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

A

absoluteUris(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler

Sets the flag used when exporting a BioPAX model to RDF/XML: true - to always write full URI in rdf:resource and use rdf:about instead rdf:ID (does not matter xml:base is set or not).

AbstractAddRemoveCommand - Class in org.biopax.paxtools.command

AbstractAddRemoveCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.AbstractAddRemoveCommand

AbstractFilterSet<F,E> - Class in org.biopax.paxtools.util

Base class for implementing various filter sets.

AbstractFilterSet(Set<? extends F>) - Constructor for class org.biopax.paxtools.util.AbstractFilterSet

AbstractPropertyCommand<D extends BioPAXElement,R> - Class in org.biopax.paxtools.command

AbstractPropertyEditor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller

This is the base class for all property editors.

AbstractPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.AbstractPropertyEditor

Constructor.

AbstractTraverser - Class in org.biopax.paxtools.controller

This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required.

AbstractTraverser(EditorMap, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.AbstractTraverser

access(E) - Method in class org.biopax.paxtools.util.AccessibleSet

access(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper

AccessibleSet<E> - Class in org.biopax.paxtools.util

This is a decorator set for capturing a set member that is equal to the given parameter.

AccessibleSet() - Constructor for class org.biopax.paxtools.util.AccessibleSet

add(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl

add(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model

This method add the given onject to this model.

add(E) - Method in class org.biopax.paxtools.util.BiopaxSafeSet

add(T) - Method in class org.biopax.paxtools.util.EquivalenceGrouper

addAuthor(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

addAuthor(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref

addAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref

addAvailability(String) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

addAVAILABILITY(String) - Method in interface org.biopax.paxtools.model.level2.entity

This method adds the given text to the avaialability set.

addAvailability(String) - Method in interface org.biopax.paxtools.model.level3.Entity

This method adds the given text to the avaialability set.

addCofactor(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

addCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis

addCofactor(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.

AddCommand - Class in org.biopax.paxtools.command

AddCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.AddCommand

addComment(String) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

addCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.Level2Element

addComment(String) - Method in interface org.biopax.paxtools.model.level3.Level3Element

A textual comment about this individual.

addComponent(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

addComponent(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Complex

Defines the PhysicalEntity subunits of this complex.

addCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex

addComponentStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

addComponentStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Complex

The stoichiometry of components in a complex.

addConfidence(Score) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

Confidence in the containing instance.

addCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence

addConfidence(Score) - Method in interface org.biopax.paxtools.model.level3.Evidence

Confidence in the containing instance.

addControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl

addCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control

addControlled(Process) - Method in interface org.biopax.paxtools.model.level3.Control

The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.

addController(Controller) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

addController(Controller) - Method in class org.biopax.paxtools.impl.level3.ControlImpl

addCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control

addController(Controller) - Method in interface org.biopax.paxtools.model.level3.Control

The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.

addDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity

This method adds the given value to the DATA_SOURCE set.

addDataSource(Provenance) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

addDataSource(Provenance) - Method in interface org.biopax.paxtools.model.level3.Entity

This method adds the given value to the DATA_SOURCE set.

addDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

addDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

addDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

addDeltaG(DeltaG) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

addDeltaG(DeltaG) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

addDeltaH(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

addDeltaH(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

addDeltaS(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

addDeltaS(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

addEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

addECNumber(String) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

addECNumber(String) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

addEntityFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

addEntityFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.

addEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

addEntityReferenceType(EntityReferenceTypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Adds the given cv to the list of types

addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

addEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

addEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process

This method adds the given evidence to this process.

addEvidence(Evidence) - Method in interface org.biopax.paxtools.model.level3.Observable

addEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence

addEvidenceCode(EvidenceCodeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

addEvidenceCode(EvidenceCodeVocabulary) - Method in interface org.biopax.paxtools.model.level3.Evidence

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

addEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence

addEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm

addExperimentalFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

addExperimentalFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm

This method adds an experimental feature

addExperimentalForm(ExperimentalForm) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

addExperimentalForm(ExperimentalForm) - Method in interface org.biopax.paxtools.model.level3.Evidence

Adds an experimental form.

addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm

Adds an experimental form description.

addFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

addFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl

addFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

addFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

addINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction

addInteractionType(InteractionVocabulary) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl

addInteractionType(InteractionVocabulary) - Method in interface org.biopax.paxtools.model.level3.Interaction

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".

addKEQ(KPrime) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

addKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

addKEQ(KPrime) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

This quantity is dimensionless and is usually a single number.

addLeft(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

addLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion

addLeft(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion

Adds a participant to the left side of the conversion interaction.

addMaxCardinalityRestriction(Class<? extends D>, int) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

addMaxCardinalityRestriction(Class<? extends D>, int) - Method in interface org.biopax.paxtools.controller.PropertyEditor

Sets a maximum cardinality for a domain.

addMemberEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

addMemberEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Adds the given entityReference to the member list

addMemberFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

addMemberFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature

An entity feature that belongs to this homology grouping.

addMemberPhysicalEntity(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

addMemberPhysicalEntity(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

addMethod - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor

This variable stores the method to invoke for adding the given value to the property managed by this commander.

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

addSubRegion(NucleicAcidRegionReference) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

addSubRegion(NucleicAcidRegionReference) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference

addSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.entity

This method adds the given value to the SYNONYMS set.

addSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

addTerm(String) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

addTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary

addTerm(String) - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary

addUrl(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

addURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref

addUrl(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref

addXref(Xref) - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl

addXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable

addXref(Xref) - Method in interface org.biopax.paxtools.model.level3.XReferrable

applies(BioPAXElement) - Method in class org.biopax.paxtools.controller.PathAccessor

atEquivalentLocation(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

atEquivalentLocation(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature

AutoComplete - Annotation Type in org.biopax.paxtools.util

Interface for demarcating excise-able boundaries of the object graph.

B

base - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

baseSet - Variable in class org.biopax.paxtools.util.AbstractFilterSet

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.

bindArrays(ObjectPropertyEditor, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory

bindArrays(String, BioPAXElement[], BioPAXElement[]) - Method in class org.biopax.paxtools.impl.MockFactory

BindingFeature - Interface in org.biopax.paxtools.model.level3

BindingFeatureImpl - Class in org.biopax.paxtools.impl.level3

BindingFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.BindingFeatureImpl

bindInPairs(ObjectPropertyEditor, BioPAXElement...) - Method in class org.biopax.paxtools.impl.MockFactory

bindInPairs(String, BioPAXElement...) - Method in class org.biopax.paxtools.impl.MockFactory

bindValue(String, PropertyEditor, BioPAXElement, Model) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

This method binds the value to the bpe.

BiochemicalPathwayStep - Interface in org.biopax.paxtools.model.level3

Definition: Imposes ordering on a step in a biochemical pathway.

BiochemicalPathwayStepImpl - Class in org.biopax.paxtools.impl.level3

BiochemicalPathwayStepImpl() - Constructor for class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

biochemicalReaction - Interface in org.biopax.paxtools.model.level2

A conversion interaction in which one or more entities (substrates) undergo ovalent changes to become one or more other entities (products).

BiochemicalReaction - Interface in org.biopax.paxtools.model.level3

Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).

BiochemicalReactionImpl - Class in org.biopax.paxtools.impl.level3

BiochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

BioPAXElement - Interface in org.biopax.paxtools.model

This class represents a general BioPAXElement, regardless of Level.

BioPAXElementImpl - Class in org.biopax.paxtools.impl

BioPAXElementImpl() - Constructor for class org.biopax.paxtools.impl.BioPAXElementImpl

BioPAXFactory - Class in org.biopax.paxtools.model

Abstract factory class for instantiating BioPAX classes.

BioPAXFactory() - Constructor for class org.biopax.paxtools.model.BioPAXFactory

Protected Constructor without parameters.

BioPaxIOException - Exception in org.biopax.paxtools.util

This exception is thrown if a problem occurs during an input/output operation related to BioPAX Handlers.

BioPaxIOException(Throwable) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException

BioPaxIOException(String) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException

BioPaxIOException(String, Throwable) - Constructor for exception org.biopax.paxtools.util.BioPaxIOException

BioPAXIOHandler - Interface in org.biopax.paxtools.io

This interface defines IO related operations that can be performed on BioPAX models.

BioPAXIOHandlerAdapter - Class in org.biopax.paxtools.io

BioPAXIOHandlerAdapter() - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

BioPAXIOHandlerAdapter(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

BioPAXIOHandlerAdapter(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

BioPAXLevel - Enum in org.biopax.paxtools.model

Enumeration type for BioPAX levels.

BiopaxSafeSet<E extends BioPAXElement> - Class in org.biopax.paxtools.util

A thread-safe set of BioPAX objects that also prevents adding several elements having the same URI.

BiopaxSafeSet() - Constructor for class org.biopax.paxtools.util.BiopaxSafeSet

bioSource - Interface in org.biopax.paxtools.model.level2

The biological source of an entity (e.g.

BioSource - Interface in org.biopax.paxtools.model.level3

Definition: The biological source of an entity (e.g.

BioSourceImpl - Class in org.biopax.paxtools.impl.level3

BioSourceImpl() - Constructor for class org.biopax.paxtools.impl.level3.BioSourceImpl

bp - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

BP_PREFIX - Static variable in enum org.biopax.paxtools.model.BioPAXLevel

This is the prefix used for all biopax releases.

BPCollections - Enum in org.biopax.paxtools.util

BPCollections.CollectionProvider - Interface in org.biopax.paxtools.util

This interface is responsible for setting the class and initialize and load factor for all sets and maps used in all model objects for performance purposes.

buildCustomEditorMap(BioPAXLevel, InputStream) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

C

canInstantiate(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.model.BioPAXFactory

Checks whether objects of a BioPAX model interface can be created (some types are not official BioPAX types, abstract classes).

canRedo() - Method in class org.biopax.paxtools.command.CommandManager

canRedo() - Method in class org.biopax.paxtools.command.PropertyAddCommand

canRedo() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

canUndo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand

canUndo() - Method in class org.biopax.paxtools.command.CommandManager

canUndo() - Method in class org.biopax.paxtools.command.PropertyAddCommand

canUndo() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

catalysis - Interface in org.biopax.paxtools.model.level2

A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.

Catalysis - Interface in org.biopax.paxtools.model.level3

Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.

CatalysisDirectionType - Enum in org.biopax.paxtools.model.level3

This enum represents the direction of a catalysis under all physiological conditions if there is one.

CatalysisImpl - Class in org.biopax.paxtools.impl.level3

CatalysisImpl() - Constructor for class org.biopax.paxtools.impl.level3.CatalysisImpl

CellularLocationVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.

CellularLocationVocabularyImpl - Class in org.biopax.paxtools.impl.level3

CellularLocationVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl

CellVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: A reference to the Cell Type Ontology (CL).

CellVocabularyImpl - Class in org.biopax.paxtools.impl.level3

CellVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.CellVocabularyImpl

checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl

checkControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ModulationImpl

checkERFeatureSet(EntityReference, boolean) - Static method in class org.biopax.paxtools.controller.ModelUtils

Finds and adds all (missing) entity features to given entity reference from all its owner simple physical entities ('feature' and 'notFeature' properties).

checkRestrictions - Static variable in class org.biopax.paxtools.controller.AbstractPropertyEditor

checkRestrictions(R, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

Checks if the bean and the value are consistent with the cardinality rules of the model.

checkRestrictions(R, D) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

checkRestrictions(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler

If set to true, property editors will check restrictions at the subclass level and throw an exception if violated.

ChemicalConstant - Interface in org.biopax.paxtools.model.level3

ChemicalConstantImpl - Class in org.biopax.paxtools.impl.level3

ChemicalConstantImpl() - Constructor for class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

chemicalStructure - Interface in org.biopax.paxtools.model.level2

Describes a small molecule structure.

ChemicalStructure - Interface in org.biopax.paxtools.model.level3

Definition: The chemical structure of a small molecule.

ChemicalStructureImpl - Class in org.biopax.paxtools.impl.level3

ChemicalStructureImpl() - Constructor for class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

ClassFilterSet<E,F extends E> - Class in org.biopax.paxtools.util

A FilterSet that filters based on the class.

ClassFilterSet(Set<? extends E>, Class<F>) - Constructor for class org.biopax.paxtools.util.ClassFilterSet

classToEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl

A map from classes to their registered editors.

classToEditorSet - Variable in class org.biopax.paxtools.controller.EditorMapImpl

Another map to keep editors as a set rather than a map.

classToInverseEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl

A map from classes to their registered inverse editors

clone(Model, Set<BioPAXElement>) - Method in class org.biopax.paxtools.controller.Cloner

For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored.

