.
getLeftRoot() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
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.io.jena.JenaEditorMap
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
getLinkedElements(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.constraint.LinkedPE
getListed() - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the IDs of the blacklisted molecules.
getLocalId(BioPAXElement) - Static method in class org.biopax.paxtools.converter.LevelUpgrader: Gets the local part of the BioPAX element ID.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.model.AbstractNode
getLowerEquivalent() - Method in interface org.biopax.paxtools.query.model.Node
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control cannot have an equivalent.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events do not have equivalent objects.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control cannot have an equivalent.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events do not have equivalent objects.
getLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getMap() - Method in class org.biopax.paxtools.io.sif.level3.GroupMap
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.
getMaxHitsPerPage() - Method in class org.biopax.paxtools.search.SearchEngine: Gets the maximum no.
getMaxHitsPerPage() - Method in class org.biopax.paxtools.search.SearchResult
getMaxInd() - Method in class org.biopax.paxtools.pattern.MappedConst: Gets the maximum index.
getMediatorIDs() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects IDs of mediators.
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which essential BioPAX elements mediated this relation, then they need to override this method and pass the labels of elements.
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getMediatorLabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getMediators() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Gets other related elements of the interaction.
getMediatorsInString() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Gets the mediator IDs in a String with a space between each ID.
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.
getMiners() - Method in enum org.biopax.paxtools.pattern.miner.SIFEnum
getMiners() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Gets the list of SIFMiner classes that can search this type of SIF edge in a BioPAX model.
getModel() - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3
getModel() - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected
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
getModifications(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets modifications of the given element in a string.
getModifications(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets modifications of the given elements in a string set.
getModifications() - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Collects modifications from the elements of the chain.
getModificationTerm(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the String term of the modification feature.
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.
getName() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets name of the miner.
getName() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the name of the miner.
getName(SmallMoleculeReference) - Method in class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer: Gets the standard name of the small molecule.
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.
getNeighbors(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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
getNonUbiqueObjects(Set) - Method in class org.biopax.paxtools.pattern.util.Blacklist
getNonUbiques(Set<PhysicalEntity>, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the non-ubiquitous physical entities in the given set and in the given context.
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).
getObjectBiopaxPropertyValues(BioPAXElement, String) - Static method in class org.biopax.paxtools.examples.UseOfReflection: Example 1.
getObjectMap() - Method in class org.biopax.paxtools.query.model.AbstractGraph
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.
getOrganisms() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl: Deprecated.
use getAnnotations() instead
getPackageName() - Method in enum org.biopax.paxtools.model.BioPAXLevel
getPage() - Method in class org.biopax.paxtools.search.SearchResult
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.
getParentPathways() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl: Deprecated.
use getAnnotations() instead
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.
getPathSign() - Method in class org.biopax.paxtools.query.model.AbstractNode
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
getPathwayNames() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects the names of the related pathways.
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
getPathways() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects Pathway objects that the Interactions among the mediators are members.
getPatoData() - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl
getPatoData() - Method in interface org.biopax.paxtools.model.level3.PhenotypeVocabulary
getPattern() - Method in interface org.biopax.paxtools.pattern.miner.Miner: Gets the pattern to use for mining the graph.
getPattern() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the pattern, constructs if null.
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
getPhysicalEntity() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getPhysicalEntity() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getPhysicalEntityClass() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getPk() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl: Gets Primary Key.
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
getPositionInString(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the position of the modification feature as a String.
getPositionStart(ModificationFeature) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Gets the first position of the modification feature.
getPositionStatus() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl
getPositionStatus() - Method in interface org.biopax.paxtools.model.level3.SequenceSite
getPrecedingStates(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.
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
getPubmedIDs() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects PMIDs from mediators.
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.
getRDFId() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
getRDFId() - Method in class org.biopax.paxtools.io.sif.level3.Group
getRDFId() - Method in interface org.biopax.paxtools.model.BioPAXElement: This method returns the full URI of the element (despite it is called RDFId).
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
getRelatedEntrezGeneID(XReferrable) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Searches for the Entrez Gene ID in the references.
getRelatedPhysicalEntities(BioPAXElement, Set<PhysicalEntity>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.
getRelatedPhysicalEntityMap(Collection<BioPAXElement>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Maps each BioPAXElement to its related PhysicalEntity objects.
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.
getRelationType() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if the relation captured by match has a type.
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.
getReverse() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
getRight() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
getRight() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
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.
getRightRoot() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
getRootElements(Model, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils: Finds "root" BioPAX objects that belong to a particular class (incl.
getRules(BioPAXLevel) - Static method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Gets all available interaction rules for the given level.
getRuleTypes() - Method in interface org.biopax.paxtools.io.sif.InteractionRule: Gets a list of the rule types that this class implements.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.AffectsRule: Gets supported interactions types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ControlRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ControlRule: Gets supported interaction types.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ExpressionRule: Gets a list of the rule types that this class implements.
getRuleTypes() - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule: Gets supported interaction types.
getSbgn2BPMap() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Gets the mapping from SBGN IDs to BioPAX IDs.
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.
getSeedInteractions(Collection<BioPAXElement>, Graph) - Static method in class org.biopax.paxtools.query.QueryExecuter: Extracts the querible interactions from the elements.
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
getSIFType() - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner
getSIFType() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the type of the interaction.
getSign() - Method in class org.biopax.paxtools.query.model.AbstractEdge: Edges are positive by default.
getSign() - Method in interface org.biopax.paxtools.query.model.Edge: Algorithms may need a sign for the edge.
getSign() - Method in interface org.biopax.paxtools.query.model.Node: Some nodes can have a sign (typically non-breadth nodes).
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events have a positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: PhysicalEntity have positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events have a positive sign.
getSign() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: PhysicalEntity have positive sign.
getSimpleMembers() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getSimpleMembers(Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
getSimpleMembers(PhysicalEntity, Set<SimplePhysicalEntity>) - Static method in class org.biopax.paxtools.io.sif.level3.Simplify
getSimpleMembers() - Method in interface org.biopax.paxtools.model.level3.Complex: Gets the member physical entities which are not complex.
getSortedGeneNames(Collection<SIFInteraction>, SIFType...) - Static method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Collects and sorts sourceID and targetID of the given collection of sif interactions.
getSource() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
getSource() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Gets source element.
getSOURCE() - Method in interface org.biopax.paxtools.model.level2.publicationXref
getSource() - Method in interface org.biopax.paxtools.model.level3.PublicationXref
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getSourceLabel() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the label of the source node.
getSourceLabel() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getSourceNode() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getSourceNode() - Method in interface org.biopax.paxtools.query.model.Edge
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getSourcePELabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
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.
getStandardNameX() - Method in class org.biopax.paxtools.impl.level3.NamedImpl
getStartingClass() - Method in class org.biopax.paxtools.pattern.Pattern: Gets the type of the initial element.
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
getSucceedingStates(SimplePhysicalEntity) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.
getSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene
getSymbol(String) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC
getSymbol(String) - Static method in class org.biopax.paxtools.pattern.util.HGNC
getSymbols() - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC
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
getTag() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType: Returns the tag of the binary interaction.
getTag() - Method in enum org.biopax.paxtools.pattern.miner.SIFEnum: Tag of a SIF type is derived from the enum name.
getTag() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Tag of a SIF type is derived from the enum name.
getTarget() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Gets target element.
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsDegradationIndirectMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsProductionOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getTargetLabel() - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Gets the label of the target node.
getTargetLabel() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
getTargetNode() - Method in class org.biopax.paxtools.query.model.AbstractEdge
getTargetNode() - Method in interface org.biopax.paxtools.query.model.Edge
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CatalysisPrecedesMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughBindingMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ChemicalAffectsThroughControlMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ConsumptionControlledByMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ControlsTransportOfChemicalMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOBothControllerAndParticipantMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughControllingSmallMoleculeMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.CSCOThroughDegradationMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.InComplexWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.InteractsWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.NeighborOfMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.ReactsWithMiner
getTargetPELabels() - Method in class org.biopax.paxtools.pattern.miner.UsedToProduceMiner
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
getTemplateX() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
getTempReac() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Gets the wrapped 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
getTotalHits() - Method in class org.biopax.paxtools.search.SearchResult
getType() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Gets the type of the interaction.
getType(String) - Static method in enum org.biopax.paxtools.pattern.miner.OutputColumn.Type
getUbiques(Set<PhysicalEntity>, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Gets the ubiquitous small molecules among the given set and in the given context.
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
getUniprotNameForHuman(ProteinReference) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the uniprot name of the given human EntityReference.
getUniprotNameForHuman(Match, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Searches for the uniprot name of the given human EntityReference.
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.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.model.AbstractNode
getUpperEquivalent() - Method in interface org.biopax.paxtools.query.model.Node
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control cannot have an equivalent.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events do not have equivalent objects.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control cannot have an equivalent.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events do not have equivalent objects.
getUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
getUpstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Gets the upstream edges.
getUpstream() - Method in interface org.biopax.paxtools.query.model.Node
getUpstreamConversions(Collection<Interaction>) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Gets the conversions at the upstream of this PhysicalEntity.
getUpstreamNoInit() - Method in class org.biopax.paxtools.query.model.AbstractNode: This class gets the upstream links but does not initialize.
getUrl() - Method in class org.biopax.paxtools.client.BiopaxValidatorClient
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.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Creates values for the result file columns.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method has to be overridden if writeResultDetailed method is used.
getValue(Match, int) - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Gets the ids of the small molecule reference and its physical entities.
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.
getValues() - Method in class org.biopax.paxtools.util.BasicFilterFactory: Deprecated.
getVariables() - Method in class org.biopax.paxtools.pattern.Match: Getter for the element array.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Gets the variable size of the constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.Empty: Variable size is one less than the wrapped Constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Size of this constraint is one less than con1 if con2 is null, otherwise it is two less than the total of size of con1 and con2.
getVariableSize() - Method in interface org.biopax.paxtools.pattern.Constraint: Number of variables to check consistency.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.HasAnID: Returns 1.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.IDConstraint: Returns 1.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.NOT: Size is equal to the of the negated constraint
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.OR: Checks the inner mapping of the wrapped constraints and figures the size.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Returns size of the wrapped constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.constraint.Size: Size is one less than the size of wrapped constraint.
getVariableSize() - Method in class org.biopax.paxtools.pattern.MappedConst: Gets variable size of the wrapped constraint.
getVisitor() - Method in class org.biopax.paxtools.controller.Traverser
getWidth() - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound
getWrappedSet(Set<? extends GraphObject>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the wrapped objects of the given wrapper set.
getWrappedSet(Set<? extends GraphObject>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets the wrapped objects of the given wrappers.
getWrappedSet(Set<? extends GraphObject>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets the wrapped objects of the given wrappers.
getWrapperMap(Set<?>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets a map from objects to their wrappers.
getWrapperMap(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets an element-to-wrapper map for the given elements.
getWrapperMap(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets an element-to-wrapper map for the given elements.
getWrapperSet(Set<?>) - Method in interface org.biopax.paxtools.query.model.Graph: Gets the set of wrappers for the given wrapped object set.
getWrapperSet(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: Gets wrappers of given elements
getWrapperSet(Set<?>) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Gets wrappers of given elements
getXmlBase() - Method in class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter
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
glyph - Variable in class org.biopax.paxtools.io.sbgn.VNode
GOUnificationXREFtoRelationshipXREFConverter - Class in org.biopax.paxtools.examples: User: Emek Demir Date: Jan 18, 2007 Time: 4:56:53 PM In this example we get all the unification xrefs in the model and check if they point to the Gene Ontology.
GOUnificationXREFtoRelationshipXREFConverter() - Constructor for class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
graph - Variable in class org.biopax.paxtools.query.model.AbstractNode: Owner graph.
Graph - Interface in org.biopax.paxtools.query.model: This graph interface is used in graph algorithms.
GraphL3 - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for L3 Graphs.
GraphL3(Model, Filter...) - Constructor for class org.biopax.paxtools.query.wrapperL3.GraphL3: Constructor with the model and the IDs of the ubiquitous molecules.
GraphL3Undirected - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for L3 Graphs.
GraphL3Undirected(Model, Filter...) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Constructor with the model and the IDs of the ubiquitous molecules.
GraphObject - Interface in org.biopax.paxtools.query.model: A graph object is the common interface for nodes and edges in a graph.
graphQuery(Model, PhysicalEntity, PhysicalEntity, PhysicalEntity) - Method in class org.biopax.paxtools.examples.Tutorial
GRAY - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color gray indicates that the node is in queue waiting to be procecessed.
Group - Class in org.biopax.paxtools.io.sif.level3: This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.
Grouper - Class in org.biopax.paxtools.io.sif.level3
Grouper() - Constructor for class org.biopax.paxtools.io.sif.level3.Grouper
GroupMap - Class in org.biopax.paxtools.io.sif.level3
GroupMap(Map<BioPAXElement, Group>) - Constructor for class org.biopax.paxtools.io.sif.level3.GroupMap
groupTypeToString() - Method in class org.biopax.paxtools.io.sif.level3.Group
GSEAConverter - Class in org.biopax.paxtools.io.gsea: Converts a BioPAX model to the GMT format (used by GSEA software).
GSEAConverter() - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter: Constructor.
GSEAConverter(String, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter: Constructor.
GSEAConverter(String, boolean, boolean) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter: Constructor.
GSEAConverter(String, boolean, Set<Provenance>) - Constructor for class org.biopax.paxtools.io.gsea.GSEAConverter: Constructor.

