All Classes Interface Summary Class Summary Enum Summary Exception Summary Error Summary
| Class |
Description |
| AbstractAvailability |
A text describing the availability of data, e.g.
|
| AbstractAvailabilityRef |
Abstract class for Availability ref
|
| AbstractAvailabilityRef |
Abstract class for Availability ref
|
| AbstractAvailabilityRef |
Abstract class for Availability ref
|
| AbstractBaseEntry<T extends Interaction> |
Abstract class for Entry
|
| AbstractBaseEntry.AbstractJAXBAnnotationsWrapper |
|
| AbstractBaseEntry.AbstractJAXBInteractionsWrapper<T> |
|
| AbstractBaseEntry.AbstractJAXBInteractorsWrapper |
|
| AbstractBaseXmlInteractor |
The Xml implementation of Interactor
|
| AbstractBaseXmlInteractor.AbstractJAXBAttributeWrapper |
|
| AbstractBinaryInteraction<T extends Participant> |
Abstract class for BinaryInteraction.
|
| AbstractBinaryInteractionWrapper<I extends Interaction<T>,T extends Participant> |
Abstract class for binary interactions that wrap an Interaction.
|
| AbstractBipartiteExpansion<T extends Interaction,B extends BinaryInteraction> |
Abstract class for BipartiteExpansion.
|
| AbstractCachedFetcher |
Abstract class for fetchers
|
| AbstractCollectionWrapper<T> |
Abstract list which is updating some properties when adding/removing elements.
|
| AbstractCompactXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence> |
Abstract class for a compact PSI-XML writer of mixed interactions
|
| AbstractCompactXmlWriter<T extends Interaction> |
Abstract class for Compact XML writers.
|
| AbstractComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction> |
Abstract class for ComplexExpansionMethod.
|
| AbstractComplexRef |
Abstract class for references to a complex
|
| AbstractComplexRef |
Abstract class for references to a complex
|
| AbstractComplexRef |
Abstract class for references to a complex
|
| AbstractCsvInteractionEvidenceParser<T extends InteractionEvidence> |
Abstract class for crosslink CSV parser
|
| AbstractCsvSource<T extends InteractionEvidence> |
Abstract class for an InteractionSource coming from a Crosslink CSV file.
|
| AbstractCsvStreamSource<T extends InteractionEvidence> |
abstract class for Crosslink Csv datasource.
|
| AbstractEntity<F extends Feature> |
Abstract class for Entity
|
| AbstractEntityRef<T extends Feature> |
Abstract entity reference
|
| AbstractEntityRef<T extends Feature> |
Abstract entity reference
|
| AbstractEntityRef<T extends Feature> |
Abstract entity reference
|
| AbstractEntry<T extends Interaction> |
Abstract class for Entry
|
| AbstractEntry<T extends Interaction> |
Abstract class for Entry
|
| AbstractEntry<T extends Interaction> |
Abstract class for Entry
|
| AbstractEntry.JAXBAnnotationsWrapper |
|
| AbstractEntry.JAXBAnnotationsWrapper |
|
| AbstractEntry.JAXBAnnotationsWrapper |
|
| AbstractEntry.JAXBInteractionsWrapper<T> |
|
| AbstractEntry.JAXBInteractionsWrapper<T> |
|
| AbstractEntry.JAXBInteractionsWrapper<T> |
|
| AbstractEntry.JAXBInteractorsWrapper |
|
| AbstractEntry.JAXBInteractorsWrapper |
|
| AbstractEntry.JAXBInteractorsWrapper |
|
| AbstractEntrySet<T extends AbstractBaseEntry> |
Abstract class for Psi-XML root node.
|
| AbstractExpandedXmlMixWriter<I extends Interaction,M extends ModelledInteraction,E extends InteractionEvidence> |
Abstract class for an expanded PSI-XML writer of mixed interactions
|
| AbstractExpandedXmlWriter<T extends Interaction> |
Abstract class for expanded PSI-xml writers
|
| AbstractExperimentalInteractor |
Java class for experimentalInteractor complex type.