Cloner - Class in org.biopax.paxtools.controller

Specifically "Clones" the BioPAX elements set (traverses to obtain dependent elements), puts them to the new model using the visitor and traverser framework; ignores elements that are not in the source list (compare to Fetcher)

Cloner(EditorMap, BioPAXFactory) - Constructor for class org.biopax.paxtools.controller.Cloner

collectSimpleMembersRecursive(PhysicalEntity, Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

Command - Interface in org.biopax.paxtools.command

CommandManager - Class in org.biopax.paxtools.command

This is a class for manipulating a BioPAX model via undoable commands

CommandManager(Model) - Constructor for class org.biopax.paxtools.command.CommandManager

compareTo(Object) - Method in class org.biopax.paxtools.controller.ConversionScore

complete(Collection<BioPAXElement>, Model) - Method in class org.biopax.paxtools.controller.Completer

Completer - Class in org.biopax.paxtools.controller

This class is used for getting a valid subgraph from a set of BioPAX elements.

Completer(EditorMap) - Constructor for class org.biopax.paxtools.controller.Completer

complex - Interface in org.biopax.paxtools.model.level2

A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.

Complex - Interface in org.biopax.paxtools.model.level3

Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.

complexAssembly - Interface in org.biopax.paxtools.model.level2

A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.

ComplexAssembly - Interface in org.biopax.paxtools.model.level3

Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.

ComplexAssemblyImpl - Class in org.biopax.paxtools.impl.level3

ComplexAssemblyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl

ComplexImpl - Class in org.biopax.paxtools.impl.level3

ComplexImpl() - Constructor for class org.biopax.paxtools.impl.level3.ComplexImpl

CompositeIterator<T> - Class in org.biopax.paxtools.util

A composite iterator that iterates over multiple iterators.

CompositeIterator(Collection<? extends Collection<? extends T>>) - Constructor for class org.biopax.paxtools.util.CompositeIterator

This constructor creates an iterator instance from a set of collections

confidence - Interface in org.biopax.paxtools.model.level2

Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure.

contains(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl

This method returns true if given element is the same object ("==") as the object stored in the model usually (for self-consistent models) but not necessarily under the element's ID.

contains(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model

This method returns true if the parameter is contained within this model.

contains(Object) - Method in class org.biopax.paxtools.util.AbstractFilterSet

contains(Object) - Method in class org.biopax.paxtools.util.BiopaxSafeSet

containsEquivalent(Set<? extends BioPAXElement>, BioPAXElement) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker

containsID(String) - Method in class org.biopax.paxtools.impl.ModelImpl

containsID(String) - Method in interface org.biopax.paxtools.model.Model

This method checks for the biopax element with the given id, returns true if the object with the given id exists.

control - Interface in org.biopax.paxtools.model.level2

Control - Interface in org.biopax.paxtools.model.level3

Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.

ControlImpl - Class in org.biopax.paxtools.impl.level3

ControlImpl() - Constructor for class org.biopax.paxtools.impl.level3.ControlImpl

ControlledVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: This class represents a term from an external controlled vocabulary (CV).

ControlledVocabularyImpl - Class in org.biopax.paxtools.impl.level3

ControlledVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

Constructor.

Controller - Interface in org.biopax.paxtools.model.level3

This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.

ControlType - Enum in org.biopax.paxtools.model.level2

User: root Date: Aug 1, 2006 Time: 5:37:34 PM_DOT

ControlType - Enum in org.biopax.paxtools.model.level3

Defines the nature of the control relationship between the controller and the controlled entities.

conversion - Interface in org.biopax.paxtools.model.level2

Conversion - Interface in org.biopax.paxtools.model.level3

Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.

ConversionDirectionType - Enum in org.biopax.paxtools.model.level3

This enum is used for specifying the direction of a Conversion.

ConversionImpl - Class in org.biopax.paxtools.impl.level3

ConversionImpl() - Constructor for class org.biopax.paxtools.impl.level3.ConversionImpl

ConversionScore - Class in org.biopax.paxtools.controller

Encapsulation of scores of conversions, and related information

ConversionScore(conversion, conversion, Double, Map<physicalEntityParticipant, physicalEntityParticipant>, boolean) - Constructor for class org.biopax.paxtools.controller.ConversionScore

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.

convertToOWL(Model, OutputStream) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler

This method will write the model to the output stream.

convertToOWL(Model, OutputStream, String...) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler

This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.

convertToOWL(Model, OutputStream, String...) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Similar to BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) (org.biopax.paxtools.model.Model, Object)}, but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.

convertToOWL(Model, OutputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler

Converts a model into BioPAX (OWL) format, and writes it into the outputStream.

convertToOwl(Model) - Static method in class org.biopax.paxtools.io.SimpleIOHandler

Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string.

copy(Model, T, String) - Method in class org.biopax.paxtools.controller.ShallowCopy

Creates a copy of the BioPAX object with all its properties are the same, and also adds it to a model.

copy(T, String) - Method in class org.biopax.paxtools.controller.ShallowCopy

Returns a copy of the BioPAX element (with all the property values are same)

copyPEPFields() - Method in class org.biopax.paxtools.controller.ReusedPEPHelper

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.

createAndBind(Model) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.

createAndBind(Model) - Method in class org.biopax.paxtools.io.SimpleIOHandler

createAndRegisterBeanEditor(String, Class, Map<Class<? extends BioPAXElement>, Set<Class<? extends BioPAXElement>>>) - Method in class org.biopax.paxtools.controller.EditorMapImpl

createMap() - Method in interface org.biopax.paxtools.util.BPCollections.CollectionProvider

createMap() - Method in enum org.biopax.paxtools.util.BPCollections

createModel() - Method in class org.biopax.paxtools.model.BioPAXFactory

Creates a new BioPAX model.

createPropertyEditor(Class<D>, String) - Static method in class org.biopax.paxtools.controller.AbstractPropertyEditor

This method creates a property reflecting on the domain and property.

createSafeSet() - Method in enum org.biopax.paxtools.util.BPCollections

createSet() - Method in interface org.biopax.paxtools.util.BPCollections.CollectionProvider

createSet() - Method in enum org.biopax.paxtools.util.BPCollections

D

DataPropertyEditor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller

Created by igor on 13/08/15.

dataSource - Interface in org.biopax.paxtools.model.level2

XREF Should be only unification and publication xrefs

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.

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

Degradation - Interface in org.biopax.paxtools.model.level3

Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.

DegradationImpl - Class in org.biopax.paxtools.impl.level3

DegradationImpl() - Constructor for class org.biopax.paxtools.impl.level3.DegradationImpl

DeltaG - Interface in org.biopax.paxtools.model.level3

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

DeltaGImpl - Class in org.biopax.paxtools.impl.level3

DeltaGImpl() - Constructor for class org.biopax.paxtools.impl.level3.DeltaGImpl

deltaGprimeO - Interface in org.biopax.paxtools.model.level2

detectRange(Method) - Static method in class org.biopax.paxtools.controller.AbstractPropertyEditor

Given the multiple cardinality feature, the range of the get method is returned.

Direction - Enum in org.biopax.paxtools.model.level2

Catalysis direction controlled vocabulary

dna - Interface in org.biopax.paxtools.model.level2

Dna - Interface in org.biopax.paxtools.model.level3

Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.

DnaImpl - Class in org.biopax.paxtools.impl.level3

DnaImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaImpl

DnaReference - Interface in org.biopax.paxtools.model.level3

A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.

DnaReferenceImpl - Class in org.biopax.paxtools.impl.level3

DnaReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaReferenceImpl

DnaRegion - Interface in org.biopax.paxtools.model.level3

Definition: A region on a DNA molecule.

DnaRegionImpl - Class in org.biopax.paxtools.impl.level3

DnaRegionImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaRegionImpl

DnaRegionReference - Interface in org.biopax.paxtools.model.level3

Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.

DnaRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3

DnaRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl

domain - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter

This is the Class representing the domain of the property.

domain - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple

E

editor(String, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.impl.MockFactory

EditorMap - Interface in org.biopax.paxtools.controller

This class contains methods that eases to use editors for specific or a set of property.

editorMap - Variable in class org.biopax.paxtools.controller.Traverser

editorMap - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

EditorMapImpl - Class in org.biopax.paxtools.controller

This is the base adapter for all editor maps.

EditorMapImpl(BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.EditorMapImpl

entity - Interface in org.biopax.paxtools.model.level2

This class represents a discrete biological unit used when describing pathways.

Entity - Interface in org.biopax.paxtools.model.level3

This class represents a discrete biological unit used when describing pathways.

EntityFeature - Interface in org.biopax.paxtools.model.level3

Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.

EntityFeatureImpl - Class in org.biopax.paxtools.impl.level3

EntityFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityFeatureImpl

EntityImpl - Class in org.biopax.paxtools.impl.level3

EntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityImpl

Helper object for managing names

EntityReference - Interface in org.biopax.paxtools.model.level3

Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists.

EntityReferenceImpl - Class in org.biopax.paxtools.impl.level3

EntityReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityReferenceImpl

Constructor.

EntityReferenceTypeVocabulary - Interface in org.biopax.paxtools.model.level3

Definiiton: A reference to a term from an entity reference group ontology.

EntityReferenceTypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3

EntityReferenceTypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl

EnumeratedPropertyEditor<D extends BioPAXElement,R extends Enum> - Class in org.biopax.paxtools.controller

Provides an ENUM class compatible editor by extending the PropertyEditor.

EnumeratedPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.EnumeratedPropertyEditor

equals(Object) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

true if and only if the other obj has the same biopax type (same BioPAXElement.getModelInterface(), not a subclass) and same URI.

equivalenceCode() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl

equivalenceCode() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

equivalenceCode() - Method in interface org.biopax.paxtools.model.BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

EquivalenceGrouper<T extends BioPAXElement> - Class in org.biopax.paxtools.util

Utility class for equivalence based comparison of a set of BioPAXElements.

EquivalenceGrouper(Set<? extends T>) - Constructor for class org.biopax.paxtools.util.EquivalenceGrouper

EquivalenceGrouper() - Constructor for class org.biopax.paxtools.util.EquivalenceGrouper

evidence - Interface in org.biopax.paxtools.model.level2

Evidence - Interface in org.biopax.paxtools.model.level3

Definition: The support for a particular assertion, such as the existence of an interaction or pathway.

EvidenceCodeVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".

EvidenceCodeVocabularyImpl - Class in org.biopax.paxtools.impl.level3

EvidenceCodeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl

evidenceFilter - Static variable in class org.biopax.paxtools.controller.Fetcher

A property filter to ignore 'evidence' ('EVIDENCE' in L2) property (it can eventually lead to other organism, experimental entities)

EvidenceImpl - Class in org.biopax.paxtools.impl.level3

EvidenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.EvidenceImpl

Constructor.

experimentalForm - Interface in org.biopax.paxtools.model.level2

ExperimentalForm - Interface in org.biopax.paxtools.model.level3

Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.

ExperimentalFormImpl - Class in org.biopax.paxtools.impl.level3

ExperimentalFormImpl() - Constructor for class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

Constructor.

ExperimentalFormVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: A term that describes the form of the physical entity in the context of the experiment.

ExperimentalFormVocabularyImpl - Class in org.biopax.paxtools.impl.level3

ExperimentalFormVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl

externalReferenceUtilityClass - Interface in org.biopax.paxtools.model.level2

F

factory - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

fetch(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.Fetcher

Adds the element and all its children (found via traversing into object properties that pass all the filters defined in the Constructor, and also taking #isSkipSubPathways into account) to the target model.

fetch(BioPAXElement) - Method in class org.biopax.paxtools.controller.Fetcher

Recursively finds and collects all child objects, while escaping possible infinite loops.

fetch(BioPAXElement, int) - Method in class org.biopax.paxtools.controller.Fetcher

Recursively collects unique child objects from BioPAX object type properties that pass all the filters (as set via Constructor).

fetch(BioPAXElement, Class<T>) - Method in class org.biopax.paxtools.controller.Fetcher

Goes over object type biopax properties to collect nested objects (using only properties that pass all the filters set in Constructor, and taking #isSkipSubPathways into account) of the given biopax element, its children, etc.

Fetcher - Class in org.biopax.paxtools.controller

This class is used to fetch an element (traverse it to obtain its dependent elements) and to add this element into a model using the visitor and traverse functions.

Fetcher(EditorMap, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.Fetcher

Constructor.

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_ECNUMBER - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_KEYWORD - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_NAME - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_ORGANISM - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_PATHWAY - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_SEQUENCE - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_TERM - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_XREFDB - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_XREFID - Static variable in class org.biopax.paxtools.impl.BioPAXElementImpl

filter(Model) - Method in interface org.biopax.paxtools.controller.ModelFilter

filter(PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.Traverser

filter(Model) - Method in class org.biopax.paxtools.converter.LevelUpgrader

Converts a BioPAX Model, Level 1 or 2, to the Level 3.

filter(E) - Method in class org.biopax.paxtools.util.ClassFilterSet

This filter method implementation filters based on isInstance function.

Filter<T> - Interface in org.biopax.paxtools.util

Generic interface for defining filter decorators.

filter(T) - Method in interface org.biopax.paxtools.util.Filter

Can e.g., analyze, modify or convert the given object (or model) to another format.