H

HasAnID - Class in org.biopax.paxtools.pattern.constraint: Checks if the element has a valid ID.
HasAnID(IDFetcher, Map<BioPAXElement, Set<String>>) - Constructor for class org.biopax.paxtools.pattern.constraint.HasAnID: Constructor with the ID fetcher.
hasDifferentCompartments() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if two physical entities have non-empty and different compartments.
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)
hashCode() - Method in class org.biopax.paxtools.io.sif.level3.Group
hashCode() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
hashCode() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: This method returns a hashcode based on the source, target and types hashcodes.
hashCode() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
hashCode() - Method in class org.biopax.paxtools.query.model.AbstractEdge
hasIDs() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
hasInverseLink() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
hasLabel(String) - Method in class org.biopax.paxtools.pattern.Pattern: Checks if the label is already in use.
hasLabel(int) - Method in class org.biopax.paxtools.pattern.Pattern: Checks if the given location has a label.
hasNext() - Method in class org.biopax.paxtools.util.CompositeIterator
hasNonSelfEffect() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not associated with the EntityReference of the initial PhysicalEntity.
hasSolution(Pattern, BioPAXElement...) - Method in class org.biopax.paxtools.pattern.Searcher: Checks if there is any match for the given pattern if search starts from the given element.
hasXref(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the object has an Xref with the given ID.
height - Variable in class org.biopax.paxtools.io.sbgn.VNode.Bound
help() - Static method in class org.biopax.paxtools.PaxtoolsMain
HGNC - Class in org.biopax.paxtools.io.sbgn.idmapping: This class provides a mapping between HGNC IDs and approved gene symbols.
HGNC() - Constructor for class org.biopax.paxtools.io.sbgn.idmapping.HGNC
HGNC - Class in org.biopax.paxtools.pattern.util: This class provides a mapping between HGNC IDs and Symbols.
HGNC() - Constructor for class org.biopax.paxtools.pattern.util.HGNC
highlightWorkaround() - Method in class org.biopax.paxtools.examples.Tutorial

I

IDConstraint - Class in org.biopax.paxtools.pattern.constraint: Checks if the element has the desired ID.
IDConstraint(Set<String>) - Constructor for class org.biopax.paxtools.pattern.constraint.IDConstraint: Constructor with desired IDs.
IDFetcher - Interface in org.biopax.paxtools.pattern.miner
idFetcher - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: ID fetcher is used for skipping objects that cannot generate a valid ID during the search.
idMap - Variable in class org.biopax.paxtools.impl.ModelImpl
idMap - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Memory for object IDs.
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
inComplexWith() - Static method in class org.biopax.paxtools.pattern.PatternBox: Two proteins have states that are members of the same complex.
InComplexWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the degradation pattern.
InComplexWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.InComplexWithMiner: Constructor that sets edge type.
index() - Method in interface org.biopax.paxtools.search.Indexer
index() - Method in class org.biopax.paxtools.search.SearchEngine
Indexer - Interface in org.biopax.paxtools.search
indexOf(String) - Method in class org.biopax.paxtools.pattern.Pattern: Gets the index of the given label.
inferGroups(Model) - Static method in class org.biopax.paxtools.io.sif.level3.Grouper
inferInteractions(InteractionSet, BioPAXElement, Model) - Method in interface org.biopax.paxtools.io.sif.InteractionRule: This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
inferInteractions(InteractionSet, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor: Uses physicalEntity as source of the interaction.
inferInteractions(InteractionSet, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Selects only PhysicalEntity as seed.
inferInteractions(Model) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Infers simple interactions from the interactions found in the model for every interaction rule given; and returns this inferred simple interactions.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.AffectsRule: Infers interactions using the given physicalEntity as seed.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule: Infer starting from the given physicalEntity.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ConsecutiveCatalysisRule: Infers using the given physicalEntity as source.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ControlRule: When options map is null, then all rules are generated.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ControlsTogetherRule: Infers interactions using A as source.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in interface org.biopax.paxtools.io.sif.level2.InteractionRuleL2: This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
inferInteractionsFromPE(InteractionSet, physicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule: Infer using given physicalEntity as source.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule: Infer interactions where A = the given PhysicalEntity.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ConsecutiveCatalysisRule: Infers interactions using the given PhysicalEntity as seed.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ControlRule: When options map is null, then all rules are generated.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ControlsTogetherRule
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ExpressionRule: Searches the transcriptional relations using the pattern, then decides the interaction type according to the type of the Control.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in interface org.biopax.paxtools.io.sif.level3.InteractionRuleL3: This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
inferInteractionsFromPE(InteractionSetL3, PhysicalEntity, Model) - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule: Infers interactions starting from the given PhysicalEntity.
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() - Method in class org.biopax.paxtools.io.jena.JenaEditorMap
init(InputStream) - Method in class org.biopax.paxtools.io.jena.JenaIOHandler
init(InputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler
init() - Method in class org.biopax.paxtools.query.model.AbstractNode: Does nothing yet.
init() - Method in interface org.biopax.paxtools.query.model.Node: Initializes the node.
init() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Extracts the sign and the type of the Control.
init() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Extracts the direction, creates the reverse if necessary.
init() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Extracts the sign and the type of the Control.
initBanned() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the set of banned nodes.
initDownstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the downstream connections.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Binds the controlled objects.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Binds products.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Binds to downstream interactions.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds to products.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Binds the controlled objects.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds to participants and controllers.
initDownstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Binds to downstream interactions.
initLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Finds member nodes if this is a homology node
initLowerEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Finds member nodes if this is a homology node
initMaps() - Method in class org.biopax.paxtools.query.algorithm.BFS: Initializes maps used during query.
initOptions(Map) - Method in interface org.biopax.paxtools.io.sif.InteractionRule: Uses the parameter map as options for the rule.
initOptions(Map) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor: Initializes options.
initOptions(Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Initializes the options.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ComponentRule: Initializes options.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ControlRule: Initializes option.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor: Does nothing here.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level2.ParticipatesRule: Initializes options.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ComponentRule: Initializes options.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ControlRule: Initializes options.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor: Does nothing for this class.
initOptionsNotNull(Map) - Method in class org.biopax.paxtools.io.sif.level3.ParticipatesRule: Initializes options.
initPortIdToGlyphMap(List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: This method initializes map for glyphs and their respective ports.
initUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Finds homology parent.
initUpperEquivalent() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Finds homology parent.
initUpstream() - Method in class org.biopax.paxtools.query.model.AbstractNode: Initializes the upstream connections.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Binds the controller and other Controls that controls this control.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Binds inputs and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Binds to upstream interactions.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Binds to template and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Binds the controller and other Controls that controls this control.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Binds to participants and controllers.
initUpstream() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Binds to upstream interactions.
inSameActiveComplex() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has an activity.
inSameComplex() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
inSameComplexEffectingConversion() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex is controlling a Conversion.
inSameComplexHavingTransActivity() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has transcriptional activity.
inSamePathway() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the two interactions are members of the same pathway.
insertPointConstraint(Constraint, int...) - Method in class org.biopax.paxtools.pattern.Pattern: A point constraint deals with only one element in a match, checks its validity.
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.
integrate(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
Integrator - Class in org.biopax.paxtools.controller: This class is intended to merge and to integrate biopax 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
InteractionRule - Interface in org.biopax.paxtools.io.sif: This interface defines a rule which can be run on BioPAX model to derive simple interactions.
InteractionRuleL2 - Interface in org.biopax.paxtools.io.sif.level2: This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.
InteractionRuleL2Adaptor - Class in org.biopax.paxtools.io.sif.level2: Base class for level 2 rules.
InteractionRuleL2Adaptor() - Constructor for class org.biopax.paxtools.io.sif.level2.InteractionRuleL2Adaptor
InteractionRuleL3 - Interface in org.biopax.paxtools.io.sif.level3: This interface defines a rule which can be run on BioPAX model L2 to derive simple interactions.
InteractionRuleL3Adaptor - Class in org.biopax.paxtools.io.sif.level3: Base class for level 3 interactions rules.
InteractionRuleL3Adaptor() - Constructor for class org.biopax.paxtools.io.sif.level3.InteractionRuleL3Adaptor
InteractionSet - Class in org.biopax.paxtools.io.sif: This is a set of binary interactions.
InteractionSet() - Constructor for class org.biopax.paxtools.io.sif.InteractionSet
InteractionSetL3 - Class in org.biopax.paxtools.io.sif.level3: Set of inferred interactions.
InteractionSetL3(Model) - Constructor for class org.biopax.paxtools.io.sif.level3.InteractionSetL3: Constructor with the model.
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
InteractionWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for Interaction class, excluding Control objects.
InteractionWrapper(Interaction, GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Constructor with the Interaction and the owner graph.
InteractsWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "interacts-with" relation.
InteractsWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.InteractsWithMiner: Constructor that sets sif type.
intersects(PhysicalEntityChain) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if two chains intersect without ignoring endpoint intersection.
intersects(PhysicalEntityChain, boolean) - Method in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Checks if two chains intersect.
interToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the upstream Control (and its upstream Control recursively).
interToController() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the controlling Controls recursively, and their controller PEs.
InterToPartER - Class in org.biopax.paxtools.pattern.constraint: This constraint is used to collect related EntityReference of the participant physical entities.
InterToPartER(int) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with parameters.
InterToPartER(InterToPartER.Direction, int) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with parameters.
InterToPartER() - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor without parameters.
InterToPartER(InterToPartER.Direction) - Constructor for class org.biopax.paxtools.pattern.constraint.InterToPartER: Constructor with direction.
InterToPartER.Direction - Enum in org.biopax.paxtools.pattern.constraint
interToPE() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the related PhysicalEntity.
invokeMethod(Method, D, R) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor: Calls the method onto bean with the value as its parameter.
IO(InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial
IS_UBIQUE - Static variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Ubique label.
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.
isBait() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if the molecule is a bait of a Y2H experiment.
isBreadthNode() - Method in interface org.biopax.paxtools.query.model.Node: This method is critical when the algorithm needs to calculate a path length.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Control is not a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events are not breadth nodes.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: PhysicalEntity is a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Control is not a breadth node.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events are not breadth nodes.
isBreadthNode() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: PhysicalEntity is a breadth node.
isChildless(Glyph) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Returns true if a glyph includes child glyphs (state and info glyphs are out of count!)
isCompleteBackward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
isCompleteForward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor
isComplex() - Method in class org.biopax.paxtools.io.sif.level3.Group
isCOMPONENTof() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant
isCONTROLLEDOf() - Method in interface org.biopax.paxtools.model.level2.process
isConvertingFromLevel1ToLevel2() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This flag will allow reader to automatically convert level1 classes to corresponding level 2 classes.
isConvertingFromLevel1ToLevel2() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
isDirected() - Method in enum org.biopax.paxtools.io.sif.BinaryInteractionType: Returns true, if the interaction is directed.
isDirected() - Method in enum org.biopax.paxtools.pattern.miner.SIFEnum: Asks if the edge is directed.
isDirected() - Method in interface org.biopax.paxtools.pattern.miner.SIFType: Asks if the edge is directed.
isEmpty() - Method in class org.biopax.paxtools.io.sif.level3.Group
isEmptyOK() - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Gets the option to accept empty fields.
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl
isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.level3.Group
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
isEquivalentInTheSet(Node, Set<Node>) - Method in class org.biopax.paxtools.query.algorithm.BFS: Checks if an equivalent of the given node is in the set.
isEquivalentInTheSet(Node, boolean, Set<Node>) - Method in class org.biopax.paxtools.query.algorithm.BFS: Checks if an equivalent of the given node is in the set.
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.
isFlattenComplexContent() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter
isHuman() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the EntityReference or the PhysicalEntity belongs to human.
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
isInhibition(Control) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if the type of a Control is inhibition.
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
isPrey() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Checks if the molecule is a prey of a Y2H experiment.
isReverseMatch() - Method in class org.biopax.paxtools.controller.ConversionScore
isSafe(Node, Edge) - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Checks whether an edge is on an unwanted cycle.
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.Fetcher
isSTEP_INTERACTIONSOf() - Method in interface org.biopax.paxtools.model.level2.process
isTranscription() - Method in class org.biopax.paxtools.query.model.AbstractNode: Nodes are not transcription by default.
isTranscription() - Method in interface org.biopax.paxtools.query.model.Edge
isTranscription() - Method in interface org.biopax.paxtools.query.model.Node: A node may be related to a transcription and an algorithm can depend on this information.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.EdgeL3
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Say if the event is a transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: This is transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Say if the event is a transcription.
isTranscription() - Method in class org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper: Being a transcription is not relevant in the undirected context.
isTreatNilAsNull() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.
isTreatNilAsNull() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Deprecated.
This problem is fixed and this option is no longer needed for recent BioCyc exports. Enable only if you are parsing a legacy export.
isUbique(PhysicalEntity) - Method in class org.biopax.paxtools.io.sbgn.ListUbiqueDetector: Checks if the ID of the PhysicalEntity is in the set.
isUbique(PhysicalEntity) - Method in interface org.biopax.paxtools.io.sbgn.UbiqueDetector: Checks if the PhysicalEntity is a ubiquitous molecule.
isUbique(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted in at least one context.
isUbique(PhysicalEntity, Conversion, ConversionDirectionType, RelType) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted for the given Conversion assuming the Conversion flows towards the given direction, and the entity is in given context.
isUbique() - Method in interface org.biopax.paxtools.query.model.Node: In biological graphs, some nodes are used ubiquitously like ATP, H2O, etc.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Controls are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.EventWrapper: Events are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Controls are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper: Events are not ubiquitous molecules.
isUbique() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
isUbiqueInBothContexts(PhysicalEntity) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Checks if the given entity is blacklisted in both context together.
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
isUseTwoGlyphsForReversibleConversion() - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Getter class for the parameter useTwoGlyphsForReversibleConversion.
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