|
| AbstractExperimentalInteractor.AbstractJAXBExperimentRefWrapper |
|
| AbstractExperimentRef |
Abstract class for an ModelledInteractionRef
|
| AbstractExperimentRef |
Abstract class for an ModelledInteractionRef
|
| AbstractExperimentRef |
Abstract class for an ModelledInteractionRef
|
| AbstractExtendedXmlBinaryInteraction<P extends Participant> |
Abstract class for xml binary interactions
|
| AbstractFailingFetcher<T> |
A mock fetcher for testing behaviour of bridgeFailedExceptions.
|
| AbstractFeature<P extends Entity,F extends Feature> |
Abstract class for Feature
|
| AbstractFeatureRef<E extends Entity,F extends Feature> |
Abstract feature reference
|
| AbstractFullPsiXmlParser<T extends Interaction> |
This class if for parser that will load the all file in memory
|
| AbstractInferredInteraction |
Java class for inferredInteraction complex type.
|
| AbstractInferredInteraction.AbstractJAXBExperimentRefWrapper |
|
| AbstractInferredInteractionParticipant |
Participant of the inferred interaction.
|
| AbstractInteraction<T extends Participant> |
Abstract class for interactions
|
| AbstractInteractionEvidenceLineParser<T extends InteractionEvidence> |
Abstract class for Interaction evidence parsers
|
| AbstractInteractionLineParser<T extends Interaction,P extends Participant,F extends Feature> |
Abstract mitab line parser
|
| AbstractInteractorEnricher<T extends Interactor> |
Abstract class for enricher of interactors
Minimal enrichment:
- enrich fullname of an interactor.
|
| AbstractInteractorRef |
An implementation of XmlIdReference for interactors
|
| AbstractInteractorRef |
An implementation of XmlIdReference for interactors
|
| AbstractInteractorRef |
An implementation of XmlIdReference for interactors
|
| AbstractInteractorUpdater<T extends Interactor> |
Abstract class for updater of interactors
Minimal update:
- enrich shortname of an interactor.
|
| AbstractLightInteractionLineParser<T extends Interaction> |
Abstract class for InteractionLine parsers
|
| AbstractListHavingProperties<T> |
Abstract list which is updating some properties when adding/removing elements.
|
| AbstractMatrixExpansion<T extends Interaction,B extends BinaryInteraction> |
Abstract class for Matrix expansion
|
| AbstractMIEdge<T> |
Abstract class for MIEdge interface.
|
| AbstractMIEnricher<T> |
Abstract implementation of a MIEnricher
|
| AbstractMIHtmlWriter<T extends Interaction,P extends Participant,F extends Feature> |
Abstract class for MI HTML writer
|
| AbstractMIJsonBinaryWriter<I extends BinaryInteraction> |
Abstract JSON writer for binary interactions (binary json format)
|
| AbstractMIJsonWriter<I extends Interaction,B extends BinaryInteraction> |
The jsonWriter which writes the interactions
|
| AbstractMIJsonWriter<I extends Interaction> |
Abstract JSON writer for interactions (n-ary json format)
|
| AbstractMIOntologyAccess |
abstract class for OntologyAccess
|
| AbstractMitab25BinaryWriter<T extends BinaryInteraction,P extends Participant> |
Abstract class for BinaryInteraction writer.
|
| AbstractMitab26BinaryWriter<T extends BinaryInteraction,P extends Participant> |
Abstract class for MITAB 2.6 writer of binary interactions
|
| AbstractMitab27BinaryWriter<T extends BinaryInteraction,P extends Participant> |
Abstract mitab 2.7 writer for binary interactions
|
| AbstractMitab28BinaryWriter<T extends BinaryInteraction,P extends Participant> |
Abstract mitab 2.8 writer for binary interactions
|
| AbstractMitabColumnFeeder<T extends BinaryInteraction,P extends Participant> |
Abstract Mitab 2.5 column feeder
|
| AbstractMitabIterator<T extends Interaction,P extends Participant,F extends Feature> |
Abstract class for mitab iterator
|
| AbstractMitabSource<T extends Interaction,P extends Participant,F extends Feature> |
Abstract class for an InteractionSource coming from a MITAB file.
|
| AbstractMitabStreamSource<T extends Interaction,P extends Participant,F extends Feature> |
abstract class for Mitab datasource.
|
| AbstractMitabWriter<T extends Interaction,B extends BinaryInteraction,P extends Participant> |
Abstract writer for Mitab 2.5.
|
| AbstractMockFetcher<T> |
A general mock fetcher which can be used to quickly make new mocks with predictable behaviour.