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

findCommonPublications(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable

findCommonRelationships(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable

findCommonUnifications(XReferrable) - Method in interface org.biopax.paxtools.model.level2.XReferrable

findEquivalentIntersection(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker

findFeaturesAddedToSecond(PhysicalEntity, PhysicalEntity, boolean) - Static method in class org.biopax.paxtools.controller.ModelUtils

findInverseGetMethod() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

fixDanglingInverseProperties(BioPAXElement, Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

Unlinks inverse properties of the BioPAX object from values the 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.

fixReusedPEP(physicalEntityParticipant, BioPAXElement) - Method in class org.biopax.paxtools.controller.ReusedPEPHelper

fixReusedPEPs(boolean) - Method in interface org.biopax.paxtools.io.BioPAXIOHandler

This option is only applicable two level 2 models.

fixReusedPEPs(boolean) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Enables (true) or disables (false) the fixing of reused peps.

FragmentFeature - Interface in org.biopax.paxtools.model.level3

Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.

FragmentFeatureImpl - Class in org.biopax.paxtools.impl.level3

FragmentFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

G

Gene - Interface in org.biopax.paxtools.model.level3

Definition: A continuant that encodes information that can be inherited through replication.

GeneImpl - Class in org.biopax.paxtools.impl.level3

GeneImpl() - Constructor for class org.biopax.paxtools.impl.level3.GeneImpl

generateClassMetrics(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

Generates simple counts of different elements in the model.

GeneticInteraction - Interface in org.biopax.paxtools.model.level3

Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.

GeneticInteractionImpl - Class in org.biopax.paxtools.impl.level3

GeneticInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.GeneticInteractionImpl

get(BioPAXLevel) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

To obtain a copy of the editor map for the corresponding level, use the

get(String) - Method in class org.biopax.paxtools.util.BiopaxSafeSet

Gets a BioPAX element by URI.

getAbsoluteRegion() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

getAbsoluteRegion() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference

getAddedElements() - Method in class org.biopax.paxtools.controller.Merger

After a merge is accomplished, this set will contain the newly added elements.

getAddMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getAddMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor

getAllChildren(BioPAXElement, Filter<PropertyEditor>...) - Static method in class org.biopax.paxtools.controller.ModelUtils

Gets all the child BioPAX elements of a given BioPAX element (using the "tuned" Fetcher) and adds them to a new model.

getAllInteractions() - Method in interface org.biopax.paxtools.model.level2.physicalEntity

getAllInteractions(Class<T>) - Method in interface org.biopax.paxtools.model.level2.physicalEntity

getAnnotations() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

getAnnotations() - Method in interface org.biopax.paxtools.model.BioPAXElement

A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.

getAuthor() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getAuthor() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

getAUTHORS() - Method in interface org.biopax.paxtools.model.level2.publicationXref

getAvailability() - Method in class org.biopax.paxtools.impl.level3.EntityImpl

getAVAILABILITY() - Method in interface org.biopax.paxtools.model.level2.entity

The contents of this set can be modified but semantic consistency is not guaranteed.

getAvailability() - Method in interface org.biopax.paxtools.model.level3.Entity

The contents of this set can be modified but semantic consistency is not guaranteed.

getBindsTo() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl

getBindsTo() - Method in interface org.biopax.paxtools.model.level3.BindingFeature

A binding feature represents a "half" of the bond between two entities.

getBuckets() - Method in class org.biopax.paxtools.util.EquivalenceGrouper

getByID(String) - Method in class org.biopax.paxtools.impl.ModelImpl

getByID(String) - Method in interface org.biopax.paxtools.model.Model

This method returns the biopax element with the given id, returns null if the object with the given id does not exist in this model.

getCatalysisDirection() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

getCatalysisDirection() - Method in interface org.biopax.paxtools.model.level3.Catalysis

This property represents the direction of this catalysis under all physiological conditions if there is one.

getCellType() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

getCELLTYPE() - Method in interface org.biopax.paxtools.model.level2.bioSource

getCellType() - Method in interface org.biopax.paxtools.model.level3.BioSource

A cell type, e.g.

getCELLULAR_LOCATION() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

getCellularLocation() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getCellularLocation() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

A cellular location, e.g.

getCHEMICAL_FORMULA() - Method in interface org.biopax.paxtools.model.level2.smallMolecule

getChemicalFormula() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

getChemicalFormula() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference

getCofactor() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

getCOFACTOR() - Method in interface org.biopax.paxtools.model.level2.catalysis

getCofactor() - Method in interface org.biopax.paxtools.model.level3.Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.

getComment() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

getCOMMENT() - Method in interface org.biopax.paxtools.model.level2.Level2Element

getComment() - Method in interface org.biopax.paxtools.model.level3.Level3Element

A textual comment about this individual.

getComponent() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getComponent() - Method in interface org.biopax.paxtools.model.level3.Complex

Defines the PhysicalEntity subunits of this complex.

getComponentOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getComponentOf() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

getCOMPONENTS() - Method in interface org.biopax.paxtools.model.level2.complex

getComponentStoichiometry() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getComponentStoichiometry() - Method in interface org.biopax.paxtools.model.level3.Complex

The stoichiometry of components in a complex.

getConfidence() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

Confidence in the containing instance.

getCONFIDENCE() - Method in interface org.biopax.paxtools.model.level2.evidence

getConfidence() - Method in interface org.biopax.paxtools.model.level3.Evidence

Confidence in the containing instance.

getCONFIDENCE_VALUE() - Method in interface org.biopax.paxtools.model.level2.confidence

The value of the confidence measure.

getCONTROL_TYPE() - Method in interface org.biopax.paxtools.model.level2.control

getControlled() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getCONTROLLED() - Method in interface org.biopax.paxtools.model.level2.control

getControlled() - Method in interface org.biopax.paxtools.model.level3.Control

The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.

getControlledOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf() - Method in interface org.biopax.paxtools.model.level3.Process

getController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getCONTROLLER() - Method in interface org.biopax.paxtools.model.level2.control

getController() - Method in interface org.biopax.paxtools.model.level3.Control

The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.

getControllerOf() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

getControllerOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getControllerOf() - Method in interface org.biopax.paxtools.model.level3.Controller

This method returns the list of Control interactions that this entity controls.

getControlType() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getControlType() - Method in interface org.biopax.paxtools.model.level3.Control

Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities.

getConversion1() - Method in class org.biopax.paxtools.controller.ConversionScore

getConversion2() - Method in class org.biopax.paxtools.controller.ConversionScore

getConversionDirection() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

getConversionDirection() - Method in interface org.biopax.paxtools.model.level3.Conversion

This property represents the direction of the reaction.

getDATA_SOURCE() - Method in interface org.biopax.paxtools.model.level2.entity

This method returns a set of free text descriptions of the source of this data, e.g.

getDataSource() - Method in class org.biopax.paxtools.impl.level3.EntityImpl

getDataSource() - Method in interface org.biopax.paxtools.model.level3.Entity

This method returns a set of free text descriptions of the source of this data, e.g.

getDatasources(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils

Collects all Provenance objects associated with this one as follows: - if the element is Entity (has 'dataSource' property) or is Provenence itself, get the values and quit; - if the biopax element is PathwayStep or EntityReference, traverse into some of its object/inverse properties to collect dataSource values from associated entities.

getDatasources() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

Deprecated.

use getAnnotations() instead

getDb() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

getDB() - Method in interface org.biopax.paxtools.model.level2.xref

getDb() - Method in interface org.biopax.paxtools.model.level3.Xref

getDB_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref

getDbVersion() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

getDbVersion() - Method in interface org.biopax.paxtools.model.level3.Xref

getDefaultFactory() - Method in enum org.biopax.paxtools.model.BioPAXLevel

This method returns the default factory for this level

getDELTA_G() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

getDELTA_G_PRIME_O() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO

getDELTA_H() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

getDELTA_S() - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

getDeltaG() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

getDeltaG() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

getDeltaGPrime0() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl

getDeltaGPrime0() - Method in interface org.biopax.paxtools.model.level3.DeltaG

For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

getDeltaH() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

getDeltaH() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

getDeltaS() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

getDeltaS() - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

getDirectChildren(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils

Gets direct children of a given BioPAX element and adds them to a new model.

getDirectChildrenAsSet(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils

Collects direct children of a given BioPAX element.

getDIRECTION() - Method in interface org.biopax.paxtools.model.level2.catalysis

getDisplayName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl

getDisplayName() - Method in interface org.biopax.paxtools.model.level3.Named

An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.

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.

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()

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.

getGenericEntityReferences() - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

getGenericEntityReferences() - Method in interface org.biopax.paxtools.model.level3.SimplePhysicalEntity

This method returns: The entity reference of this PhysicalEntity plus If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively

getGetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getGetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor

getId() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

getId() - Method in class org.biopax.paxtools.io.SimpleIOHandler

getID() - Method in interface org.biopax.paxtools.model.level2.xref

getId() - Method in interface org.biopax.paxtools.model.level3.Xref

getID_VERSION() - Method in interface org.biopax.paxtools.model.level2.xref

getIdVersion() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

getIdVersion() - Method in interface org.biopax.paxtools.model.level3.Xref

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.

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.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'.

getLeft() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

getLEFT() - Method in interface org.biopax.paxtools.model.level2.conversion

getLeft() - Method in interface org.biopax.paxtools.model.level3.Conversion

The participants on the left side of the conversion interaction.

getLevel() - Method in interface org.biopax.paxtools.controller.EditorMap

Returns the BioPAX level for which editor map is created.

getLevel() - Method in class org.biopax.paxtools.controller.EditorMapImpl

getLevel() - Method in enum org.biopax.paxtools.controller.SimpleEditorMap

getLevel() - Method in class org.biopax.paxtools.impl.MockFactory

getLevel() - Method in class org.biopax.paxtools.impl.ModelImpl

getLevel() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler

getLevel() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

getLevel() - Method in class org.biopax.paxtools.model.BioPAXFactory

Gets the level.

getLevel() - Method in interface org.biopax.paxtools.model.Model

This method returns the level of the objects that are contained within this model.

getLevelFileAsStream() - Method in enum org.biopax.paxtools.model.BioPAXLevel

This method loads the level file as resource and returns it as an input stream

getLevelFromNameSpace(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel

getLocalId(BioPAXElement) - Static method in class org.biopax.paxtools.converter.LevelUpgrader

Gets the local part of the BioPAX element ID.

getMatch(physicalEntityParticipant) - Method in class org.biopax.paxtools.controller.ConversionScore

getMatchedPEPs() - Method in class org.biopax.paxtools.controller.ConversionScore

getMatchingEnum(Object) - Method in class org.biopax.paxtools.converter.LevelUpgrader

getMaxCardinality(Class<? extends D>) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getMaxCardinality(Class<? extends D>) - Method in interface org.biopax.paxtools.controller.PropertyEditor

Return the maximum cardinality that is defined for the property to which editor is belong.

getMemberEntityReference() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

getMemberEntityReference() - Method in interface org.biopax.paxtools.model.level3.EntityReference

getMemberEntityReferenceOf() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

getMemberEntityReferenceOf() - Method in interface org.biopax.paxtools.model.level3.EntityReference

Reverse of EntityReference.getMemberEntityReference()

getMemberFeature() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

getMemberFeature() - Method in interface org.biopax.paxtools.model.level3.EntityFeature

An entity feature that belongs to this homology grouping.

getMemberFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

getMemberFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature

Reverse of EntityFeature.getMemberFeature()

getMemberPhysicalEntity() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getMemberPhysicalEntity() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

Please avoid using this property in your BioPAX L3 models unless absolutely sure/required, for there is an alternative way (using PhysicalEntity/entityReference/memberEntityReference), and this will probably be deprecated in the future BioPAX releases.

getMemberPhysicalEntityOf() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getMemberPhysicalEntityOf() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

getMemberReferences() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getMemberReferences() - Method in interface org.biopax.paxtools.model.level3.Complex

Gets the EntityReferences of the member simple physical entities.

getMergedElements() - Method in class org.biopax.paxtools.controller.Merger

After a merge is accomplished, this set will contain the merged elements.

getMethod - Variable in class org.biopax.paxtools.controller.SimplePropertyAccessor

This variable stores the method to invoke for getting the value of the property on a given bean.