J

JenaEditorMap - Class in org.biopax.paxtools.io.jena: This class is an editor map that uses Jena to read BioPAX OWL definition and creates property editors for BioPAX interfaces.
JenaEditorMap(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.jena.JenaEditorMap
JenaIOHandler - Class in org.biopax.paxtools.io.jena: Provides I/O support for BioPAX models presented in OWL format using the com.hp.hpl.jena package.
JenaIOHandler() - Constructor for class org.biopax.paxtools.io.jena.JenaIOHandler: If set to true, "error-mode: strict" option will be passed to Jena reader.
JenaIOHandler(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.jena.JenaIOHandler
JenaIOHandler(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.jena.JenaIOHandler
JsonldBiopaxConverter - Class in org.biopax.paxtools.io.jsonld
JsonldBiopaxConverter() - Constructor for class org.biopax.paxtools.io.jsonld.JsonldBiopaxConverter
JsonldConverter - Interface in org.biopax.paxtools.io.jsonld
JVM_PROPERTY_URL - Static variable in class org.biopax.paxtools.client.BiopaxValidatorClient: The Java Option to set a BioPAX Validator URL (if set, overrides the default and URL provided by the Constructor arg.)

K

keyPressed(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog
keyReleased(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog
keyTyped(KeyEvent) - Method in class org.biopax.paxtools.pattern.miner.Dialog: Listens key pressing events.
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

L1ToL2Fixes(PropertyEditor, BioPAXElement, Model, String) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Deprecated.
BioPAX Level 1 exports are extremely rare and obsolete.
L3ElementImpl - Class in org.biopax.paxtools.impl.level3: Base BioPAX Level3 element.
L3ElementImpl() - Constructor for class org.biopax.paxtools.impl.level3.L3ElementImpl
L3ToSBGNPDConverter - Class in org.biopax.paxtools.io.sbgn: This class converts BioPAX L3 model into SBGN PD.
L3ToSBGNPDConverter() - Constructor for class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Empty constructor.
L3ToSBGNPDConverter(UbiqueDetector, FeatureDecorator, boolean) - Constructor for class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Constructor with parameters.
label(String, int) - Method in class org.biopax.paxtools.pattern.Pattern: Puts the given label for the given index.
labeledInactive(Match, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks if a PE chain is labeled as inactive.
labelEquivRecursive(Node, boolean, int, boolean, boolean) - Method in class org.biopax.paxtools.query.algorithm.BFS: Labels equivalent nodes recursively.
labelMap - Variable in class org.biopax.paxtools.pattern.Pattern: Indexes in a pattern can be labeled using this map.
lastIndex - Variable in class org.biopax.paxtools.pattern.Pattern: How many elements are there in a pattern match.
left() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to its left participants.
LEFT_TO_RIGHT - Static variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Direction LEFT_TO_RIGHT.
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
limit - Variable in class org.biopax.paxtools.query.algorithm.BFS: Stop distance.
LimitType - Enum in org.biopax.paxtools.query.algorithm: Specifies whether the length limit is a normal limit or shortest_plus_k limit.
linkedER(boolean) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox
LinkedPE - Class in org.biopax.paxtools.pattern.constraint: Many times we want to link PhysicalEntities (PE) while traversing a relation.
LinkedPE(LinkedPE.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.LinkedPE: Constructor with the linking type.
LinkedPE(LinkedPE.Type, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.LinkedPE: Constructor with the linking type.
LinkedPE.Type - Enum in org.biopax.paxtools.pattern.constraint: Two type of linking between PhysicalEntity.
linkToComplex() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
linkToComplex(Blacklist) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
linkToSimple(Blacklist) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
linkToSpecific() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
listProteinUnificationXrefsPerPathway(Model) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
ListUbiqueDetector - Class in org.biopax.paxtools.io.sbgn: Detects ubiquitous molecules using a given ID set.
ListUbiqueDetector(Set<String>) - Constructor for class org.biopax.paxtools.io.sbgn.ListUbiqueDetector: Contructor with the Ubique IDs.
listUnificationXrefsPerPathway(Model) - Static method in class org.biopax.paxtools.examples.ProteinNameLister: Here is a more elegant way of doing the previous method!
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
log - Static variable in class org.biopax.paxtools.PaxtoolsMain
log - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3: Log for logging.
log - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: Log for logging.
lowerEquivalent - Variable in class org.biopax.paxtools.query.model.AbstractNode: If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the child equivalents of this node.
lowerEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to remember if child equivalents initialized.
lowerEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to remember if child equivalents initialized.