|
| AbstractModelledInteractionLineParser<T extends ModelledInteraction> |
Abstract class for ModelledInteraction line parsers
|
| AbstractNamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| AbstractOboLoader<T extends CvTerm> |
Abstract obo loader
|
| AbstractOlsFetcher<T extends CvTerm> |
Abstract class for OlsCvTermFetcher
|
| AbstractParticipant<I extends Interaction,F extends Feature> |
Abstract class for Participant
|
| AbstractParticipantCandidate<P extends ParticipantPool,F extends Feature> |
Abstract class for participant candidate
|
| AbstractParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
Abstract class for Participant pool
|
| AbstractParticipantRef<I extends Interaction,T extends Feature> |
Abstract participant reference
|
| AbstractParticipantRef<I extends Interaction,T extends Feature> |
Abstract participant reference
|
| AbstractParticipantRef<I extends Interaction,T extends Feature> |
Abstract participant reference
|
| AbstractPsixmlBinaryParser<T extends Interaction,B extends BinaryInteraction> |
Abstract class for a binary interaction parser
|
| AbstractPsiXmlBinarySource<T extends Interaction,B extends BinaryInteraction> |
Abstract class for Psi-XML binary interaction data source which loads the full
interaction dataset
|
| AbstractPsiXmlBinaryStream<T extends Interaction,B extends BinaryInteraction> |
Abstract class for binary interaction datasources
|
| AbstractPsiXmlInteraction<T extends Participant> |
Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interface
|
| AbstractPsiXmlInteraction<T extends Participant> |
Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interface
|
| AbstractPsiXmlInteraction<T extends Participant> |
Abstract class for xml interactions implementing ExtendedPsiXmlInteraction interface
|
| AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper |
|
| AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper |
|
| AbstractPsiXmlInteraction.JAXBInferredInteractionWrapper |
|
| AbstractPsiXmlParser<T extends Interaction> |
Parser for PSI-XML
Returns an Iterator of interactions.
|
| AbstractPsiXmlSource<T extends Interaction> |
Abstract class for a PSI-XML datasource that loads the full interaction dataset
|
| AbstractPsiXmlStream<T extends Interaction> |
Abstract class for psiXml data source
|
| AbstractSpokeExpansion<T extends Interaction,B extends BinaryInteraction> |
Abstract class for SpokeExpansion
|
| AbstractXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| AbstractXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| AbstractXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| AbstractXmlBasicInteraction |
Xml implementation of interaction
|
| AbstractXmlBasicInteraction |
Xml implementation of interaction
|
| AbstractXmlBasicInteraction |
Xml implementation of interaction
|
| AbstractXmlBasicInteraction.JAXBParticipantWrapper |
|
| AbstractXmlBasicInteraction.JAXBParticipantWrapper |
|
| AbstractXmlBasicInteraction.JAXBParticipantWrapper |
|
| AbstractXmlBinaryInteraction<P extends Participant> |
Abstract class for xml binary interactions
|
| AbstractXmlBinaryInteractionEvidence |
Abstract class for Xml BinaryInteractionEvidence
|
| AbstractXmlComplex |
Xml implementation for complex
|
| AbstractXmlComplex |
Xml implementation for complex
|
| AbstractXmlComplex |
Xml implementation for complex
|
| AbstractXmlConfidence |
abstract Xml implementation of confidence
|
| AbstractXmlConfidence |
abstract Xml implementation of confidence
|
| AbstractXmlConfidence |
abstract Xml implementation of confidence
|
| AbstractXmlCooperativeEffect |
Abstract class for XML 3.0 cooperative effects
|
| AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper |
|
| AbstractXmlCooperativeEffect.JAXBAttributeWrapper |
|
| AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper |
|
| AbstractXmlCooperativeEffectWriter<C extends CooperativeEffect> |
Abstract Xml 3.0 writer for cooperative effect
|
| AbstractXmlCvTerm |
Abstract cv term
|
| AbstractXmlCvTerm |
Abstract cv term
|
| AbstractXmlCvTerm |
Abstract cv term
|
| AbstractXmlCvTerm.JAXBAttributeWrapper |
|