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CellularLocationVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CellVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ComplexAssemblyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DegradationImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaRegionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.DnaRegionReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EntityReferenceTypeVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EvidenceCodeVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.GeneImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.InteractionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ModulationImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.MolecularInteractionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProteinImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProteinReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ProvenanceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaRegionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceLocationImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceModificationVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceRegionVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TissueVocabularyImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TransportImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl

getModelInterface() - Method in class org.biopax.paxtools.impl.level3.UnificationXrefImpl

getModelInterface() - Method in interface org.biopax.paxtools.model.BioPAXElement

This method returns the actual model interface that a class implements.

getModelInterface() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

Overridden to provide better downcasting

getModificationType() - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl

getModificationType() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

getModificationType() - Method in interface org.biopax.paxtools.model.level3.ModificationFeature

getMOLECULAR_WEIGHT() - Method in interface org.biopax.paxtools.model.level2.smallMolecule

getMolecularWeight() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

getMolecularWeight() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference

getName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl

getNAME() - Method in interface org.biopax.paxtools.model.level2.bioSource

getNAME() - Method in interface org.biopax.paxtools.model.level2.dataSource

getNAME() - Method in interface org.biopax.paxtools.model.level2.entity

This method returns the preferred full name for this entity.

getNAME() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

getName() - Method in interface org.biopax.paxtools.model.level3.Named

Names for this entity, including standardName and shortName if defined.

getNameSpace() - Method in enum org.biopax.paxtools.model.BioPAXLevel

This method returns the namespace defined for this level.

getNameSpacePrefixMap() - Method in class org.biopax.paxtools.impl.ModelImpl

getNameSpacePrefixMap() - Method in interface org.biopax.paxtools.model.Model

This method returns a map of name space prefixes.

getNEXT_STEP() - Method in interface org.biopax.paxtools.model.level2.pathwayStep

getNextStep() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

getNextStep() - Method in interface org.biopax.paxtools.model.level3.PathwayStep

getNextStepOf() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

getNextStepOf() - Method in interface org.biopax.paxtools.model.level3.PathwayStep

getNotFeature() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

getNotFeature() - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

getNotFeatureOf() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

getNotFeatureOf() - Method in interface org.biopax.paxtools.model.level3.EntityFeature

Inverse of PhysicalEntity.getNotFeature() Contents of this set is generated automatically and should not be modified.

getObject(Model, String, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils

A more strict, type-safe way to ask for a biopax object from the model, unlike Model.getByID(String).

getObjects() - Method in class org.biopax.paxtools.impl.ModelImpl

getObjects(Class<T>) - Method in class org.biopax.paxtools.impl.ModelImpl

getObjects() - Method in interface org.biopax.paxtools.model.Model

This method returns a set of objects in the model.

getObjects(Class<T>) - Method in interface org.biopax.paxtools.model.Model

This method returns a set of objects in the model of the given class.

getOrganism() - Method in class org.biopax.paxtools.impl.level3.GeneImpl

getOrganism() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

getOrganism() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl

getORGANISM() - Method in interface org.biopax.paxtools.model.level2.complex

getORGANISM() - Method in interface org.biopax.paxtools.model.level2.pathway

getORGANISM() - Method in interface org.biopax.paxtools.model.level2.sequenceEntity

getOrganism() - Method in interface org.biopax.paxtools.model.level3.Gene

An organism, e.g.

getOrganism() - Method in interface org.biopax.paxtools.model.level3.Pathway

An organism, e.g.

getOrganism() - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference

An organism, e.g.

getOrganisms(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils

Collects BioSource objects from this or related elements (where it makes sense; though the biopax element might have no or empty 'organism' property at all.

getOrganisms() - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

Deprecated.

use getAnnotations() instead

getPackageName() - Method in enum org.biopax.paxtools.model.BioPAXLevel

getParentPathways(BioPAXElement) - Static method in class org.biopax.paxtools.controller.ModelUtils

Collects all parent Pathway objects recursively traversing the inverse object properties of the biopax element.

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.

getPATHWAY_COMPONENTS() - Method in interface org.biopax.paxtools.model.level2.pathway

getPathwayComponent() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

getPathwayComponent() - Method in interface org.biopax.paxtools.model.level3.Pathway

getPathwayComponentOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl

getPathwayComponentOf() - Method in interface org.biopax.paxtools.model.level3.Process

getPathwayController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getPathwayOrder() - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

getPathwayOrder() - Method in interface org.biopax.paxtools.model.level3.Pathway

getPathwayOrderOf() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

getPathwayOrderOf() - Method in interface org.biopax.paxtools.model.level3.PathwayStep

getPatoData() - Method in class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl

getPatoData() - Method in interface org.biopax.paxtools.model.level3.PhenotypeVocabulary

getPeController() - Method in class org.biopax.paxtools.impl.level3.ControlImpl

getPh() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

getPH() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO

getPH() - Method in interface org.biopax.paxtools.model.level2.kPrime

getPh() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant

A measure of acidity and alkalinity of a solution that is a number on a scale on which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution.

getPhenotype() - Method in class org.biopax.paxtools.impl.level3.GeneticInteractionImpl

getPhenotype() - Method in interface org.biopax.paxtools.model.level3.GeneticInteraction

getPHYSICAL_ENTITY() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

getPhysicalEntity() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl

getPhysicalEntity() - Method in interface org.biopax.paxtools.model.level3.Stoichiometry

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

getPositionStatus() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

getPositionStatus() - Method in interface org.biopax.paxtools.model.level3.SequenceSite

getPresentationName() - Method in class org.biopax.paxtools.command.AddCommand

getPresentationName() - Method in class org.biopax.paxtools.command.PropertyAddCommand

getPresentationName() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

getPresentationName() - Method in class org.biopax.paxtools.command.PropertySetCommand

getPresentationName() - Method in class org.biopax.paxtools.command.RemoveCommand

getPrimarySetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getPrimarySetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor

Returns the primary set method of the editor.

getProduct() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

getProduct() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction

getProperty() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getProperty() - Method in interface org.biopax.paxtools.controller.PropertyEditor

getRange() - Method in interface org.biopax.paxtools.controller.PropertyAccessor

Returns the range of the editor.

getRange() - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter

Returns the range of the editor.

getRDFCommentEditor(BioPAXElement) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Paxtools maps BioPAX:comment (L3) and BioPAX:COMMENT (L2) to rdf:comment.

getRDFId() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

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

getRELATIONSHIP_TYPE() - Method in interface org.biopax.paxtools.model.level2.relationshipXref

getRelationshipType() - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl

getRelationshipType() - Method in interface org.biopax.paxtools.model.level3.RelationshipXref

Definition:A controlled vocabulary term that defines the type of relationship that this xref defines.

getRemoveMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getRemoveMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor

getRestrictedRanges() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

getRestrictedRangesFor(Class<? extends D>) - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

getReusedPEPHelper() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

This is a helper class initialized only if fixReusedPEPs is true.

getRight() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

getRIGHT() - Method in interface org.biopax.paxtools.model.level2.conversion

getRight() - Method in interface org.biopax.paxtools.model.level3.Conversion

The participants on the right side of the conversion interaction.

getRootElements(Model, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils

Finds "root" BioPAX objects that belong to a particular class (incl.

getScore() - Method in class org.biopax.paxtools.controller.ConversionScore

getScoreSource() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl

getScoreSource() - Method in interface org.biopax.paxtools.model.level3.Score

This property defines the source of the scoring methodology.

getSequence() - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl

getSEQUENCE() - Method in interface org.biopax.paxtools.model.level2.sequenceEntity

getSequence() - Method in interface org.biopax.paxtools.model.level3.SequenceEntityReference

Polymer sequence in uppercase letters.

getSEQUENCE_FEATURE_LIST() - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant

getSEQUENCE_INTERVAL_BEGIN() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval

getSEQUENCE_INTERVAL_END() - Method in interface org.biopax.paxtools.model.level2.sequenceInterval

getSEQUENCE_POSITION() - Method in interface org.biopax.paxtools.model.level2.sequenceSite

getSequenceIntervalBegin() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

getSequenceIntervalBegin() - Method in interface org.biopax.paxtools.model.level3.SequenceInterval

getSequenceIntervalEnd() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

getSequenceIntervalEnd() - Method in interface org.biopax.paxtools.model.level3.SequenceInterval

getSequencePosition() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

getSequencePosition() - Method in interface org.biopax.paxtools.model.level3.SequenceSite

getSetMethod() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getSetMethod() - Method in interface org.biopax.paxtools.controller.PropertyEditor

getSHORT_NAME() - Method in interface org.biopax.paxtools.model.level2.entity

This method sets an abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity.

getSHORT_NAME() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

getSimpleMembers() - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getSimpleMembers(Set<SimplePhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

getSimpleMembers() - Method in interface org.biopax.paxtools.model.level3.Complex

Gets the member physical entities which are not complex.

getSource() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getSOURCE() - Method in interface org.biopax.paxtools.model.level2.publicationXref

getSource() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

getSpontaneous() - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

getSPONTANEOUS() - Method in interface org.biopax.paxtools.model.level2.conversion

getSpontaneous() - Method in interface org.biopax.paxtools.model.level3.Conversion

Specifies whether a conversion occurs spontaneously or not.

getStandardName() - Method in class org.biopax.paxtools.impl.level3.NamedImpl

getStandardName() - Method in interface org.biopax.paxtools.model.level3.Named

The preferred full name for this entity, if exists assigned by a standard nomenclature organization such as HUGO Gene Nomenclature Committee.

getStandardNameX() - Method in class org.biopax.paxtools.impl.level3.NamedImpl

getSTEP_INTERACTIONS() - Method in interface org.biopax.paxtools.model.level2.pathwayStep

getStepConversion() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

getStepConversion() - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep

This method returns the central conversion of this BiochemicalPathwayStep.

getStepDirection() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

getStepDirection() - Method in interface org.biopax.paxtools.model.level3.BiochemicalPathwayStep

This property can be used for annotating direction of enzymatic activity.

getStepProcess() - Method in class org.biopax.paxtools.impl.level3.BiochemicalPathwayStepImpl

getStepProcess() - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

getStepProcess() - Method in interface org.biopax.paxtools.model.level3.PathwayStep

getStepProcessOf() - Method in class org.biopax.paxtools.impl.level3.ProcessImpl

getStepProcessOf() - Method in interface org.biopax.paxtools.model.level3.Process

getSTOICHIOMETRIC_COEFFICIENT() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

getStoichiometricCoefficient() - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl

getStoichiometricCoefficient() - Method in interface org.biopax.paxtools.model.level3.Stoichiometry

Stoichiometric coefficient of the physicalEntity specified by Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.

getStructure() - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

getSTRUCTURE() - Method in interface org.biopax.paxtools.model.level2.smallMolecule

getStructure() - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference

getSTRUCTURE_DATA() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure

getSTRUCTURE_FORMAT() - Method in interface org.biopax.paxtools.model.level2.chemicalStructure

getStructureData() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

getStructureData() - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure

This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI.

getStructureFormat() - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

getStructureFormat() - Method in interface org.biopax.paxtools.model.level3.ChemicalStructure

This property specifies which format is used to define chemical structure.

getSubclassEditorsForProperty(String, Class<D>) - Method in interface org.biopax.paxtools.controller.EditorMap

This method returns the set of editors intended to handle property named property.

getSubclassEditorsForProperty(String, Class<D>) - Method in class org.biopax.paxtools.controller.EditorMapImpl

getSubclassEditorsForProperty(String, Class<D>) - Method in enum org.biopax.paxtools.controller.SimpleEditorMap

getSubRegion() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

getSubRegion() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference

getSubRegionOf() - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

getSubRegionOf() - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference

getSYNONYMS() - Method in interface org.biopax.paxtools.model.level2.entity

The contents of this set can be modified but semantic consistency is not guaranteed.

getSYNONYMS() - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

getTAXON_XREF() - Method in interface org.biopax.paxtools.model.level2.bioSource

getTemperature() - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.deltaGprimeO

getTEMPERATURE() - Method in interface org.biopax.paxtools.model.level2.kPrime

getTemperature() - Method in interface org.biopax.paxtools.model.level3.ChemicalConstant

getTemplate() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

getTemplate() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction

getTemplateDirection() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

getTemplateDirection() - Method in interface org.biopax.paxtools.model.level3.TemplateReaction

getTemplateX() - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

getTerm() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

getTERM() - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary

getTerm() - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary

getThreshold() - Method in class org.biopax.paxtools.controller.Integrator

Returns the threshold value (the smallest score for integrating two conversions)

getTissue() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

getTISSUE() - Method in interface org.biopax.paxtools.model.level2.bioSource

getTissue() - Method in interface org.biopax.paxtools.model.level3.BioSource

An external controlled vocabulary of tissue types.

getTitle() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getTITLE() - Method in interface org.biopax.paxtools.model.level2.publicationXref

getTitle() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

getUndoPresentationName() - Method in class org.biopax.paxtools.command.AddCommand

getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertyAddCommand

getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

getUndoPresentationName() - Method in class org.biopax.paxtools.command.PropertySetCommand

getUndoPresentationName() - Method in class org.biopax.paxtools.command.RemoveCommand

getUnknown() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

getUnknown() - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor

getUnknown() - Method in interface org.biopax.paxtools.controller.PropertyEditor

Gets the unknown value.

getUrl() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getURL() - Method in interface org.biopax.paxtools.model.level2.publicationXref

getUrl() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

getValue() - Method in class org.biopax.paxtools.impl.level3.ScoreImpl

getValue() - Method in interface org.biopax.paxtools.model.level3.Score

This property defines the value of the score.