M

Macros - Class in org.biopax.paxtools.examples: Created with IntelliJ IDEA.
Macros() - Constructor for class org.biopax.paxtools.examples.Macros
main(String[]) - Static method in class org.biopax.paxtools.examples.GOUnificationXREFtoRelationshipXREFConverter
main(String[]) - Static method in class org.biopax.paxtools.examples.PathwayGenesExtractor
main(String[]) - Static method in class org.biopax.paxtools.examples.ProteinNameLister
main(String[]) - Static method in class org.biopax.paxtools.examples.PublicationStatisticsAnalyzer
main(String[]) - Static method in class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix
main(String[]) - Static method in class org.biopax.paxtools.examples.SifnxExportExample
main(String[]) - Static method in class org.biopax.paxtools.examples.SimpleIOExample
main(String[]) - Static method in class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
Main - Class in org.biopax.paxtools.io.json
Main() - Constructor for class org.biopax.paxtools.io.json.Main
main(String[]) - Static method in class org.biopax.paxtools.io.json.Main
main(String[]) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.EntrezGene
main(String[]) - Static method in class org.biopax.paxtools.io.sbgn.idmapping.HGNC
main(String[]) - Static method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
main(String[]) - Static method in class org.biopax.paxtools.pattern.miner.Dialog: Runs the program showing the dialog.
main(String[]) - Static method in class org.biopax.paxtools.pattern.util.ChemicalNameNormalizer
main(String[]) - Static method in class org.biopax.paxtools.pattern.util.HGNC
main(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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.
MappedConst - Class in org.biopax.paxtools.pattern: This is a mapping from a constraint to the elements in a match.
MappedConst(Constraint, int...) - Constructor for class org.biopax.paxtools.pattern.MappedConst: Constructor with the constraint and the index mapping.
Match - Class in org.biopax.paxtools.pattern: A pattern match is an array of biopax elements that satisfies the list of mapped constraints in a pattern.
Match(int) - Constructor for class org.biopax.paxtools.pattern.Match: Constructor with size.
matrix - Variable in class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Edges matrix.
max(int[]) - Method in class org.biopax.paxtools.pattern.constraint.OR: Gets the max value.
maxDegree(int) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the participant degree (number of Conversions that this is a participant) of the PhysicalEntity is less than or equal to the parameter.
MaximumInteractionThresholdExceedException - Exception in org.biopax.paxtools.io.sif: This exception is thrown when there are more than a maximum number of interactions generated.
MaximumInteractionThresholdExceedException(String) - Constructor for exception org.biopax.paxtools.io.sif.MaximumInteractionThresholdExceedException: Constructor with the message.
md5hex(String) - Static method in class org.biopax.paxtools.controller.ModelUtils: Calculates MD5 hash code (as 32-byte hex.
mediators - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
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(EditorMap, Model, Model) - Static method in class org.biopax.paxtools.examples.Tutorial
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.
merge(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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.
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
mergeWith(SIFInteraction) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction: Merges publications of the parameter equivalent sif with this one.
mineAndCollect(Model) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
Miner - Interface in org.biopax.paxtools.pattern.miner: A miner provides a pattern to mine, and knows how to use the result set to prepare the text output.
MinerAdapter - Class in org.biopax.paxtools.pattern.miner: Adapter class for a miner.
MinerAdapter(String, String) - Constructor for class org.biopax.paxtools.pattern.miner.MinerAdapter: Constructor with name and description.
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.
model - Variable in class org.biopax.paxtools.query.wrapperL3.GraphL3: The model to be wrapped.
model - Variable in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: The model to be wrapped.
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.
ModificationChangeConstraint - Class in org.biopax.paxtools.pattern.constraint: This class checks if there exists a desired type of modification change among two PhysicalEntity.
ModificationChangeConstraint(ModificationChangeConstraint.Type, String...) - Constructor for class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Constructor with the desired change and maps to activating and inactivating features.
ModificationChangeConstraint.Type - Enum in org.biopax.paxtools.pattern.constraint
modificationConstraint(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity or any linked PE contains the modification term.
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
modifiedPESimple() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for an EntityReference has distinct PhysicalEntities associated with both left and right of a Conversion.
modifierConv() - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for finding Conversions that an EntityReference is participating.
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.
molecularInteraction() - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last molecules are participants of a MolecularInteraction.
MolecularInteractionImpl - Class in org.biopax.paxtools.impl.level3
MolecularInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.MolecularInteractionImpl
moreControllerThanParticipant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity is controlling more reactions than it participates (excluding complex assembly).
MultiPathConstraint - Class in org.biopax.paxtools.pattern.constraint: Logical OR of several PathConstraints.
MultiPathConstraint(String...) - Constructor for class org.biopax.paxtools.pattern.constraint.MultiPathConstraint: Constructor with specifier string of the path constraints.
multipleCardinality - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter: This is false if there is a cardinality restriction of one on the property.
myFirstModel() - Static method in class org.biopax.paxtools.examples.Tutorial

N

name - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Name of the miner.
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
nameEquals(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Filters Named to contain a specific name.
nameEquals(String...) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Filters Named to contain a name from the input set.
names - Variable in class org.biopax.paxtools.pattern.util.AdjacencyMatrix: Unique node names.
namespaces - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
NEGATIVE - Static variable in interface org.biopax.paxtools.query.model.Node: Negative sign.
NeighborhoodQuery - Class in org.biopax.paxtools.query.algorithm: Searches the neighborhood of given source set of nodes
NeighborhoodQuery(Set<Node>, Direction, int) - Constructor for class org.biopax.paxtools.query.algorithm.NeighborhoodQuery: Constructor with parameters.
neighborOf() - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last proteins are related through an interaction.
NeighborOfMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "neighbor-of" relation.
NeighborOfMiner() - Constructor for class org.biopax.paxtools.pattern.miner.NeighborOfMiner: Constructor that sets sif type.
NEUTRAL - Static variable in interface org.biopax.paxtools.query.model.Node: Neutral sign.
next() - Method in class org.biopax.paxtools.util.CompositeIterator
nextInteraction() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Starts from an Interaction and gets next Interactions in temporal order, if ever defined in a Pathway.
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.
Node - Interface in org.biopax.paxtools.query.model: Node interface to use in graph algorithms.
NonUbique - Class in org.biopax.paxtools.pattern.constraint: This is a non-generative constraint that checks if the small molecule is ubiquitous in any context.
NonUbique(Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.NonUbique
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')
NOT - Class in org.biopax.paxtools.pattern.constraint: Negation of a constraint.
NOT(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.NOT: Constructor with the wrapped constraint.
notAParticipant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the second element (PhysicalEntity) is not a participant of the first element (Interaction).
notControlled() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the Interaction has no Control
notControlsThis() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure the second element (Control) is not a controller to the first element (Interaction).
notGeneric() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the PhysicalEntity do not have member physical entities..
notLabeledInactive() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not labeled as inactive.
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

objectMap - Variable in class org.biopax.paxtools.query.model.AbstractGraph: Objects are stored in this map.
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.
objectToString(Object) - Method in class org.biopax.paxtools.util.SetStringBridge: Deprecated.
Observable - Interface in org.biopax.paxtools.model.level3: User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.Filter: Checks if it is ok to traverse the given level 3 element.
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Checks if the related values of the object are among valid values.
okToTraverse(Level3Element) - Method in class org.biopax.paxtools.query.wrapperL3.UbiqueFilter: Checks if the ID of the given element is in the black list.
OldFormatWriter - Class in org.biopax.paxtools.pattern.miner: This class is used for writing the binary interactions to a text output stream in the old EXTENDED_BINARY_SIF format.
OldFormatWriter() - Constructor for class org.biopax.paxtools.pattern.miner.OldFormatWriter
open(String) - Static method in class org.biopax.paxtools.examples.Macros
openControlledVocabulary - Interface in org.biopax.paxtools.model.level2
optimizeConstraintOrder() - Method in class org.biopax.paxtools.pattern.Pattern
OR - Class in org.biopax.paxtools.pattern.constraint: Logical OR of several constraints.
OR(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.OR: Constructor with the array of mapped constraints.
org.biopax.paxtools - package org.biopax.paxtools
org.biopax.paxtools.client - package org.biopax.paxtools.client: A simple client for the BioPAX validator..
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.converter.psi - package org.biopax.paxtools.converter.psi
org.biopax.paxtools.examples - package org.biopax.paxtools.examples: This package contains several examples that uses Paxtools to demonstrate basic functionality.
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.io.gsea - package org.biopax.paxtools.io.gsea: This package contains a simple GSEA converter.
org.biopax.paxtools.io.jena - package org.biopax.paxtools.io.jena: This package contains a Jena bases reader/writer for reading BioPAX files.
org.biopax.paxtools.io.json - package org.biopax.paxtools.io.json
org.biopax.paxtools.io.jsonld - package org.biopax.paxtools.io.jsonld
org.biopax.paxtools.io.sbgn - package org.biopax.paxtools.io.sbgn: This package contains a BioPAX to SBGN-PD converter and associated classes.
org.biopax.paxtools.io.sbgn.idmapping - package org.biopax.paxtools.io.sbgn.idmapping: This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.io.sif - package org.biopax.paxtools.io.sif: This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
org.biopax.paxtools.io.sif.level2 - package org.biopax.paxtools.io.sif.level2
org.biopax.paxtools.io.sif.level3 - package org.biopax.paxtools.io.sif.level3: This package contains the SIF rules for BioPAX Level 3.
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.pattern - package org.biopax.paxtools.pattern: Main package.
org.biopax.paxtools.pattern.constraint - package org.biopax.paxtools.pattern.constraint: Package for constraints.
org.biopax.paxtools.pattern.example - package org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner - package org.biopax.paxtools.pattern.miner: Package for pattern miner utility.
org.biopax.paxtools.pattern.util - package org.biopax.paxtools.pattern.util: Package for several utility classes.
org.biopax.paxtools.query - package org.biopax.paxtools.query: Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other molecules that is reachable through some specific paths using the BioPAX data model.
org.biopax.paxtools.query.algorithm - package org.biopax.paxtools.query.algorithm: This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.model - package org.biopax.paxtools.query.model: This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.wrapperL3 - package org.biopax.paxtools.query.wrapperL3: This package contains TODO annotate!
org.biopax.paxtools.query.wrapperL3undirected - package org.biopax.paxtools.query.wrapperL3undirected: This package contains TODO annotate!
org.biopax.paxtools.search - package org.biopax.paxtools.search: Public interfaces and classes (API) for indexing and full-text searching BioPAX models.
org.biopax.paxtools.trove - package org.biopax.paxtools.trove
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.
OrganismFieldBridge - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
OrganismFieldBridge() - Constructor for class org.biopax.paxtools.util.OrganismFieldBridge: Deprecated.
OrganismFilter - Class in org.biopax.paxtools.query.wrapperL3: Filter by organism.
OrganismFilter(String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.OrganismFilter: Constructor.
OrganismFilterFactory - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
OrganismFilterFactory() - Constructor for class org.biopax.paxtools.util.OrganismFilterFactory: Deprecated.
OtherSide - Class in org.biopax.paxtools.pattern.constraint: Deprecated.
OtherSide() - Constructor for class org.biopax.paxtools.pattern.constraint.OtherSide: Deprecated.

Constructor.
output(Model) - Static method in class org.biopax.paxtools.examples.SimpleIOExample
OutputColumn - Class in org.biopax.paxtools.pattern.miner: This class is used for defining a custom column in the te
OutputColumn(String) - Constructor for class org.biopax.paxtools.pattern.miner.OutputColumn: Constructor with output type.
OutputColumn.Type - Enum in org.biopax.paxtools.pattern.miner: Type of the output column.
owl - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

P

ParentPathwayFieldBridge - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
ParentPathwayFieldBridge() - Constructor for class org.biopax.paxtools.util.ParentPathwayFieldBridge: Deprecated.
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
participant() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to its PhysicalEntity participants.
Participant - Class in org.biopax.paxtools.pattern.constraint: Gets input or output participants of a Conversion.
Participant(RelType, Blacklist, boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, Blacklist, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
Participant(RelType, boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.Participant: Constructor with parameters.
participantER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Interaction to the related EntityReference of its participants.
participatesInConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the Conversion that it participates.
ParticipatesInConv - Class in org.biopax.paxtools.pattern.constraint: Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired.
ParticipatesInConv(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Constructor with parameters.
ParticipatesInConv(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatesInConv: Constructor with parameters.
participatesInInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the Interaction that it participates.
ParticipatesRule - Class in org.biopax.paxtools.io.sif.level2: Finds pairs of molecules that are participants of the same interaction.
ParticipatesRule() - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule: Constructor with default values.
ParticipatesRule(int) - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule: Constructor with participant number threshold.
ParticipatesRule(int, boolean) - Constructor for class org.biopax.paxtools.io.sif.level2.ParticipatesRule: Constructor with participant number threshold and option to suppress exceptions.
ParticipatesRule - Class in org.biopax.paxtools.io.sif.level3: Finds pairs of molecules that are participants of the same interaction for the INTERACTS_WITH type, and participants of the same Conversion for the REACTS_WITH type.
ParticipatesRule() - Constructor for class org.biopax.paxtools.io.sif.level3.ParticipatesRule
ParticipatingPE - Class in org.biopax.paxtools.pattern.constraint: Deprecated.
ParticipatingPE(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatingPE: Deprecated.