| AbstractXmlCvTerm.JAXBAttributeWrapper |
|
| AbstractXmlCvTerm.JAXBAttributeWrapper |
|
| AbstractXmlEntity<F extends Feature> |
Abstract class for XmlEntity
|
| AbstractXmlEntity<F extends Feature> |
Abstract class for XmlEntity
|
| AbstractXmlEntity<F extends Feature> |
Abstract class for XmlEntity
|
| AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature> |
|
| AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature> |
|
| AbstractXmlEntity.JAXBFeatureWrapper<F extends Feature> |
|
| AbstractXmlExperiment |
Xml im
|
| AbstractXmlExperiment |
Xml im
|
| AbstractXmlExperiment |
Xml im
|
| AbstractXmlExperiment.JAXBAttributeWrapper |
|
| AbstractXmlExperiment.JAXBAttributeWrapper |
|
| AbstractXmlExperiment.JAXBAttributeWrapper |
|
| AbstractXmlExperiment.JAXBConfidenceWrapper |
|
| AbstractXmlExperiment.JAXBConfidenceWrapper |
|
| AbstractXmlExperiment.JAXBConfidenceWrapper |
|
| AbstractXmlExperiment.JAXBHostOrganismWrapper |
|
| AbstractXmlExperiment.JAXBHostOrganismWrapper |
|
| AbstractXmlExperiment.JAXBHostOrganismWrapper |
|
| AbstractXmlExperiment.JAXBVariableParameterWrapper |
|
| AbstractXmlExperiment.JAXBVariableParameterWrapper |
|
| AbstractXmlExperiment.JAXBVariableParameterWrapper |
|
| AbstractXmlExperimentalInteractorWriter |
Abstract class for experimental interactor XML writer
|
| AbstractXmlExperimentWriter |
Abstract PSI-XML experiment writer
|
| AbstractXmlFeature<P extends Entity,F extends Feature> |
Abstract class for Xml features
|
| AbstractXmlFeature<P extends Entity,F extends Feature> |
Abstract class for Xml features
|
| AbstractXmlFeature<P extends Entity,F extends Feature> |
Abstract class for Xml features
|
| AbstractXmlFeature.JAXBAttributeWrapper |
|
| AbstractXmlFeature.JAXBAttributeWrapper |
|
| AbstractXmlFeature.JAXBAttributeWrapper |
|
| AbstractXmlFeature.JAXBRangeWrapper |
|
| AbstractXmlFeature.JAXBRangeWrapper |
|
| AbstractXmlFeature.JAXBRangeWrapper |
|
| AbstractXmlFeatureEvidenceWriter |
Abstract class for feature evidence 2.5 writers
|
| AbstractXmlFeatureEvidenceWriter |
Abstract class for feature evidence 3.0 writers
|
| AbstractXmlFeatureWriter<F extends Feature> |
Abstract writer for Xml25Feature.
|
| AbstractXmlFeatureWriter<F extends Feature> |
Abstract writer for Xml25Feature.
|
| AbstractXmlFeatureWriter<F extends Feature> |
Abstract writer for Xml30Feature.
|
| AbstractXmlIdReference |
Abstract implementation for XmlIdReference
|
| AbstractXmlInteraction<T extends Participant> |
Abstract class for xml interactions
|
| AbstractXmlInteraction<T extends Participant> |
Abstract class for xml interactions
|
| AbstractXmlInteraction<T extends Participant> |
Abstract class for xml interactions
|
| AbstractXmlInteraction.JAXBAttributeWrapper |
|
| AbstractXmlInteraction.JAXBAttributeWrapper |
|
| AbstractXmlInteraction.JAXBAttributeWrapper |
|
| AbstractXmlInteraction.JAXBParticipantWrapper<T extends Participant> |
|
| AbstractXmlInteraction.JAXBParticipantWrapper<T extends Participant> |
|
| AbstractXmlInteraction.JAXBParticipantWrapper<T extends Participant> |
|
| AbstractXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| AbstractXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| AbstractXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| AbstractXmlInteractionEvidence.JAXBConfidenceWrapper |
|
| AbstractXmlInteractionEvidence.JAXBConfidenceWrapper |
|
| AbstractXmlInteractionEvidence.JAXBConfidenceWrapper |
|
| AbstractXmlInteractionEvidence.JAXBExperimentWrapper |
|
| AbstractXmlInteractionEvidence.JAXBExperimentWrapper |
|
| AbstractXmlInteractionEvidence.JAXBExperimentWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParameterWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParameterWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParameterWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParticipantWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParticipantWrapper |
|
| AbstractXmlInteractionEvidence.JAXBParticipantWrapper |
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers in PSI-MI XML 3.0
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.)