getValueFromBean(D) - Method in class org.biopax.paxtools.controller.FilteredPropertyAccessor

getValueFromBean(BioPAXElement) - Method in class org.biopax.paxtools.controller.PathAccessor

getValueFromBean(D) - Method in interface org.biopax.paxtools.controller.PropertyAccessor

Returns the value of the bean using the default getMethod.

getValueFromBean(D) - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor

Returns the value of the bean using the default SimplePropertyAccessor.getMethod.

getValueFromBean(D) - Method in class org.biopax.paxtools.controller.TransitivePropertyAccessor

getValueFromBean(D) - Method in class org.biopax.paxtools.controller.UnionPropertyAccessor

getValueFromBeans(Collection<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.PathAccessor

getValueFromBeans(Collection<? extends D>) - Method in interface org.biopax.paxtools.controller.PropertyAccessor

Returns the values for a collection of beans using the default getMethod.

getValueFromBeans(Collection<? extends D>) - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter

getValueFromModel(Model) - Method in class org.biopax.paxtools.controller.PathAccessor

This method runs the path query on all the elements within the model.

getValues() - Method in class org.biopax.paxtools.util.BasicFilterFactory

Deprecated.

getVisitor() - Method in class org.biopax.paxtools.controller.Traverser

getXmlBase() - Method in class org.biopax.paxtools.impl.ModelImpl

getXmlBase() - Method in interface org.biopax.paxtools.model.Model

Gets the model's xml:base (URI prefix/namespace), which normally the majority of the BioPAX object's absolute URIs in the model begin with.

getXmlStreamInfo() - Method in class org.biopax.paxtools.io.SimpleIOHandler

This may be required for external applications to access the specific information (e.g., location) when reporting XML exceptions.

getXref() - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl

getXREF() - Method in interface org.biopax.paxtools.model.level2.XReferrable

getXref() - Method in interface org.biopax.paxtools.model.level3.XReferrable

getXrefOf() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

getXrefOf() - Method in interface org.biopax.paxtools.model.level3.Xref

getYear() - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

getYEAR() - Method in interface org.biopax.paxtools.model.level2.publicationXref

getYear() - Method in interface org.biopax.paxtools.model.level3.PublicationXref

H

hasElement(BioPAXElement) - Method in enum org.biopax.paxtools.model.BioPAXLevel

hasEquivalentCellularLocation(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

hasEquivalentCellularLocation(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

hasEquivalentFeatures(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

hasEquivalentFeatures(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

hasEquivalentIntersection(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker

hashCode() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

This method is consistent with the overridden BioPAXElementImpl.equals(Object) method (biopax type and URI are what matters)

hasInverseLink() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

hasNext() - Method in class org.biopax.paxtools.util.CompositeIterator

I

idMap - Variable in class org.biopax.paxtools.impl.ModelImpl

IllegalBioPAXArgumentException - Exception in org.biopax.paxtools.util

This exception is thrown typically when BioPAX domain or cardinality restrictions are violated.

IllegalBioPAXArgumentException() - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException

IllegalBioPAXArgumentException(Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException

IllegalBioPAXArgumentException(String) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException

IllegalBioPAXArgumentException(String, Throwable) - Constructor for exception org.biopax.paxtools.util.IllegalBioPAXArgumentException

impl - Variable in class org.biopax.paxtools.controller.DecoratingPropertyAccessor

init(InputStream) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to perform the initial reading from the input stream.

init(InputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler

integrate() - Method in class org.biopax.paxtools.controller.Integrator

Integrates target and source(s) and returns a sorted (desc) list of conversion scores.

integrate(List<ConversionScore>) - Method in class org.biopax.paxtools.controller.Integrator

Does the integration using user-provided scores list.

Integrator - Class in org.biopax.paxtools.controller

This class is intended to merge and to integrate biopax models not necessarily from the same resource - if models allow such a thing.

Integrator(EditorMap, Model, Model...) - Constructor for class org.biopax.paxtools.controller.Integrator

interaction - Interface in org.biopax.paxtools.model.level2

Interaction - Interface in org.biopax.paxtools.model.level3

Definition: A biological relationship between two or more entities.

InteractionImpl - Class in org.biopax.paxtools.impl.level3

InteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.InteractionImpl

InteractionParticipant - Interface in org.biopax.paxtools.model.level2

marker interface for entities and PEPs

InteractionVocabulary - Interface in org.biopax.paxtools.model.level3

A reference to the PSI Molecular Interaction ontology (MI) interaction type.

InteractionVocabularyImpl - Class in org.biopax.paxtools.impl.level3

InteractionVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.InteractionVocabularyImpl

invokeMethod(Method, D, R) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

Calls the method onto bean with the value as its parameter.

isAbsoluteUris() - Method in class org.biopax.paxtools.io.SimpleIOHandler

isAddDependencies() - Method in class org.biopax.paxtools.impl.ModelImpl

isAddDependencies() - Method in interface org.biopax.paxtools.model.Model

When addDependencies is false, the model will not check for the dependent objects of a newly added object.

isCompleteBackward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

isCompleteForward() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

isCOMPONENTof() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

isCONTROLLEDOf() - Method in interface org.biopax.paxtools.model.level2.process

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

isEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

isEquivalent(BioPAXElement) - Method in interface org.biopax.paxtools.model.BioPAXElement

This method compares the given element for equivalency.

isEquivalent(Set<? extends T>, Set<? extends T>) - Static method in class org.biopax.paxtools.util.SetEquivalenceChecker

isFixReusedPEPs() - Method in interface org.biopax.paxtools.io.BioPAXIOHandler

This option is only applicable two level 2 models.

isFixReusedPEPs() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Workaround for a very common Level 2 issue.

isInBioPAXNameSpace(String) - Method in class org.biopax.paxtools.controller.EditorMapImpl

isInBioPAXNameSpace(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel

This method returns true if the given string starts with the BP_PREFIX

isInEquivalentState(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

isInstanceOfAtLeastOne(Set<Class<? extends BioPAXElement>>, Object) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

Checks if value is an instance of one of the classes given in a set.

isInverseMultipleCardinality() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

isInverseOnly() - Method in class org.biopax.paxtools.controller.TraverserBilinked

isMergeDuplicates() - Method in class org.biopax.paxtools.io.SimpleIOHandler

isMultipleCardinality() - Method in interface org.biopax.paxtools.controller.PropertyAccessor

Checks if the property to which editor is assigned has multiple cardinality.

isMultipleCardinality() - Method in class org.biopax.paxtools.controller.PropertyAccessorAdapter

Checks if the property to which editor is assigned has multiple cardinality.

isMultipleCardinality(Method) - Static method in class org.biopax.paxtools.controller.SimplePropertyAccessor

isNEXT_STEPof() - Method in interface org.biopax.paxtools.model.level2.pathwayStep

isNormalizeNameSpaces() - Method in class org.biopax.paxtools.io.SimpleIOHandler

isPARTICIPANTSof() - Method in interface org.biopax.paxtools.model.level2.InteractionParticipant

This method returns the interaction that this entity/pep takes part in.

isPATHWAY_COMPONENTSof() - Method in interface org.biopax.paxtools.model.level2.pathwayComponent

isPATHWAY_COMPONENTSof() - Method in interface org.biopax.paxtools.model.level2.process

isPHYSICAL_ENTITYof() - Method in interface org.biopax.paxtools.model.level2.physicalEntity

isReverseMatch() - Method in class org.biopax.paxtools.controller.ConversionScore

isSignificant() - Method in class org.biopax.paxtools.command.PropertyAddCommand

isSignificant() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

isSkipSubPathways() - Method in class org.biopax.paxtools.controller.Fetcher

isSTEP_INTERACTIONSOf() - Method in interface org.biopax.paxtools.model.level2.process

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.

isUnknown(Object) - Method in class org.biopax.paxtools.controller.DecoratingPropertyAccessor

isUnknown(Object) - Method in class org.biopax.paxtools.controller.PathAccessor

isUnknown(Object) - Method in class org.biopax.paxtools.controller.PrimitivePropertyEditor

According the editor type, this methods checks if value equals to one of the unknown values defined under BioPAXElement or is an empty set or set of "unknown" values.

isUnknown(Object) - Method in interface org.biopax.paxtools.controller.PropertyAccessor

Checks if the value is unkown.

isUnknown(Object) - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor

Checks if the value is unkown.

isUnknown(Object) - Method in class org.biopax.paxtools.controller.UnionPropertyAccessor

isXREFof() - Method in interface org.biopax.paxtools.model.level2.xref

iterator() - Method in interface org.biopax.paxtools.controller.EditorMap

iterator() - Method in class org.biopax.paxtools.controller.EditorMapImpl

iterator() - Method in enum org.biopax.paxtools.controller.SimpleEditorMap

iterator() - Method in class org.biopax.paxtools.util.AbstractFilterSet

iterator() - Method in class org.biopax.paxtools.util.BiopaxSafeSet

K

kPrime - Interface in org.biopax.paxtools.model.level2

KPrime - Interface in org.biopax.paxtools.model.level3

The apparent equilibrium constant, K', and associated values.

KPrimeImpl - Class in org.biopax.paxtools.impl.level3

KPrimeImpl() - Constructor for class org.biopax.paxtools.impl.level3.KPrimeImpl

L

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

level - Variable in class org.biopax.paxtools.controller.EditorMapImpl

level - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Level2Element - Interface in org.biopax.paxtools.model.level2

Created by IntelliJ IDEA.

Level3Element - Interface in org.biopax.paxtools.model.level3

A Level 3 specific element.

LevelUpgrader - Class in org.biopax.paxtools.converter

Upgrades BioPAX L1 and L2 to Level 3.

LevelUpgrader() - Constructor for class org.biopax.paxtools.converter.LevelUpgrader

Default Constructor that also loads 'classesmap' and 'propsmap' from the properties files.

LevelUpgrader(BioPAXFactory) - Constructor for class org.biopax.paxtools.converter.LevelUpgrader

Constructor

locationAndFeatureCode() - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

locationCode() - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

log - Static variable in class org.biopax.paxtools.controller.AbstractPropertyEditor

log - Static variable in class org.biopax.paxtools.controller.PathAccessor

M

mapClassName(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.impl.MockFactory

mapClassName(Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.model.BioPAXFactory

Maps a BioPAX type (model interface) to the full-qualified class name of an implementing class.

md5hex(String) - Static method in class org.biopax.paxtools.controller.ModelUtils

Calculates MD5 hash code (as 32-byte hex.

merge(Model, Model...) - Method in class org.biopax.paxtools.controller.Merger

Merges the source models into target model.

merge(Model, Model...) - Method in class org.biopax.paxtools.controller.SimpleMerger

Merges the source models into target model, one after another (in the order they are listed).

merge(Model, Collection<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.SimpleMerger

Merges the elements and all their child biopax objects into the target model.

merge(Model, BioPAXElement) - Method in class org.biopax.paxtools.controller.SimpleMerger

Merges the source element (and its "downstream" dependents) into target model.

merge(Model) - Method in class org.biopax.paxtools.impl.ModelImpl

This is default implementation that uses the id-based merging (SimpleMerger.merge(Model, Model...)) NOTE: some applications, such as those dealing with persistence/transactions or advanced BioPAX alignment/comparison algorithms (like the Patch), may have to implement and use a more specific method instead.

merge(Model) - Method in interface org.biopax.paxtools.model.Model

Merges the source model into this one.

mergeDuplicates(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler

If set to true, the reader will merge duplicate individuals, i.e.

mergeEquivalentInteractions(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

Merges equivalent interactions.

Merger - Class in org.biopax.paxtools.controller

Utility class to merge multiple biopax models into one.

Merger(EditorMap) - Constructor for class org.biopax.paxtools.controller.Merger

MockFactory - Class in org.biopax.paxtools.impl

This factory returns decorated objects for testing.

MockFactory(BioPAXLevel) - Constructor for class org.biopax.paxtools.impl.MockFactory

Model - Interface in org.biopax.paxtools.model

A model acts as a container for BioPAX elements.

ModelFilter - Interface in org.biopax.paxtools.controller

A generic filter interface for Models.

ModelImpl - Class in org.biopax.paxtools.impl

This is the default implementation of the Model.

ModelImpl() - Constructor for class org.biopax.paxtools.impl.ModelImpl

ModelImpl(BioPAXLevel) - Constructor for class org.biopax.paxtools.impl.ModelImpl

ModelImpl(BioPAXFactory) - Constructor for class org.biopax.paxtools.impl.ModelImpl

ModelUtils - Class in org.biopax.paxtools.controller

Several useful algorithms and examples, e.g., to extract root or child BioPAX L3 elements, remove dangling, replace elements or URIs, fix/infer property values, etc.

ModificationFeature - Interface in org.biopax.paxtools.model.level3

Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.

ModificationFeatureImpl - Class in org.biopax.paxtools.impl.level3

ModificationFeatureImpl() - Constructor for class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

modulation - Interface in org.biopax.paxtools.model.level2

get controlled should be catalysis

Modulation - Interface in org.biopax.paxtools.model.level3

Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.