Constructor with parameters.
ParticipatingPE(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.ParticipatingPE: Deprecated.

Constructor with parameters.
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.
PathConstraint - Class in org.biopax.paxtools.pattern.constraint: PathConstraint encapsulates PathAccessor of Paxtools.
PathConstraint(String) - Constructor for class org.biopax.paxtools.pattern.constraint.PathConstraint: Constructor with the constructor String of PathAccessor.
PathsBetweenQuery - Class in org.biopax.paxtools.query.algorithm: Finds the paths between the specified source set of states within the boundaries of a specified length limit.
PathsBetweenQuery(Collection<Set<Node>>, int) - Constructor for class org.biopax.paxtools.query.algorithm.PathsBetweenQuery: Constructor with parameters
PathsFromToQuery - Class in org.biopax.paxtools.query.algorithm: Finds the paths from a specified source set of states or entities to a specified target set of states or entities within the boundaries of a specified length limit.
PathsFromToQuery(Set<Node>, Set<Node>, LimitType, int, boolean) - Constructor for class org.biopax.paxtools.query.algorithm.PathsFromToQuery: Constructor with parameters.
pathSign - Variable in class org.biopax.paxtools.query.model.AbstractNode: This variable can be used by algorithms that need to label nodes with a path sign (typically the current path).
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
PathwayComponentLister - Class in org.biopax.paxtools.examples: This example shows how to list all components of a pathway.
PathwayComponentLister() - Constructor for class org.biopax.paxtools.examples.PathwayComponentLister
PathwayGenesExtractor - Class in org.biopax.paxtools.examples: Prints all the genes (aka proteins) in the L2 pathway and sub-pathways (*conditions apply), and also - trace where they come from.
PathwayGenesExtractor(pathway) - Constructor for class org.biopax.paxtools.examples.PathwayGenesExtractor
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.
pattern - Variable in class org.biopax.paxtools.pattern.miner.MinerAdapter: Pattern to use for mining.
Pattern - Class in org.biopax.paxtools.pattern: A pattern is a list of mapped constraints.
Pattern(Class<? extends BioPAXElement>, Constraint, String...) - Constructor for class org.biopax.paxtools.pattern.Pattern: Constructor with the first constraint and labels it uses.
Pattern(Class<? extends BioPAXElement>, String) - Constructor for class org.biopax.paxtools.pattern.Pattern: Constructor with a label for the element at index 0.
pattern(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
PatternBox - Class in org.biopax.paxtools.pattern: This class contains several pattern samples.
PatternBox() - Constructor for class org.biopax.paxtools.pattern.PatternBox
PaxtoolsMain - Class in org.biopax.paxtools: A command line accessible utility for basic Paxtools operations.
PaxtoolsMain() - Constructor for class org.biopax.paxtools.PaxtoolsMain
pe - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Wrapped PhysicalEntity.
pe - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Wrapped PhysicalEntity.
PE2FEAT - Static variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Accessor to the modification term.
PE2TERM - Static variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Accessor to the modification term.
PEChainsIntersect - Class in org.biopax.paxtools.pattern.constraint: This constraint checks if two chains of linked physical entities are intersecting or not.
PEChainsIntersect(boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Constructor with the desired result.
PEChainsIntersect(boolean, boolean) - Constructor for class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Constructor with the desired result and endpoint ignore option.
peInOut() - Static method in class org.biopax.paxtools.pattern.PatternBox
peNotRelatedToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Makes sure that the given physical entity is not related to the entity reference.
pes - Variable in class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Array that links two ends of the chain.
PEStateChange - Class in org.biopax.paxtools.io.sif.level3: This experimental class is used by Activity Network Analyzer to capture state change events.
PEStateChange(SimplePhysicalEntity, SimplePhysicalEntity, PhysicalEntity, PhysicalEntity, BioPAXElement, Conversion) - Constructor for class org.biopax.paxtools.io.sif.level3.PEStateChange
peToControl() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Control
peToControlledConv() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Conversion.
peToControlledInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the downstream Interaction.
peToER() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From SimplePhysicalEntity to its EntityReference.
peToInter() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to the related Interaction.
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
PhysicalEntityChain - Class in org.biopax.paxtools.pattern.util: This class takes two PhysicalEntity objects linked with generic or complex member relationships, and prepares an array of PEs that link those.
PhysicalEntityChain(PhysicalEntity, PhysicalEntity) - Constructor for class org.biopax.paxtools.pattern.util.PhysicalEntityChain: Constructor with endpoints.
PhysicalEntityChain.Activity - Enum in org.biopax.paxtools.pattern.util: Values for activity.
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
PhysicalEntityWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for PhysicalEntity.
PhysicalEntityWrapper(PhysicalEntity, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Constructor with the wrapped PhysicalEntity and the owner graph.
PhysicalEntityWrapper - Class in org.biopax.paxtools.query.wrapperL3undirected: Wrapper for PhysicalEntity.
PhysicalEntityWrapper(PhysicalEntity, GraphL3Undirected) - Constructor for class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Constructor with the wrapped PhysicalEntity and the owner graph.
physicalInteraction - Interface in org.biopax.paxtools.model.level2
placeStateAndInfoGlyphs() - Method in class org.biopax.paxtools.io.sbgn.VNode: Places state and info glyphs of this node
populateCompartmentOccurencesMap(Glyph, HashMap<String, Integer>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Updates a hashmap by incrementing the number of nodes in the compartment glyph that includes targetGlyph.
PositionStatusType - Enum in org.biopax.paxtools.model.level2
PositionStatusType - Enum in org.biopax.paxtools.model.level3
POSITIVE - Static variable in interface org.biopax.paxtools.query.model.Node: Positive sign.
preparePep2PEIDMap(Model) - Method in class org.biopax.paxtools.converter.LevelUpgrader
prepareSingleNodeSet(Set<BioPAXElement>, Graph) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the related wrappers of the given elements in a set.
preProcessFile(InputStream) - Method in class org.biopax.paxtools.io.jsonld.JsonldBiopaxConverter
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
printPathwayComponents(Model) - Static method in class org.biopax.paxtools.examples.PathwayComponentLister
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
processNode(Node) - Method in class org.biopax.paxtools.query.algorithm.BFS: Processes a node.
processNode2(Node) - Method in class org.biopax.paxtools.query.algorithm.CycleBreaker: Continue the search from the node.
product() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From TemplateReaction to its products.
ProgressWatcher - Interface in org.biopax.paxtools.pattern.util: This interface is to use for tracking progress of a process.
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
ProteinNameLister - Class in org.biopax.paxtools.examples: This example class processes all the Level2 BioPAX OWL files in the input directory to find all the protein names Notes: - recent fix: it doesn't traverse into the NEXT-STEP property, as it may lead beyond the boundaries of the pathway of interest! - one may prefer using the Paxtools' jenaIO instead of the simpleIO: import org.biopax.paxtools.io.jena.JenaIOHandler; JenaIOHandler handler = new JenaIOHandler(null, BioPAXLevel.L2);
ProteinNameLister() - Constructor for class org.biopax.paxtools.examples.ProteinNameLister
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
Prune - Class in org.biopax.paxtools.query.algorithm: This algorithm is used internally by PathsBetween and PathsFromTo algorithms.
Prune(Set<GraphObject>, Set<Node>) - Constructor for class org.biopax.paxtools.query.algorithm.Prune: Constructor with the input.
PsiToBiopax3Converter - Class in org.biopax.paxtools.converter.psi: The PSIMI 2.5 to BioPAX Level3 converter.
PsiToBiopax3Converter() - Constructor for class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter: Constructor.
PsiToBiopax3Converter(String) - Constructor for class org.biopax.paxtools.converter.psi.PsiToBiopax3Converter: Constructor.
PublicationStatisticsAnalyzer - Class in org.biopax.paxtools.examples: A simple method that prints the publication statistics.
PublicationStatisticsAnalyzer() - Constructor for class org.biopax.paxtools.examples.PublicationStatisticsAnalyzer
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.

Q

QueryExecuter - Class in org.biopax.paxtools.query: This class provides static methods to execute graph queries.
QueryExecuter() - Constructor for class org.biopax.paxtools.query.QueryExecuter
queue - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS queue.

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
ReactomeEntitySetUnificationXrefFix - Class in org.biopax.paxtools.examples: This is a class I wrote for fixing the unification xref problem in Reactome entity sets.
ReactomeEntitySetUnificationXrefFix() - Constructor for class org.biopax.paxtools.examples.ReactomeEntitySetUnificationXrefFix
reactsWith(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first and last small molecules are substrates to the same biochemical reaction.
ReactsWithMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "reacts-with" relation.
ReactsWithMiner() - Constructor for class org.biopax.paxtools.pattern.miner.ReactsWithMiner: Constructor that sets sif type.
readJenaModel(InputStream) - Method in class org.biopax.paxtools.io.jena.JenaIOHandler
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.jena.JenaIOHandler
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
REDUCE_COMPLEXES - Static variable in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Option to reduce complexes or use them as they are in interactions.
REDUCE_GENERICS - Static variable in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Option to reduce complexes or use them as they are in interactions.
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.
RelatedControl - Class in org.biopax.paxtools.pattern.constraint: After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to the Control.
RelatedControl(RelType) - Constructor for class org.biopax.paxtools.pattern.constraint.RelatedControl: Constructor with the relation type between PhysicalEntity and Conversion.
RelatedControl(RelType, Blacklist) - Constructor for class org.biopax.paxtools.pattern.constraint.RelatedControl: Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.
RelatedGenesOfInteractionsMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the related genes (participant or controller) of interactions.
RelatedGenesOfInteractionsMiner() - Constructor for class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Constructor that sets name and description.
relatedProteinRefOfInter(Class<? extends Interaction>...) - Static method in class org.biopax.paxtools.pattern.PatternBox: Finds ProteinsReference related to an interaction.
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
RelType - Enum in org.biopax.paxtools.pattern.util: Distinguishes between input and output.
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.
removeCommon(Set<String>, Set<String>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
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
removeInteractionsWithBlackListMolecules(Set<SimpleInteraction>, Set<String>) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Filters out interactions whose source or target are in black list.
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.
removeLastConstraint() - Method in class org.biopax.paxtools.pattern.Pattern: Removes the last constraint added to the pattern.
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
removePortsFromArcs(List<Arc>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: This method replaces ports of arc objects with their owners.
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.
replaceXrefsWithRelatedER(Collection<BioPAXElement>) - Static method in class org.biopax.paxtools.query.QueryExecuter: Replaces Xref objects with the related EntityReference objects.
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.jena.JenaIOHandler
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)
resolveFeatures(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils: TODO annotate or deprecate...
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
right() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Conversion to its right participants.
RIGHT_TO_LEFT - Static variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Direction RIGHT_TO_LEFT.
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
run() - Method in class org.biopax.paxtools.query.algorithm.BFS: Executes the algorithm.
run() - Method in class org.biopax.paxtools.query.algorithm.CommonStreamQuery: Method to run the query.
run() - Method in class org.biopax.paxtools.query.algorithm.NeighborhoodQuery: Executes the query.
run() - Method in class org.biopax.paxtools.query.algorithm.PathsBetweenQuery
run() - Method in class org.biopax.paxtools.query.algorithm.PathsFromToQuery: Executes the algorithm.
run() - Method in class org.biopax.paxtools.query.algorithm.Prune: Executes the algorithm.
runCommonStream(Set<BioPAXElement>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the elements in the common upstream or downstream of the seed
runCommonStreamWithPOI(Set<BioPAXElement>, Model, Direction, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: First finds the common stream, then completes it with the paths between seed and common stream.
runGOI(Set<BioPAXElement>, Model, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Deprecated.
Use runPathsBetween instead
runNeighborhood(Set<BioPAXElement>, Model, int, Direction, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets neighborhood of the source set.
runPathsBetween(Set<BioPAXElement>, Model, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets the graph constructed by the paths between the given seed nodes.
runPathsFromTo(Set<BioPAXElement>, Set<BioPAXElement>, Model, LimitType, int, Filter...) - Static method in class org.biopax.paxtools.query.QueryExecuter: Gets paths the graph composed of the paths from a source node, and ends at a target node.