ModulationImpl - Class in org.biopax.paxtools.impl.level3

ModulationImpl() - Constructor for class org.biopax.paxtools.impl.level3.ModulationImpl

MolecularInteraction - Interface in org.biopax.paxtools.model.level3

Definition: An interaction in which at least one participant is a physical entity, e.g.

MolecularInteractionImpl - Class in org.biopax.paxtools.impl.level3

MolecularInteractionImpl() - Constructor for class org.biopax.paxtools.impl.level3.MolecularInteractionImpl

multipleCardinality - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter

This is false if there is a cardinality restriction of one on the property.

N

Named - Interface in org.biopax.paxtools.model.level3

Interface for all classes that can have names in BioPAX.

NamedImpl - Class in org.biopax.paxtools.impl.level3

NamedImpl() - Constructor for class org.biopax.paxtools.impl.level3.NamedImpl

namespaces - Variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

next() - Method in class org.biopax.paxtools.util.CompositeIterator

nextStepFilter - Static variable in class org.biopax.paxtools.controller.Fetcher

This property filter can be used to ignore 'nextStep' ('NEXT-STEP' in L2) property when fetching a sub-graph of child biopax elements, because using this property can eventually lead outside current pathway context into peer pathways, etc.

normalizeGenerics(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

Converts generic simple physical entities, i.e., physical entities except Complexes that have not empty memberPhysicalEntity property, into equivalent physical entities with generic entity references (which have members); this is a better and less error prone way to model generic molecules in BioPAX L3.

normalizeNameSpaces(boolean) - Method in class org.biopax.paxtools.io.SimpleIOHandler

Sets the flag used when exporting a BioPAX model to RDF/XML: true - to clean up current namespaces (e.g., those read from a file) and use defaults instead (prefixes: 'rdf', 'rdfs', 'owl', 'xsd')

NucleicAcid - Interface in org.biopax.paxtools.model.level3

Tagger interface for DNA and RNA

NucleicAcidImpl - Class in org.biopax.paxtools.impl.level3

NucleicAcidImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidImpl

NucleicAcidReference - Interface in org.biopax.paxtools.model.level3

Role interface for NucleicAcidReferences, namely DNA and RNA.

NucleicAcidReferenceImpl - Class in org.biopax.paxtools.impl.level3

NucleicAcidReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

NucleicAcidRegionReference - Interface in org.biopax.paxtools.model.level3

NucleicAcidRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3

NucleicAcidRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

O

objectPropertiesOnlyFilter - Static variable in class org.biopax.paxtools.controller.Fetcher

A property filter to visit only biopax object type properties.

ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement> - Class in org.biopax.paxtools.controller

Provides an editor for all object value types, e.g.

ObjectPropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.ObjectPropertyEditor

Full constructor.

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

openControlledVocabulary - Interface in org.biopax.paxtools.model.level2

org.biopax.paxtools.command - package org.biopax.paxtools.command

This package contains classes for implementing undoable editing the model.

org.biopax.paxtools.controller - package org.biopax.paxtools.controller

This package contains various methods and algorithms for traversing and manipulating the model.

org.biopax.paxtools.converter - package org.biopax.paxtools.converter

This package contains a tools for upgrading BioPAX L1 and L2 to L3.

org.biopax.paxtools.impl - package org.biopax.paxtools.impl

This package contains the default BioPAX Model implementations.

org.biopax.paxtools.impl.level2 - package org.biopax.paxtools.impl.level2

This package contains the default implementation for BioPAX Level 2.

org.biopax.paxtools.impl.level3 - package org.biopax.paxtools.impl.level3

This package contains the default implementation for BioPAX Level 3.

org.biopax.paxtools.io - package org.biopax.paxtools.io

This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..

org.biopax.paxtools.model - package org.biopax.paxtools.model

This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.

org.biopax.paxtools.model.level2 - package org.biopax.paxtools.model.level2

This package contains the interfaces that maps to the BioPAX level 2 specification.

org.biopax.paxtools.model.level3 - package org.biopax.paxtools.model.level3

This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.

org.biopax.paxtools.util - package org.biopax.paxtools.util

This package contains various collections and utilities that is used by the other packages and modules of paxtools.

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.

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.

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

PathAccessor - Class in org.biopax.paxtools.controller

This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.

PathAccessor(List<PropertyAccessor<? extends BioPAXElement, ?>>, BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.PathAccessor

Constructor for defining the access path with a list of accessors.

PathAccessor(String, BioPAXLevel) - Constructor for class org.biopax.paxtools.controller.PathAccessor

Constructor for defining the access path via a XPath like string.

PathAccessor(String) - Constructor for class org.biopax.paxtools.controller.PathAccessor

This constructor defaults to BioPAX Level 3.

pathway - Interface in org.biopax.paxtools.model.level2

Pathway - Interface in org.biopax.paxtools.model.level3

pathwayComponent - Interface in org.biopax.paxtools.model.level2

Interface for pathway steps and processes

PathwayImpl - Class in org.biopax.paxtools.impl.level3

PathwayImpl() - Constructor for class org.biopax.paxtools.impl.level3.PathwayImpl

pathwayStep - Interface in org.biopax.paxtools.model.level2

This represents a set of pathway events.

PathwayStep - Interface in org.biopax.paxtools.model.level3

This represents a set of pathway events.

PathwayStepImpl - Class in org.biopax.paxtools.impl.level3

PathwayStepImpl() - Constructor for class org.biopax.paxtools.impl.level3.PathwayStepImpl

Constructor.

PhenotypeVocabulary - Interface in org.biopax.paxtools.model.level3

PhenotypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3

PhenotypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.PhenotypeVocabularyImpl

physicalEntity - Interface in org.biopax.paxtools.model.level2

PhysicalEntity - Interface in org.biopax.paxtools.model.level3

PhysicalEntityImpl - Class in org.biopax.paxtools.impl.level3

PhysicalEntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

physicalEntityParticipant - Interface in org.biopax.paxtools.model.level2

physicalInteraction - Interface in org.biopax.paxtools.model.level2

PositionStatusType - Enum in org.biopax.paxtools.model.level2

PositionStatusType - Enum in org.biopax.paxtools.model.level3

preparePep2PEIDMap(Model) - Method in class org.biopax.paxtools.converter.LevelUpgrader

PrimitivePropertyEditor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller

Provides a primitive (int, float, double) class compatible editor by extending the PropertyEditor.

PrimitivePropertyEditor(String, Method, Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.PrimitivePropertyEditor

process - Interface in org.biopax.paxtools.model.level2

Tagging interface for entities that needs evidence and can be targeted by a control : Pathway and Interaction

Process - Interface in org.biopax.paxtools.model.level3

Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction

ProcessImpl - Class in org.biopax.paxtools.impl.level3

ProcessImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProcessImpl

property - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor

Local OWL name of the property

property - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple

PropertyAccessor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller

Allows generic access to the properties or a path of properties from a bean.

PropertyAccessorAdapter<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller

Adapter class for all property accessors.

PropertyAccessorAdapter(Class<D>, Class<R>, boolean) - Constructor for class org.biopax.paxtools.controller.PropertyAccessorAdapter

PropertyAddCommand - Class in org.biopax.paxtools.command

PropertyEditor<D extends BioPAXElement,R> - Interface in org.biopax.paxtools.controller

PropertyFilterBilinked - Interface in org.biopax.paxtools.controller

A generic interface for bidirectional property filter

PropertyRemoveCommand - Class in org.biopax.paxtools.command

PropertySetCommand<D extends BioPAXElement,R> - Class in org.biopax.paxtools.command

propertyToEditorMap - Variable in class org.biopax.paxtools.controller.EditorMapImpl

A map from property names to actual property editors.

protein - Interface in org.biopax.paxtools.model.level2

Protein - Interface in org.biopax.paxtools.model.level3

ProteinImpl - Class in org.biopax.paxtools.impl.level3

ProteinImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProteinImpl

ProteinReference - Interface in org.biopax.paxtools.model.level3

Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.

ProteinReferenceImpl - Class in org.biopax.paxtools.impl.level3

ProteinReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProteinReferenceImpl

Provenance - Interface in org.biopax.paxtools.model.level3

Definition: The direct source of a pathway data or score.

ProvenanceImpl - Class in org.biopax.paxtools.impl.level3

ProvenanceImpl() - Constructor for class org.biopax.paxtools.impl.level3.ProvenanceImpl

publicationXref - Interface in org.biopax.paxtools.model.level2

PublicationXref - Interface in org.biopax.paxtools.model.level3

PublicationXrefImpl - Class in org.biopax.paxtools.impl.level3

PublicationXrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.PublicationXrefImpl

Constructor.

R

range - Variable in class org.biopax.paxtools.controller.PropertyAccessorAdapter

This is the Class representing the range of the property.

range - Variable in class org.biopax.paxtools.io.SimpleIOHandler.Triple

rdf - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

rdfs - Static variable in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

readNameSpaces() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

This method provides a hook for the implementers of this abstract class to set the namespaces of the model.

readNameSpaces() - Method in class org.biopax.paxtools.io.SimpleIOHandler

redo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand

redo() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand

redo() - Method in interface org.biopax.paxtools.command.Command

redo() - Method in class org.biopax.paxtools.command.CommandManager

redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand

redoAction() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand

redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AddCommand

redoAction() - Method in class org.biopax.paxtools.command.PropertyAddCommand

redoAction() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

redoAction() - Method in class org.biopax.paxtools.command.PropertySetCommand

redoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.RemoveCommand

registerEditorsWithSubClasses(PropertyEditor, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.EditorMapImpl

This method registers an editor with sub classes - i.e.

registerModelClass(String) - Method in class org.biopax.paxtools.controller.EditorMapImpl

This method inserts the class into internal hashmaps and initializes the value collections.

RelationshipTypeVocabulary - Interface in org.biopax.paxtools.model.level3

Vocabulary for defining relationship Xref types.

RelationshipTypeVocabularyImpl - Class in org.biopax.paxtools.impl.level3

RelationshipTypeVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.RelationshipTypeVocabularyImpl

relationshipXref - Interface in org.biopax.paxtools.model.level2

RelationshipXref - Interface in org.biopax.paxtools.model.level3

Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.

RelationshipXrefImpl - Class in org.biopax.paxtools.impl.level3

RelationshipXrefImpl() - Constructor for class org.biopax.paxtools.impl.level3.RelationshipXrefImpl

remove(BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl

remove(BioPAXElement) - Method in interface org.biopax.paxtools.model.Model

This method removes the given BioPAX Element from the model.

remove() - Method in class org.biopax.paxtools.util.CompositeIterator

removeAuthor(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

removeAuthor(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref

removeAUTHORS(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref

removeAvailability(String) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

removeAVAILABILITY(String) - Method in interface org.biopax.paxtools.model.level2.entity

This method removes the given text from the avaialability set.

removeAvailability(String) - Method in interface org.biopax.paxtools.model.level3.Entity

This method removes the given text from the avaialability set.

removeCofactor(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

removeCOFACTOR(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.catalysis

removeCofactor(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Catalysis

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.