S

satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ActivityConstraint: Checks if the PhysicalEntity controls anything.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Checks the gained and and lost features to predict the activity change is the desired change.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.AND: Checks if all the constraints satisfy.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Use this method only if constraint canGenerate, and satisfaction criteria is that simple.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ControlsNotParticipant: Checks if the controlled Interaction contains a controller as a participant.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Empty: Checks if the wrapped Constraint can generate any elements.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Equality: Checks if the two elements are identical or not identical as desired.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Field: Checks if the element in the first index has the desired value.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.FieldOfMultiple: Checks if the generated elements from the first mapped element has either the desired value, or has some value in common with the elements generated from second mapped element.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.HasAnID: Checks if the element has one of the desired IDs.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.IDConstraint: Checks if the element has one of the desired IDs.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Checks the any of the changed modifications match to any of the desired modifications.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.NonUbique
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.NOT: Negates the satisfies value of the wrapped constraint.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.OR: Checks if any of the wrapped constraints satisfy.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PathConstraint: Checks if the PathAccessor is generating the second mapped element.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.PEChainsIntersect: Creates two PhysicalEntity chains with the given endpoints, and checks if they are intersecting.
satisfies(Match, int...) - Method in interface org.biopax.paxtools.pattern.Constraint: Checks if the variables in the Match satisfies this constraint.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.SelfOrThis: Checks if the last index is either generated or equal to the first element.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Size: Checks if generated element size is in limits.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.Type: Checks if the element is assignable to a variable of the desired type.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.constraint.XOR: Checks if constraints satisfy in xor pattern.
satisfies(Match, int...) - Method in class org.biopax.paxtools.pattern.MappedConst: Directs to satisfies method of the wrapped constraint with index translation.
sbgn2BPMap - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Mapping from SBGN IDs to the IDs of the related objects in BioPAX.
SBGNLayoutManager - Class in org.biopax.paxtools.io.sbgn: SBGNLayoutManager Class: Applies layout by using ChiLay to Sbgn graph generated by paxtools.
SBGNLayoutManager() - Constructor for class org.biopax.paxtools.io.sbgn.SBGNLayoutManager
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
search(Match, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from the given match.
search(BioPAXElement, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from the given element.
search(Model, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern in the given model.
search(Model, Pattern, ProgressWatcher) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern in the given model.
search(Collection<? extends BioPAXElement>, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given elements.
search(String, int, Class<? extends BioPAXElement>, String[], String[]) - Method in class org.biopax.paxtools.search.SearchEngine
search(String, int, Class<? extends BioPAXElement>, String[], String[]) - Method in interface org.biopax.paxtools.search.Searcher: Full-text search for BioPAX elements.
searchAndCollect(Model, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a model for the given pattern, then collects the specified elements of the matches and returns.
searchAndCollect(Collection<? extends BioPAXElement>, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
searchAndCollect(BioPAXElement, Pattern, int, Class<T>) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
SearchEngine - Class in org.biopax.paxtools.search: A full-text searcher/indexer for BioPAX L3 models.
SearchEngine(Model, String) - Constructor for class org.biopax.paxtools.search.SearchEngine: Main Constructor.
SearchEngine.HitAnnotation - Enum in org.biopax.paxtools.search: A Key for the value in a BioPAX element's annotations map where additional information about corresponding search hit will be stored.
Searcher - Class in org.biopax.paxtools.pattern: Searcher for searching a given pattern in a model.
Searcher() - Constructor for class org.biopax.paxtools.pattern.Searcher
Searcher - Interface in org.biopax.paxtools.search
searchInFile(Pattern, String, String) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
searchInFile(Pattern, String, String, int, int) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches a pattern reading the model from the given file, and creates another model that is excised using the matching patterns.
searchPlain(Model, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern in a given model, but instead of a match map, returns all matches in a list.
searchPlain(Collection<? extends BioPAXElement>, Pattern) - Static method in class org.biopax.paxtools.pattern.Searcher: Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.
searchRecursive(Match, List<MappedConst>, int) - Static method in class org.biopax.paxtools.pattern.Searcher: Continues searching with the mapped constraint at the given index.
SearchResult - Class in org.biopax.paxtools.search
SearchResult() - Constructor for class org.biopax.paxtools.search.SearchResult
searchSIF(Model) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIF(Model, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIF(Model, OutputStream, boolean) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIF(Model, OutputStream, SIFToText) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
searchSIFGetMatrix(Model) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Searches the given model with the contained miners.
SelfOrThis - Class in org.biopax.paxtools.pattern.constraint: When a constraint excludes the origin element, but it is needed to be among them, use this constraint.
SelfOrThis(Constraint) - Constructor for class org.biopax.paxtools.pattern.constraint.SelfOrThis: Constructor with the wrapped constraint.
SelfOrThis(Constraint, int) - Constructor for class org.biopax.paxtools.pattern.constraint.SelfOrThis: Constructor with the wrapped constraint and index of self.
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
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
set(BioPAXElement, int) - Method in class org.biopax.paxtools.pattern.Match: Sets the given element to the given index.
set(String, Object, Document, LuceneOptions) - Method in class org.biopax.paxtools.util.DataSourceFieldBridge: Deprecated.
set(String, Object, Document, LuceneOptions) - Method in class org.biopax.paxtools.util.OrganismFieldBridge: Deprecated.
set(String, Object, Document, LuceneOptions) - Method in class org.biopax.paxtools.util.ParentPathwayFieldBridge: Deprecated.
set(String, Object, Document, LuceneOptions) - Method in class org.biopax.paxtools.util.XrefFieldBridge: Deprecated.
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.
setAuthor(Set<String>) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
setAUTHORS(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setAvailability(Set<String>) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
setAVAILABILITY(Set<String>) - Method in interface org.biopax.paxtools.model.level2.entity: This method overrides existing set with the new set.
setBanned(Set<Node>) - Method in class org.biopax.paxtools.query.model.AbstractNode
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.
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sets the blacklist to use during SIF search.
setBlacklist(Blacklist) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Sets the blacklist that can be used during the search.
setBlacklist(Blacklist) - Method in class org.biopax.paxtools.pattern.miner.SIFSearcher: Sets the blacklist that manages IDs of ubique molecules.
setBounds(float, float) - Method in class org.biopax.paxtools.io.sbgn.VNode: Sets the bound of this VNode by given width and height
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<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl
setCOFACTOR(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.catalysis
setColor(Node, int) - Method in class org.biopax.paxtools.query.algorithm.BFS: Sets color tag
setComment(Set<String>) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl
setCOMMENT(Set<String>) - Method in interface org.biopax.paxtools.model.level2.Level2Element
setCompartmentRefForComplexMembers(Glyph, Glyph) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: This method recursively set compartmentRef fields of members of any complex glyphs as same as complex's compartmentRef
setComponent(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl
setComponentOf(Set<Complex>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
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<Score>) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl: Confidence in the containing instance.
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.
setContainsGeneralTerm(Set<String>, String) - Method in class org.biopax.paxtools.pattern.constraint.ActivityModificationChangeConstraint: Checks if any element in the set contains the term.
setCONTROL_TYPE(ControlType) - Method in interface org.biopax.paxtools.model.level2.control
setControlled(Set<Process>) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
setCONTROLLED(Set<process>) - Method in interface org.biopax.paxtools.model.level2.control
setControlledOf(Set<Control>) - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
setCONTROLLER(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.control
setControllerOf(Set<Control>) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
setControllerOf(Set<Control>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
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.
setConvertingFromLevel1ToLevel2(boolean) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: Deprecated.
BioPAX Level 1 exports are obsolete (anyway, L1 input is always converted to L2 automatically).
setConvertingFromLevel1ToLevel2(boolean) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Deprecated.
BioPAX Level 1 exports are extremely rare and obsolete.
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.
setDeltaH(Set<Float>) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
setDeltaS(Set<Float>) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
setDescription(String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
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.
setDisplayNameX(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
setEC_NUMBER(Set<String>) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction
setECNumber(Set<String>) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
setEditorMap(EditorMap) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler
setEditorMap(EditorMap) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter
setEmptyOK(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Sets the parameter to accept empty field values.
setEntityFeature(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setEntityFeatureOf(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
setEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.SimplePhysicalEntity: Reference entity for this physical entity.
setEntityReferenceOf(Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setEntityReferenceType(Set<EntityReferenceTypeVocabulary>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setEntityReferenceX(EntityReference) - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl
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 class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setEvidence(Set<Evidence>) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
setEvidence(Set<Evidence>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setEvidence(Set<Evidence>) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
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
setEvidenceCode(Set<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'.
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
setExperimentalFeature(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
setExperimentalForm(Set<ExperimentalForm>) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl
setExperimentalFormDescription(Set<ExperimentalFormVocabulary>) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl
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(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
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.
setFeatureOf(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setFlattenComplexContent(boolean) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter
setHeight(float) - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound
setHits(List<BioPAXElement>) - Method in class org.biopax.paxtools.search.SearchResult
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
setIDFetcher(IDFetcher) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sets the ID fetcher to use during SIF search.
setIDFetcher(IDFetcher) - Method in interface org.biopax.paxtools.pattern.miner.SIFMiner: Sets the idFetcher that helps to fasten the search.
setIdMap(Map<BioPAXElement, Set<String>>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
setIdVersion(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
setIdVersion(String) - Method in interface org.biopax.paxtools.model.level3.Xref
setIdx(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
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
setInteractionType(Set<InteractionVocabulary>) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
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 class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl
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'.
setLabel(GraphObject, int) - Method in class org.biopax.paxtools.query.algorithm.BFS: Sets the distance label.
setLeft(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
setLEFT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion
setMaxHitsPerPage(int) - Method in class org.biopax.paxtools.search.SearchEngine: Sets the maximum no.
setMaxHitsPerPage(long) - Method in class org.biopax.paxtools.search.SearchResult
setMemberEntity(Set<EntityReference>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setMemberEntityReference(Set<EntityReference>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setMemberEntityReferenceOf(Set<EntityReference>) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl
setMemberFeature(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setMemberFeatureOf(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
setMemberPhysicalEntity(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
setMemberPhysicalEntityOf(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
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.
setName(String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter
setNEXT_STEP(Set<pathwayStep>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
setNextStep(Set<PathwayStep>) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
setNextStepOf(Set<PathwayStep>) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl
setNormalizeModels(boolean) - Method in class org.biopax.paxtools.controller.Integrator: Fixes some of the known Open Controlled Vocabullary issues in the models.
setNotFeature(Set<EntityFeature>) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl
setNotFeatureOf(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl
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.
setPage(int) - Method in class org.biopax.paxtools.search.SearchResult
setParticipant(Set<Entity>) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl
setPARTICIPANT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.experimentalForm
setParticipantOf(Set<Interaction>) - Method in class org.biopax.paxtools.impl.level3.EntityImpl
setPARTICIPANTS(Set<InteractionParticipant>) - Method in interface org.biopax.paxtools.model.level2.interaction
setParticipantStoichiometry(Set<Stoichiometry>) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
setPathSign(int) - Method in class org.biopax.paxtools.query.model.AbstractNode
setPATHWAY_COMPONENTS(Set<pathwayComponent>) - Method in interface org.biopax.paxtools.model.level2.pathway
setPathwayComponent(Set<Process>) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
setPathwayComponentOf(Set<Pathway>) - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
setPathwayController(Set<Pathway>) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
setPathwayOrder(Set<PathwayStep>) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl
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
setPeController(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ControlImpl
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.
setRegionType(Set<SequenceRegionVocabulary>) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
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<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl
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
setSize(int) - Method in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Sets the size of the constraint.
setSizeAccordingToClass() - Method in class org.biopax.paxtools.io.sbgn.VNode: Chooses a proper bound for this VNode according to its class.
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 class org.biopax.paxtools.impl.level3.PublicationXrefImpl
setSource(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Sets source element.
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.
setStandardNameX(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl
setSTEP_INTERACTIONS(Set<process>) - Method in interface org.biopax.paxtools.model.level2.pathwayStep
setStepConversion(Conversion) - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl: This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion.
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.
setStepProcessOf(Set<PathwayStep>) - Method in class org.biopax.paxtools.impl.level3.ProcessImpl
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.
SetStringBridge - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
SetStringBridge() - Constructor for class org.biopax.paxtools.util.SetStringBridge: Deprecated.
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.
setSubRegion(Set<NucleicAcidRegionReference>) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl
setSubRegionOf(Set<NucleicAcidReference>) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl
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
setTarget(BioPAXElement) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Sets target element.
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
setTemplateX(NucleicAcid) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl
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
setTotalHits(long) - Method in class org.biopax.paxtools.search.SearchResult
setTotalTicks(int) - Method in interface org.biopax.paxtools.pattern.util.ProgressWatcher: Sets how many ticks are there in total.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Make or not make this control related to a transcription.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.EdgeL3: Set the transcription flag.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Make or not make this control related to a transcription.
setTranscription(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.EdgeL3: Set the transcription flag.
setType(BinaryInteractionType) - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Sets the type of the interaction.
setType(SIFType) - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner
setUbique(boolean) - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Set the ubique flag.
setUbique(boolean) - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Set the ubique flag.
setUrl(String) - Method in class org.biopax.paxtools.client.BiopaxValidatorClient
setUrl(Set<String>) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl
setURL(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref
setUseTwoGlyphsForReversibleConversion(boolean) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Sets the option to use two glyphs for the reversible conversion.
setUseUniprotIDs(boolean) - Method in class org.biopax.paxtools.pattern.miner.CommonIDFetcher
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.
setValues(String[]) - Method in class org.biopax.paxtools.util.BasicFilterFactory: Deprecated.
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
setWidth(float) - Method in class org.biopax.paxtools.io.sbgn.VNode.Bound
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
setXrefOf(Set<XReferrable>) - Method in class org.biopax.paxtools.impl.level3.XrefImpl
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.
SIFEnum - Enum in org.biopax.paxtools.pattern.miner: Enum for representing supported SIF edge types.
SIFInteraction - Class in org.biopax.paxtools.pattern.miner
SIFInteraction(String, String, BioPAXElement, BioPAXElement, SIFType, Set<BioPAXElement>, Set<BioPAXElement>, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.pattern.miner.SIFInteraction
SIFMiner - Interface in org.biopax.paxtools.pattern.miner: This interface tells that the miner supports SIF output.
SifnxExportExample - Class in org.biopax.paxtools.examples: This example exports A BioPAX model to SIF.
SifnxExportExample() - Constructor for class org.biopax.paxtools.examples.SifnxExportExample
SIFSearcher - Class in org.biopax.paxtools.pattern.miner: Searches a model and generates SIF network using the pattern matches.
SIFSearcher(SIFType...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with binary interaction types.
SIFSearcher(SIFMiner...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with miners.
SIFSearcher(IDFetcher, SIFType...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with ID fetcher and binary interaction types.
SIFSearcher(IDFetcher, SIFMiner...) - Constructor for class org.biopax.paxtools.pattern.miner.SIFSearcher: Constructor with ID fetcher and miners.
SIFToText - Interface in org.biopax.paxtools.pattern.miner: An interface for converting a SIF interaction to text.
SIFType - Interface in org.biopax.paxtools.pattern.miner
sign(Control) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Identifies negative and positive controls.
sign(Match, String...) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Checks the cumulative sign of the chained controls.
sign - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Sign of the control.
sign - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Sign of the control.
SimpleEditorMap - Enum in org.biopax.paxtools.controller: Provides a simple editor map for a level with a given factory.
SimpleInteraction - Class in org.biopax.paxtools.io.sif: This class implements a directed binary interaction between two entities.
SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction: Constructor with parameters, without mediators.
SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType, BioPAXElement...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction: Constructor with parameters, with mediators.
SimpleInteraction(BioPAXElement, BioPAXElement, BinaryInteractionType, Collection<BioPAXElement>) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteraction: Constructor with parameters, with mediators.
SimpleInteractionConverter - Class in org.biopax.paxtools.io.sif: Deprecated.
use the pattern (new Paxtools' module) api instead
SimpleInteractionConverter(InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Constructor with the mining rules to use.
SimpleInteractionConverter(Map, InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Constructor with mining rules and options.
SimpleInteractionConverter(Map, Set<String>, InteractionRule...) - Constructor for class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Constructor with mining rules, options, and black list.
SimpleIOExample - Class in org.biopax.paxtools.examples: A basic example that shows the basic IO operations.
SimpleIOExample() - Constructor for class org.biopax.paxtools.examples.SimpleIOExample
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
simpleMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From complex to its simple members (members which are of type SimplePhysicalEntity) recursively.
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
simplePEToConv(RelType) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From simple PhysicalEntity to related Conversion.
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
simpleTraverse() - Method in class org.biopax.paxtools.examples.Tutorial
Simplify - Class in org.biopax.paxtools.io.sif.level3
Simplify() - Constructor for class org.biopax.paxtools.io.sif.level3.Simplify
size - Variable in class org.biopax.paxtools.pattern.constraint.ConstraintAdapter: Size of the constraint.
Size - Class in org.biopax.paxtools.pattern.constraint: Checks the size of the generated elements of the wrapped constraint.
Size(Constraint, int, Size.Type) - Constructor for class org.biopax.paxtools.pattern.constraint.Size: Constructor with parameters.
size() - Method in class org.biopax.paxtools.pattern.Pattern: Gets the element size of the pattern.
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
Size.Type - Enum in org.biopax.paxtools.pattern.constraint: Type of the (in)equality.
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
source(String) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox
sourceERs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
sourceID - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
sourcePEs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
sourceSet - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS starts from source nodes.
SpontaneousType - Enum in org.biopax.paxtools.model.level2
startingClass - Variable in class org.biopax.paxtools.pattern.Pattern: Class of the first elements to match with this pattern.
stateChange(Pattern, String) - Static method in class org.biopax.paxtools.pattern.PatternBox: Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.
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
stopSet - Variable in class org.biopax.paxtools.query.algorithm.BFS: BFS will not further traverse neighbors of any node in the stopSet.
StringFieldFilter - Class in org.biopax.paxtools.query.wrapperL3: This is the base class for filters that are filtering based on values of specific fields of the objects and their related objects.
StringFieldFilter(boolean, String[]) - Constructor for class org.biopax.paxtools.query.wrapperL3.StringFieldFilter: Constructor.
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).
summarize(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
summarize(Model, PrintStream) - Static method in class org.biopax.paxtools.PaxtoolsMain

T

targetERs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
targetID - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
targetPEs - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
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
TemplateReactionWrapper - Class in org.biopax.paxtools.query.wrapperL3: Wrapper for TemplateReaction class.
TemplateReactionWrapper(TemplateReaction, GraphL3) - Constructor for class org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper: Constructor with the TemplateReaction and the owner graph.
tempted(BioPAXIOHandler, InputStream, OutputStream) - Static method in class org.biopax.paxtools.examples.Tutorial
tick(int) - Method in interface org.biopax.paxtools.pattern.util.ProgressWatcher: Ticks the progress watcher.
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
toGSEA(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toLevel3(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toSBGN(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toSif(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
toSifnx(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
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.sif.level3.Group
toString() - Method in class org.biopax.paxtools.io.sif.level3.PEStateChange
toString() - Method in class org.biopax.paxtools.io.sif.SimpleInteraction: Returns "source type target".
toString() - Method in class org.biopax.paxtools.io.SimpleIOHandler.Triple
toString() - Method in enum org.biopax.paxtools.model.level2.Direction
toString() - Method in class org.biopax.paxtools.pattern.Match: Gets name of variables.
toString() - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Uses the name as sting representation of the miner.
toString() - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
toString(boolean) - Method in class org.biopax.paxtools.pattern.miner.SIFInteraction
toString() - Method in class org.biopax.paxtools.pattern.util.AdjacencyMatrix
toString() - Method in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper
toString() - Method in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper
toString() - Method in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper
toStringSet(Set<ModificationFeature>) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Sorts the modifications and gets them in a String.
TProvider - Class in org.biopax.paxtools.trove: A Trove4j based java collections (Set, Map) provider for the paxtools-core BioPAX model.
TProvider() - Constructor for class org.biopax.paxtools.trove.TProvider
transcription - Variable in class org.biopax.paxtools.query.wrapperL3.ControlWrapper: Flag to indicate if this control is related to a transcription.
transcription - Variable in class org.biopax.paxtools.query.wrapperL3.ConversionWrapper: Flag to say this Conversion is a transcription.
transcription - Variable in class org.biopax.paxtools.query.wrapperL3undirected.ControlWrapper: Flag to indicate if this control is related to a transcription.
TransitivePropertyAccessor<R extends BioPAXElement,D extends R> - Class in org.biopax.paxtools.controller: This class is a transitive decorator for PropertyAccessors.
translate(int[]) - Method in class org.biopax.paxtools.pattern.MappedConst: This methods translates the indexes of outer constraint, to this inner constraint.
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.
treatNilAsNull(boolean) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler: This flag will fix a common legacy bug from BioCyc where the "NIL" string was used for representing unknown values.
treatNilAsNull(boolean) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter: Deprecated.
This problem is fixed and this option is no longer needed for recent BioCyc exports. Enable only if you are parsing a legacy export.
Tutorial - Class in org.biopax.paxtools.examples: This class used for a Paxtools Tutorial during Harmony 2010.
Tutorial() - Constructor for class org.biopax.paxtools.examples.Tutorial
type(Class<? extends BioPAXElement>) - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: Creates an element type constraint.
type - Variable in class org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint: Gain or loss?
Type - Class in org.biopax.paxtools.pattern.constraint: Checks if a variable is a specific type or its subclass.
Type(Class<? extends BioPAXElement>) - Constructor for class org.biopax.paxtools.pattern.constraint.Type: Constructor with the desired class.
type - Variable in class org.biopax.paxtools.pattern.miner.SIFInteraction
typeOf(String) - Static method in enum org.biopax.paxtools.pattern.miner.SIFEnum