RemoveCommand - Class in org.biopax.paxtools.command

RemoveCommand(Model, Set<BioPAXElement>) - Constructor for class org.biopax.paxtools.command.RemoveCommand

removeComment(String) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

removeCOMMENT(String) - Method in interface org.biopax.paxtools.model.level2.Level2Element

removeComment(String) - Method in interface org.biopax.paxtools.model.level3.Level3Element

A textual comment about this individual.

removeComponent(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

removeComponent(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Complex

Defines the PhysicalEntity subunits of this complex.

removeCOMPONENTS(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.complex

removeComponentStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

removeComponentStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Complex

The stoichiometry of components in a complex.

removeConfidence(Score) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

Confidence in the containing instance.

removeCONFIDENCE(confidence) - Method in interface org.biopax.paxtools.model.level2.evidence

removeConfidence(Score) - Method in interface org.biopax.paxtools.model.level3.Evidence

Confidence in the containing instance.

removeControlled(Process) - Method in class org.biopax.paxtools.impl.level3.ControlImpl

removeCONTROLLED(process) - Method in interface org.biopax.paxtools.model.level2.control

removeControlled(Process) - Method in interface org.biopax.paxtools.model.level3.Control

The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.

removeController(Controller) - Method in class org.biopax.paxtools.impl.level3.ControlImpl

removeCONTROLLER(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.control

removeController(Controller) - Method in interface org.biopax.paxtools.model.level3.Control

The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.

removeDATA_SOURCE(dataSource) - Method in interface org.biopax.paxtools.model.level2.entity

This method removes the given value from the DATA_SOURCE set.

removeDataSource(Provenance) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

removeDataSource(Provenance) - Method in interface org.biopax.paxtools.model.level3.Entity

This method removes the given value from the DATA_SOURCE set.

removeDELTA_G(deltaGprimeO) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

removeDELTA_H(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

removeDELTA_S(double) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

removeDeltaG(DeltaG) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

removeDeltaG(DeltaG) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

removeDeltaH(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

removeDeltaH(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

removeDeltaS(float) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

removeDeltaS(float) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

removeEC_NUMBER(String) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

removeECNumber(String) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

removeECNumber(String) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

removeEntityFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

removeEntityFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Variable features that are observed for the entities of this entityReference - such as known PTM or methylation sites and non-covalent bonds.

removeEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

removeEntityReferenceType(EntityReferenceTypeVocabulary) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Removes the given cv from the list of types

removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

removeEvidence(Evidence) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

removeEVIDENCE(evidence) - Method in interface org.biopax.paxtools.model.level2.process

This method remmoves the given evidence from this process.

removeEvidence(Evidence) - Method in interface org.biopax.paxtools.model.level3.Observable

removeEVIDENCE_CODE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.evidence

removeEvidenceCode(EvidenceCodeVocabulary) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

removeEvidenceCode(EvidenceCodeVocabulary) - Method in interface org.biopax.paxtools.model.level3.Evidence

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

removeEXPERIMENTAL_FORM(experimentalForm) - Method in interface org.biopax.paxtools.model.level2.evidence

removeEXPERIMENTAL_FORM_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.experimentalForm

removeExperimentalFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

removeExperimentalFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm

This method removes an experimental feature

removeExperimentalForm(ExperimentalForm) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

removeExperimentalForm(ExperimentalForm) - Method in interface org.biopax.paxtools.model.level3.Evidence

Removes an experimental form.

removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class org.biopax.paxtools.impl.level3.ExperimentalFormImpl

removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface org.biopax.paxtools.model.level3.ExperimentalForm

Removes an experimental form description.

removeFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

removeFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

removeFEATURE_LOCATION(sequenceLocation) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

removeINTERACTION_TYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalInteraction

removeInteractionType(InteractionVocabulary) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl

removeInteractionType(InteractionVocabulary) - Method in interface org.biopax.paxtools.model.level3.Interaction

Controlled vocabulary term annotating the interaction type for example, "phosphorylation reaction".

removeKEQ(KPrime) - Method in class org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

removeKEQ(kPrime) - Method in interface org.biopax.paxtools.model.level2.biochemicalReaction

removeKEQ(KPrime) - Method in interface org.biopax.paxtools.model.level3.BiochemicalReaction

This quantity is dimensionless and is usually a single number.

removeLeft(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

removeLEFT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion

removeLeft(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion

Removes a participant from the left side of the conversion interaction.

removeMemberEntityReference(EntityReference) - Method in class org.biopax.paxtools.impl.level3.EntityReferenceImpl

removeMemberEntityReference(EntityReference) - Method in interface org.biopax.paxtools.model.level3.EntityReference

Removes the given entityReference from the member list

removeMemberFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

removeMemberFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.EntityFeature

An entity feature that belongs to this homology grouping.

removeMemberPhysicalEntity(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

removeMemberPhysicalEntity(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

removeMethod - Variable in class org.biopax.paxtools.controller.AbstractPropertyEditor

This variable stores the method for removing the value of the property on a given bean.

removeName(String) - Method in class org.biopax.paxtools.impl.level3.NamedImpl

removeNAME(String) - Method in interface org.biopax.paxtools.model.level2.dataSource

removeName(String) - Method in interface org.biopax.paxtools.model.level3.Named

This method removes the given value from the name set.

removeNEXT_STEP(pathwayStep) - Method in interface org.biopax.paxtools.model.level2.pathwayStep

removeNextStep(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

removeNextStep(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.PathwayStep

removeNotFeature(EntityFeature) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

removeNotFeature(EntityFeature) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

removeObjects(Set<BioPAXElement>) - Method in class org.biopax.paxtools.command.CommandManager

removeObjectsIfDangling(Model, Class<T>) - Static method in class org.biopax.paxtools.controller.ModelUtils

Iteratively removes "dangling" elements of given type and its sub-types, e.g.

removeParticipant(Entity) - Method in class org.biopax.paxtools.impl.level3.InteractionImpl

removeParticipant(Entity) - Method in interface org.biopax.paxtools.model.level3.Interaction

The entities that participate in this interaction.

removePARTICIPANTS(InteractionParticipant) - Method in interface org.biopax.paxtools.model.level2.interaction

removeParticipantStoichiometry(Stoichiometry) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

removeParticipantStoichiometry(Stoichiometry) - Method in interface org.biopax.paxtools.model.level3.Conversion

This method removes a stoichiometry for one of the participants of this conversion.

removePATHWAY_COMPONENTS(pathwayComponent) - Method in interface org.biopax.paxtools.model.level2.pathway

removePathwayComponent(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

removePathwayComponent(Process) - Method in interface org.biopax.paxtools.model.level3.Pathway

removePathwayOrder(PathwayStep) - Method in class org.biopax.paxtools.impl.level3.PathwayImpl

removePathwayOrder(PathwayStep) - Method in interface org.biopax.paxtools.model.level3.Pathway

removePHYSICAL_ENTITYof(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.physicalEntity

removeProduct(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.TemplateReactionImpl

removeProduct(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.TemplateReaction

removeProperty(BioPAXElement, PropertyEditor, Object) - Method in class org.biopax.paxtools.command.CommandManager

removeRegionType(SequenceRegionVocabulary) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidRegionReferenceImpl

removeRegionType(SequenceRegionVocabulary) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidRegionReference

removeRight(PhysicalEntity) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

removeRIGHT(physicalEntityParticipant) - Method in interface org.biopax.paxtools.model.level2.conversion

removeRight(PhysicalEntity) - Method in interface org.biopax.paxtools.model.level3.Conversion

Removes a participant from the right side of the conversion interaction.

removeSEQUENCE_FEATURE_LIST(sequenceFeature) - Method in interface org.biopax.paxtools.model.level2.sequenceParticipant

removeSource(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

removeSOURCE(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref

removeSource(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref

removeSTEP_INTERACTIONS(process) - Method in interface org.biopax.paxtools.model.level2.pathwayStep

removeStepProcess(Process) - Method in class org.biopax.paxtools.impl.level3.PathwayStepImpl

removeStepProcess(Process) - Method in interface org.biopax.paxtools.model.level3.PathwayStep

removeSTRUCTURE(chemicalStructure) - Method in interface org.biopax.paxtools.model.level2.smallMolecule

removeSubRegion(NucleicAcidRegionReference) - Method in class org.biopax.paxtools.impl.level3.NucleicAcidReferenceImpl

removeSubRegion(NucleicAcidRegionReference) - Method in interface org.biopax.paxtools.model.level3.NucleicAcidReference

removeSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.entity

This method removes the given value from the SYNONYMS set.

removeSYNONYMS(String) - Method in interface org.biopax.paxtools.model.level2.sequenceFeature

removeTerm(String) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

removeTERM(String) - Method in interface org.biopax.paxtools.model.level2.openControlledVocabulary

removeTerm(String) - Method in interface org.biopax.paxtools.model.level3.ControlledVocabulary

removeUrl(String) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

removeURL(String) - Method in interface org.biopax.paxtools.model.level2.publicationXref

removeUrl(String) - Method in interface org.biopax.paxtools.model.level3.PublicationXref

removeValueFromBean(R, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

removeValueFromBean(Set<R>, D) - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

removeValueFromBean(R, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor

Removes the value from the bean using the default removeMethod, if such method is defined (i.e., it's a multiple cardinality property), otherwise sets unknown value using PropertyEditor.setValueToBean(Object, org.biopax.paxtools.model.BioPAXElement) (but only if )

removeValueFromBean(Set<R>, D) - Method in interface org.biopax.paxtools.controller.PropertyEditor

Removes the values from the bean using the PropertyEditor.removeValueFromBean(Object, org.biopax.paxtools.model.BioPAXElement) for each value in the set.

removeXref(Xref) - Method in class org.biopax.paxtools.impl.level3.XReferrableImpl

removeXREF(xref) - Method in interface org.biopax.paxtools.model.level2.XReferrable

removeXref(Xref) - Method in interface org.biopax.paxtools.model.level3.XReferrable

repair() - Method in class org.biopax.paxtools.impl.ModelImpl

This implementation "repairs" the model without unnecessarily copying objects: - recursively adds lost "children" (not null object property values for which Model.contains(BioPAXElement) returns False) - updates object properties (should refer to model's elements)

repair() - Method in interface org.biopax.paxtools.model.Model

Attempts to repair the model, i.e., make it self-consistent, integral.

replace(Model, Map<? extends BioPAXElement, ? extends BioPAXElement>) - Static method in class org.biopax.paxtools.controller.ModelUtils

Replaces BioPAX elements in the model with ones from the map, updates corresponding BioPAX object references.

replace(BioPAXElement, BioPAXElement) - Method in class org.biopax.paxtools.impl.ModelImpl

It does not automatically replace or clean up the old element's object properties, therefore, some child elements may become "dangling" if they were used by the replaced element only.

replace(BioPAXElement, BioPAXElement) - Method in interface org.biopax.paxtools.model.Model

Replaces existing BioPAX element with another one, of the same or possibly equivalent type, and updates all the affected references to it (object properties).

replaceEquivalentFeatures(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

This method iterates over the features in a model and tries to find equivalent objects and merges them.

reset() - Method in class org.biopax.paxtools.controller.AbstractTraverser

Clears the internal set of traversed biopax objects.

reset(InputStream) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

reset(InputStream) - Method in class org.biopax.paxtools.io.SimpleIOHandler

resetEditorMap() - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Updates the member EditorMap for the new BioPAX level and factory (different implementations of EditorMap can be used in modules, e.g.

resetEditorMap() - Method in class org.biopax.paxtools.io.SimpleIOHandler

This method resets the editor map.

resetLevel(BioPAXLevel, BioPAXFactory) - Method in class org.biopax.paxtools.io.BioPAXIOHandlerAdapter

Updates the level and factory for this I/O (final - because used in the constructor)

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

rna - Interface in org.biopax.paxtools.model.level2

Rna - Interface in org.biopax.paxtools.model.level3

RnaImpl - Class in org.biopax.paxtools.impl.level3

RnaImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaImpl

RnaReference - Interface in org.biopax.paxtools.model.level3

RnaReferenceImpl - Class in org.biopax.paxtools.impl.level3

RnaReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaReferenceImpl

RnaRegion - Interface in org.biopax.paxtools.model.level3

Definition: A region on a RNA molecule.

RnaRegionImpl - Class in org.biopax.paxtools.impl.level3

RnaRegionImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaRegionImpl

RnaRegionReference - Interface in org.biopax.paxtools.model.level3

A RNA region reference

RnaRegionReferenceImpl - Class in org.biopax.paxtools.impl.level3

RnaRegionReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.RnaRegionReferenceImpl

S

Score - Interface in org.biopax.paxtools.model.level3

Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method.

ScoreImpl - Class in org.biopax.paxtools.impl.level3

ScoreImpl() - Constructor for class org.biopax.paxtools.impl.level3.ScoreImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ChemicalConstantImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ChemicalStructureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.CovalentBindingFeatureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.DeltaGImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EntityFeatureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EntityImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.EvidenceImpl

Answers whether two Evidence objects are semantically equivalent.

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.KPrimeImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.RelationshipXrefImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceEntityReferenceImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.StoichiometryImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.UnificationXrefImpl

semanticallyEquivalent(BioPAXElement) - Method in class org.biopax.paxtools.impl.level3.XrefImpl

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(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.

setBindsTo(BindingFeature) - Method in class org.biopax.paxtools.impl.level3.BindingFeatureImpl

This method will set the paired binding feature that binds to this feature.

setBindsTo(BindingFeature) - Method in interface org.biopax.paxtools.model.level3.BindingFeature

A binding feature represents a "half" of the bond between two entities.

setCatalysisDirection(CatalysisDirectionType) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

setCatalysisDirection(CatalysisDirectionType) - Method in interface org.biopax.paxtools.model.level3.Catalysis

This property represents the direction of this catalysis under all physiological conditions if there is one.

setCellType(CellVocabulary) - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

setCELLTYPE(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.bioSource

setCellType(CellVocabulary) - Method in interface org.biopax.paxtools.model.level3.BioSource

A cell type, e.g.

setCELLULAR_LOCATION(openControlledVocabulary) - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

setCellularLocation(CellularLocationVocabulary) - Method in class org.biopax.paxtools.impl.level3.PhysicalEntityImpl

setCellularLocation(CellularLocationVocabulary) - Method in interface org.biopax.paxtools.model.level3.PhysicalEntity

A cellular location, e.g.

setCHEMICAL_FORMULA(String) - Method in interface org.biopax.paxtools.model.level2.smallMolecule

setChemicalFormula(String) - Method in class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

setChemicalFormula(String) - Method in interface org.biopax.paxtools.model.level3.SmallMoleculeReference

setCofactor(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.CatalysisImpl

setCOFACTOR(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.catalysis

setComment(Set<String>) - Method in class org.biopax.paxtools.impl.level3.L3ElementImpl

setCOMMENT(Set<String>) - Method in interface org.biopax.paxtools.model.level2.Level2Element

setComponent(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ComplexImpl

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.

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

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

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

setId(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl

setID(String) - Method in interface org.biopax.paxtools.model.level2.xref

setId(String) - Method in interface org.biopax.paxtools.model.level3.Xref

setID_VERSION(String) - Method in interface org.biopax.paxtools.model.level2.xref

setIdVersion(String) - Method in class org.biopax.paxtools.impl.level3.XrefImpl

setIdVersion(String) - Method in interface org.biopax.paxtools.model.level3.Xref

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'.

setLeft(Set<PhysicalEntity>) - Method in class org.biopax.paxtools.impl.level3.ConversionImpl

setLEFT(Set<physicalEntityParticipant>) - Method in interface org.biopax.paxtools.model.level2.conversion

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.

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.

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

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

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(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

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

setUrl(Set<String>) - Method in class org.biopax.paxtools.impl.level3.PublicationXrefImpl

setURL(Set<String>) - Method in interface org.biopax.paxtools.model.level2.publicationXref

setValue(String) - Method in class org.biopax.paxtools.impl.level3.ScoreImpl

setValue(String) - Method in interface org.biopax.paxtools.model.level3.Score

This property defines the value of the score.

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

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.

SimpleEditorMap - Enum in org.biopax.paxtools.controller

Provides a simple editor map for a level with a given factory.

SimpleIOHandler - Class in org.biopax.paxtools.io

Simple BioPAX reader/writer.

SimpleIOHandler() - Constructor for class org.biopax.paxtools.io.SimpleIOHandler

Basic constructor, defaults to Level 3 and default BioPAXFactory

SimpleIOHandler(BioPAXLevel) - Constructor for class org.biopax.paxtools.io.SimpleIOHandler

Basic constructor, defaults to level.defaultFactory

SimpleIOHandler(BioPAXFactory, BioPAXLevel) - Constructor for class org.biopax.paxtools.io.SimpleIOHandler

Full constructor

SimpleIOHandler.Triple - Class in org.biopax.paxtools.io

SimpleMerger - Class in org.biopax.paxtools.controller

A "simple" BioPAX merger, a utility class to merge 'source' BioPAX models or a set of elements into the target model, using (URI) identity only.

SimpleMerger(EditorMap) - Constructor for class org.biopax.paxtools.controller.SimpleMerger

SimpleMerger(EditorMap, Filter<BioPAXElement>) - Constructor for class org.biopax.paxtools.controller.SimpleMerger

SimplePhysicalEntity - Interface in org.biopax.paxtools.model.level3

Tagger interface for non-complex physical entities

SimplePhysicalEntityImpl - Class in org.biopax.paxtools.impl.level3

SimplePhysicalEntityImpl() - Constructor for class org.biopax.paxtools.impl.level3.SimplePhysicalEntityImpl

SimplePropertyAccessor<D extends BioPAXElement,R> - Class in org.biopax.paxtools.controller

SimplePropertyAccessor(Class<D>, Class<R>, boolean, Method) - Constructor for class org.biopax.paxtools.controller.SimplePropertyAccessor

size() - Method in class org.biopax.paxtools.util.AbstractFilterSet

This size operation runs on O(n) and should be avoided for large sets.

size() - Method in class org.biopax.paxtools.util.BiopaxSafeSet

smallMolecule - Interface in org.biopax.paxtools.model.level2

SmallMolecule - Interface in org.biopax.paxtools.model.level3

SmallMoleculeImpl - Class in org.biopax.paxtools.impl.level3

SmallMoleculeImpl() - Constructor for class org.biopax.paxtools.impl.level3.SmallMoleculeImpl

SmallMoleculeReference - Interface in org.biopax.paxtools.model.level3

SmallMoleculeReferenceImpl - Class in org.biopax.paxtools.impl.level3

SmallMoleculeReferenceImpl() - Constructor for class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

SpontaneousType - Enum in org.biopax.paxtools.model.level2

stateCode() - Method in interface org.biopax.paxtools.model.level2.physicalEntityParticipant

StepDirection - Enum in org.biopax.paxtools.model.level3

Catalysis direction controlled vocabulary

Stoichiometry - Interface in org.biopax.paxtools.model.level3

Stoichiometric coefficient of a physical entity in the context of a conversion or complex.

StoichiometryImpl - Class in org.biopax.paxtools.impl.level3

StoichiometryImpl() - Constructor for class org.biopax.paxtools.impl.level3.StoichiometryImpl

StringPropertyEditor<D extends BioPAXElement> - Class in org.biopax.paxtools.controller

Provides an String class compatible editor by extending the PropertyEditor.

StringPropertyEditor(String, Method, Class<D>, boolean) - Constructor for class org.biopax.paxtools.controller.StringPropertyEditor

StructureFormatType - Enum in org.biopax.paxtools.model.level3

subgraphContains(BioPAXElement, String, Class<? extends BioPAXElement>) - Method in class org.biopax.paxtools.controller.Fetcher

Iterates over child objects of the given biopax element, using BioPAX object-type properties, until the element with specified URI and class (including its sub-classes).

T

TemplateDirectionType - Enum in org.biopax.paxtools.model.level3

TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM

TemplateReaction - Interface in org.biopax.paxtools.model.level3

TemplateReactionImpl - Class in org.biopax.paxtools.impl.level3

TemplateReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.TemplateReactionImpl

TemplateReactionRegulation - Interface in org.biopax.paxtools.model.level3

TemplateReactionRegulationImpl - Class in org.biopax.paxtools.impl.level3

TemplateReactionRegulationImpl() - Constructor for class org.biopax.paxtools.impl.level3.TemplateReactionRegulationImpl

TissueVocabulary - Interface in org.biopax.paxtools.model.level3

Definition: A reference to the BRENDA

TissueVocabularyImpl - Class in org.biopax.paxtools.impl.level3

TissueVocabularyImpl() - Constructor for class org.biopax.paxtools.impl.level3.TissueVocabularyImpl

toString() - Method in class org.biopax.paxtools.controller.AbstractPropertyEditor

toString() - Method in class org.biopax.paxtools.controller.ObjectPropertyEditor

toString() - Method in interface org.biopax.paxtools.controller.PropertyEditor

toString() - Method in class org.biopax.paxtools.controller.SimplePropertyAccessor

toString() - Method in class org.biopax.paxtools.impl.BioPAXElementImpl

toString() - Method in class org.biopax.paxtools.impl.level3.BioSourceImpl

toString() - Method in class org.biopax.paxtools.impl.level3.ControlledVocabularyImpl

toString() - Method in class org.biopax.paxtools.impl.level3.FragmentFeatureImpl

toString() - Method in class org.biopax.paxtools.impl.level3.ModificationFeatureImpl

toString() - Method in class org.biopax.paxtools.impl.level3.ProvenanceImpl

toString() - Method in class org.biopax.paxtools.impl.level3.SequenceIntervalImpl

toString() - Method in class org.biopax.paxtools.impl.level3.SequenceSiteImpl

toString() - Method in class org.biopax.paxtools.impl.level3.XrefImpl

toString() - Method in class org.biopax.paxtools.io.SimpleIOHandler.Triple

toString() - Method in enum org.biopax.paxtools.model.level2.Direction

TransitivePropertyAccessor<R extends BioPAXElement,D extends R> - Class in org.biopax.paxtools.controller

This class is a transitive decorator for PropertyAccessors.

transport - Interface in org.biopax.paxtools.model.level2

Transport - Interface in org.biopax.paxtools.model.level3

TransportImpl - Class in org.biopax.paxtools.impl.level3

TransportImpl() - Constructor for class org.biopax.paxtools.impl.level3.TransportImpl

transportWithBiochemicalReaction - Interface in org.biopax.paxtools.model.level2

TransportWithBiochemicalReaction - Interface in org.biopax.paxtools.model.level3

TransportWithBiochemicalReactionImpl - Class in org.biopax.paxtools.impl.level3

TransportWithBiochemicalReactionImpl() - Constructor for class org.biopax.paxtools.impl.level3.TransportWithBiochemicalReactionImpl

traverse(D, Model) - Method in class org.biopax.paxtools.controller.AbstractTraverser

traverse(D, Model) - Method in class org.biopax.paxtools.controller.Traverser

Traverse and visit Visitor all properties of the element.

traverse(BioPAXElement, Model) - Method in class org.biopax.paxtools.controller.TraverserBilinked

traverseElements(BioPAXElement, Model, PropertyEditor<?, ?>, Set<?>) - Method in class org.biopax.paxtools.controller.Traverser

traverser - Variable in class org.biopax.paxtools.controller.Completer

Traverser - Class in org.biopax.paxtools.controller

This is a utility class for traversing over the dependent objects of a biopax element, based on property editors

Traverser(EditorMap, Visitor, Filter<PropertyEditor>...) - Constructor for class org.biopax.paxtools.controller.Traverser

The full constructor.

TraverserBilinked - Class in org.biopax.paxtools.controller

A bi-directional BioPAX properties traverser.

TraverserBilinked(EditorMap, Visitor, PropertyFilterBilinked...) - Constructor for class org.biopax.paxtools.controller.TraverserBilinked

Constructor.

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.

U

undo() - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand

undo() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand

undo() - Method in interface org.biopax.paxtools.command.Command

undo() - Method in class org.biopax.paxtools.command.CommandManager

undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AbstractAddRemoveCommand

undoAction() - Method in class org.biopax.paxtools.command.AbstractPropertyCommand

undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.AddCommand

undoAction() - Method in class org.biopax.paxtools.command.PropertyAddCommand

undoAction() - Method in class org.biopax.paxtools.command.PropertyRemoveCommand

undoAction() - Method in class org.biopax.paxtools.command.PropertySetCommand

undoAction(BioPAXElement) - Method in class org.biopax.paxtools.command.RemoveCommand

unificationXref - Interface in org.biopax.paxtools.model.level2

UnificationXref - Interface in org.biopax.paxtools.model.level3

Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity 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.

utilityClass - Interface in org.biopax.paxtools.model.level2

UtilityClass - Interface in org.biopax.paxtools.model.level3

V

valueOf(String) - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.BioPAXLevel

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.ControlType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.PositionStatusType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level2.SpontaneousType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.CatalysisDirectionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.ControlType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.ConversionDirectionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.PositionStatusType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.StepDirection

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.StructureFormatType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.model.level3.TemplateDirectionType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biopax.paxtools.util.BPCollections

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biopax.paxtools.controller.SimpleEditorMap

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.BioPAXLevel

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level2.ControlType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level2.Direction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level2.PositionStatusType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level2.SpontaneousType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.CatalysisDirectionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.ControlType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.ConversionDirectionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.PositionStatusType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.StepDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.StructureFormatType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.model.level3.TemplateDirectionType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biopax.paxtools.util.BPCollections

Returns an array containing the constants of this enum type, in the order they are declared.

visit(Object, BioPAXElement, Model, PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.AbstractTraverser

This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

visit(BioPAXElement, Object, Model, PropertyEditor<?, ?>) - Method in class org.biopax.paxtools.controller.AbstractTraverser

Calls the protected abstract method visit that is to be implemented in subclasses of this abstract class.

visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Cloner

visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Completer

visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.Merger

Checks whether model contains bpe element, and if it does, then it updates the value of the equivalent element for bpe by using the specific editor.

visit(BioPAXElement, Object, Model, PropertyEditor) - Method in class org.biopax.paxtools.controller.ShallowCopy

An implementation of this method should perform a BioPAX element and editor dependent operation on the model.

visit(BioPAXElement, Object, Model, PropertyEditor<?, ?>) - Method in interface org.biopax.paxtools.controller.Visitor

An implementation of this method should perform a BioPAX element and editor dependent operation on the model.

visit(Object, BioPAXElement, Model, PropertyEditor) - Method in class org.biopax.paxtools.converter.LevelUpgrader

visited - Variable in class org.biopax.paxtools.controller.AbstractTraverser

visitor - Variable in class org.biopax.paxtools.controller.Traverser

Visitor - Interface in org.biopax.paxtools.controller

Basic visitor interface for classes using Traverser.

W

writeObject(Writer, BioPAXElement) - Method in class org.biopax.paxtools.io.SimpleIOHandler

Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete).

writeRead(Model) - Static method in class org.biopax.paxtools.controller.ModelUtils

Cuts the BioPAX model off other models and BioPAX objects by essentially performing write/read to/from OWL.

X

xref - Interface in org.biopax.paxtools.model.level2

Xref - Interface in org.biopax.paxtools.model.level3

XReferrable - Interface in org.biopax.paxtools.model.level2

XReferrable - Interface in org.biopax.paxtools.model.level3

XReferrableImpl - Class in org.biopax.paxtools.impl.level3

This class helps with managing the bidirectional xref links.

XReferrableImpl() - Constructor for class org.biopax.paxtools.impl.level3.XReferrableImpl

Default constructor.

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

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