U

ubique - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to say this is a ubiquitous molecule.
ubique - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to say this is a ubiquitous molecule.
ubiqueDet - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: This class is used for detecting ubiques.
UbiqueDetector - Interface in org.biopax.paxtools.io.sbgn: Interface for ubiquitous molecule detection.
UbiqueFilter - Class in org.biopax.paxtools.query.wrapperL3: Filters out ubiquitous entities, whose IDs are supplied by user.
UbiqueFilter(Set<String>) - Constructor for class org.biopax.paxtools.query.wrapperL3.UbiqueFilter: Constructor.
UbiquitousIDMiner - Class in org.biopax.paxtools.pattern.miner: Miner for getting ubiquitous small molecules in a model.
UbiquitousIDMiner() - Constructor for class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Constructor that sets name and description.
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
UnificationIDtoRDFIDLister - Class in org.biopax.paxtools.examples: A basic example that shows how to list all unification xrefs.
UnificationIDtoRDFIDLister() - Constructor for class org.biopax.paxtools.examples.UnificationIDtoRDFIDLister
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 Rationale: Unification xrefs are critically important for data integration.
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.
unmarshal(String) - Static method in class org.biopax.paxtools.client.BiopaxValidatorClient: Converts a biopax-validator XML response to the java object.
update(LGraphObject) - Method in class org.biopax.paxtools.io.sbgn.VNode: Function that will take place when VNode objects will update in layout process of ChiLay
updateCompoundBounds(Glyph, List<Glyph>) - Method in class org.biopax.paxtools.io.sbgn.SBGNLayoutManager: Updates bounds of a compound node ( i.e.
updateLabel(String, String) - Method in class org.biopax.paxtools.pattern.Pattern: Changes a label.
updateSizeForStateAndInfo() - Method in class org.biopax.paxtools.io.sbgn.VNode: If glyph attribute of this VNode object includes any "state of information" or "unit of information" glyphs, this method updates the size of VNode accordingly.
upperEquivalent - Variable in class org.biopax.paxtools.query.model.AbstractNode: If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the parent equivalents of this node.
upperEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3.PhysicalEntityWrapper: Flag to remember if parent equivalents initialized.
upperEquivalentInited - Variable in class org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper: Flag to remember if parent equivalents initialized.
upstream - Variable in class org.biopax.paxtools.query.model.AbstractNode: Set of upstream edges.
upstreamInited - Variable in class org.biopax.paxtools.query.model.AbstractNode: Flag to remember if upstream links were created.
UPWARD - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Forward traversal direction.
USE_SECOND_ARG - Static variable in class org.biopax.paxtools.pattern.constraint.Field: Possible parameter value indicating the desired value will be given as the second element to the constraint.
usedToProduce(Blacklist) - Static method in class org.biopax.paxtools.pattern.PatternBox: Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
UsedToProduceMiner - Class in org.biopax.paxtools.pattern.miner: Miner for the "used-for-production-of" relation.
UsedToProduceMiner() - Constructor for class org.biopax.paxtools.pattern.miner.UsedToProduceMiner: Constructor that sets sif type.
UseOfReflection - Class in org.biopax.paxtools.examples: Examples on how to use Paxtools BioPAX property editors and accessors API (based on java reflection).
UseOfReflection() - Constructor for class org.biopax.paxtools.examples.UseOfReflection
useTwoGlyphsForReversibleConversion - Variable in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: SBGN process glyph can be used to show reversible reactions.
utilityClass - Interface in org.biopax.paxtools.model.level2
UtilityClass - Interface in org.biopax.paxtools.model.level3

V

validate(boolean, String, BiopaxValidatorClient.RetFormat, Behavior, Integer, String, File[], OutputStream) - Method in class org.biopax.paxtools.client.BiopaxValidatorClient: Checks a BioPAX OWL file(s) or resource using the online BioPAX Validator and prints the results to the output stream.
validate(String[]) - Static method in class org.biopax.paxtools.PaxtoolsMain
valueOf(String) - Static method in enum org.biopax.paxtools.client.BiopaxValidatorClient.RetFormat: Returns the enum constant of this type with the specified name.
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.io.sif.BinaryInteractionType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType: 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.pattern.constraint.ConversionSide.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.constraint.Field.Operation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.constraint.InterToPartER.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.constraint.LinkedPE.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.constraint.Size.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.miner.OutputColumn.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.miner.SIFEnum: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.pattern.util.RelType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.query.algorithm.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.query.algorithm.LimitType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biopax.paxtools.search.SearchEngine.HitAnnotation: 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.client.BiopaxValidatorClient.RetFormat: Returns an array containing the constants of this enum type, in the order they are declared.
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.io.sif.BinaryInteractionType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.io.sif.level3.ChangeType: 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.pattern.constraint.ConversionSide.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.constraint.Field.Operation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.constraint.InterToPartER.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.pattern.constraint.LinkedPE.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.constraint.ModificationChangeConstraint.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.constraint.Size.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.miner.OutputColumn.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.miner.SIFEnum: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.util.PhysicalEntityChain.Activity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.pattern.util.RelType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.query.algorithm.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.query.algorithm.LimitType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biopax.paxtools.search.SearchEngine.HitAnnotation: 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.
varSize() - Method in class org.biopax.paxtools.pattern.Match: Gets the array size.
varsPresent(int...) - Method in class org.biopax.paxtools.pattern.Match: Checks if all given indices are assigned.
VCompound - Class in org.biopax.paxtools.io.sbgn: VCompound Class
VCompound(Glyph) - Constructor for class org.biopax.paxtools.io.sbgn.VCompound: Default Constructor, creates a VCompound node by given glyph
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
visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.examples.PathwayGenesExtractor
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.
VNode - Class in org.biopax.paxtools.io.sbgn: VNode Class
VNode(Glyph) - Constructor for class org.biopax.paxtools.io.sbgn.VNode: Default Constructor, sets the geometry of the bounds which are attributes of this class
VNode.Bound - Class in org.biopax.paxtools.io.sbgn: Inner Class for glyph bounds

W

WHITE - Static variable in class org.biopax.paxtools.query.algorithm.BFS: Color white indicates the node is not processed.
width - Variable in class org.biopax.paxtools.io.sbgn.VNode.Bound
withComplexes() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From PhysicalEntity to parent Complex recursively, or to itself.
withComplexMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From Complex to its members, or the complex itself.
withSimpleMembers() - Static method in class org.biopax.paxtools.pattern.constraint.ConBox: From complex to its simple members recursively, or the Complex itself
wrap(Object) - Method in class org.biopax.paxtools.query.model.AbstractGraph: Creates the wrapper for the given object.
wrap(Object) - Method in class org.biopax.paxtools.query.wrapperL3.GraphL3: This method creates a wrapper for every wrappable L3 element.
wrap(Object) - Method in class org.biopax.paxtools.query.wrapperL3undirected.GraphL3Undirected: This method creates a wrapper for every wrappable L3 element.
write(Set<SIFInteraction>, OutputStream) - Static method in class org.biopax.paxtools.pattern.miner.OldFormatWriter: Writes down the given interactions into the given output stream in the old EXTENDED_BINARY_SIF format.
write(String) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Dumps data to the given file.
write(OutputStream) - Method in class org.biopax.paxtools.pattern.util.Blacklist: Dumps data to the given output stream.
writeInteractionsInSIF(Model, OutputStream) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

Infers simple interactions from the model using SimpleInteractionConverter.inferInteractions(org.biopax.paxtools.model.Model) and wrties them to an output stream.
writeInteractionsInSIFNX(Model, OutputStream, OutputStream, List<String>, List<String>, boolean) - Method in class org.biopax.paxtools.io.sif.SimpleInteractionConverter: Deprecated.

This method outputs inferred interactions in SIF annotation extended format (Sifnx).
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.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.AbstractSIFMiner: Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.ControlsStateChangeDetailedMiner: Writes the result as "A modifications-of-A B gains-of-B loss-of-B", where A and B are gene symbols, and whitespace is tab.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.DirectedRelationMiner: Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in interface org.biopax.paxtools.pattern.miner.Miner: Writes the text output to the given stream.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner: Writes the IDs of interaction, then gene symbols of related proteins in a line.
writeResult(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.UbiquitousIDMiner: Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
writeResultAsSIF(Map<BioPAXElement, List<Match>>, OutputStream, boolean, String, String) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method writes the output as pairs of gene symbols of the given two ProteinReference.
writeResultDetailed(Map<BioPAXElement, List<Match>>, OutputStream, int) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: Writes the result as a tab delimited format, where the column values are customized.
writeResults(String) - Method in class org.biopax.paxtools.pattern.example.DeltaFeatureExtractor
writeSBGN(Model, String) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Converts the given model to SBGN, and writes in the specified file.
writeSBGN(Model, OutputStream) - Method in class org.biopax.paxtools.io.sbgn.L3ToSBGNPDConverter: Converts the given model to SBGN, and writes in the specified output stream.
writeSIFsUsingSIFFramework(Map<BioPAXElement, List<Match>>, OutputStream) - Method in class org.biopax.paxtools.pattern.miner.MinerAdapter: This method writes the output as pairs of gene symbols of the given two ProteinReference.
writeStateNetworkAnalysis(OutputStream) - Method in class org.biopax.paxtools.io.sif.level3.ActivityNetworkAnalyzer: Deprecated.

This method writes out the results of the stateNetworkAnalysis for each detected state change.
writeToGSEA(Model, OutputStream) - Method in class org.biopax.paxtools.io.gsea.GSEAConverter: Converts model to GSEA (GMT) and writes to out.

X

XOR - Class in org.biopax.paxtools.pattern.constraint: Used for getting logical XOR of a set of constraints.
XOR(MappedConst...) - Constructor for class org.biopax.paxtools.pattern.constraint.XOR: Constructor with the mapped constraints.
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.
XrefFieldBridge - Class in org.biopax.paxtools.util: Deprecated.
Hibernate ORM/Search will be removed in v5
XrefFieldBridge() - Constructor for class org.biopax.paxtools.util.XrefFieldBridge: Deprecated.
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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