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.)
|
| AbstractXmlInteractionEvidenceWriter<I extends InteractionEvidence> |
Abstract class for interaction evidence writers that write expanded interactions (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.)
|
| AbstractXmlInteractionWriter<T extends Interaction,P extends Participant> |
Abstract writer of interaction
|
| AbstractXmlInteractionWriter<T extends Interaction> |
Abstract writer of interaction in PSI-XML 2.5
|
| AbstractXmlInteractionWriter<I extends Interaction> |
Abstract class for extended XML 2.5 interaction writer
|
| AbstractXmlInteractor |
The Xml implementation of Interactor
|
| AbstractXmlInteractor |
The Xml implementation of Interactor
|
| AbstractXmlInteractor |
The Xml implementation of Interactor
|
| AbstractXmlInteractor.JAXBAttributeWrapper |
|
| AbstractXmlInteractor.JAXBAttributeWrapper |
|
| AbstractXmlInteractor.JAXBAttributeWrapper |
|
| AbstractXmlIterator<T extends Interaction> |
Abstract iterator for parsing xml interactions
|
| AbstractXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| AbstractXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| AbstractXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| AbstractXmlModelledInteraction.JAXBConfidenceWrapper |
|
| AbstractXmlModelledInteraction.JAXBConfidenceWrapper |
|
| AbstractXmlModelledInteraction.JAXBConfidenceWrapper |
|
| AbstractXmlModelledInteraction.JAXBExperimentWrapper |
|
| AbstractXmlModelledInteraction.JAXBExperimentWrapper |
|
| AbstractXmlModelledInteraction.JAXBExperimentWrapper |
|
| AbstractXmlModelledInteraction.JAXBParameterWrapper |
|
| AbstractXmlModelledInteraction.JAXBParameterWrapper |
|
| AbstractXmlModelledInteraction.JAXBParameterWrapper |
|
| AbstractXmlModelledInteraction.JAXBParticipantWrapper |
|
| AbstractXmlModelledInteraction.JAXBParticipantWrapper |
|
| AbstractXmlModelledInteraction.JAXBParticipantWrapper |
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML writers of modelled interaction
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML 2.5 writers of modelled interaction
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML 3.0 writers of modelled interaction
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML writers of modelled interaction
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML 2.5 writers of modelled interaction
|
| AbstractXmlModelledInteractionWriter<I extends ModelledInteraction> |
Abstract class for XML 3.0 writers of modelled interaction
|
| AbstractXmlModelledParticipantWriter |
abstract writer for a modelled participant.
|
| AbstractXmlModelledParticipantWriter |
Abstract class for XML 2.5 writer of modelled participant
|
| AbstractXmlModelledParticipantWriter |
Abstract class for XML 3.0 writer of modelled participant
|
| AbstractXmlNamedParticipantWriter |
Abstract class for a named participant XML 2.5 writer
|
| AbstractXmlOrganismWriter |
Abstract class forPSI-XML writer for organism
|
| AbstractXmlParameter |
Abstract Xml implementation of Parameter
|
| AbstractXmlParameter |
Abstract Xml implementation of Parameter
|
| AbstractXmlParameter |
Abstract Xml implementation of Parameter
|
| AbstractXmlParameterWriter |
Abstract XML writer of a parameter
|
| AbstractXmlParticipant<I extends Interaction,F extends Feature> |
Abstract class for XmlParticipant
|
| AbstractXmlParticipant<I extends Interaction,F extends Feature> |
Abstract class for XmlParticipant
|
| AbstractXmlParticipant<I extends Interaction,F extends Feature> |
Abstract class for XmlParticipant
|
| AbstractXmlParticipant.JAXBAttributeWrapper |
|
| AbstractXmlParticipant.JAXBAttributeWrapper |
|
| AbstractXmlParticipant.JAXBAttributeWrapper |
|
| AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
|
| AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
|
| AbstractXmlParticipant.JAXBInteractorCandidateWrapper<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
|
| AbstractXmlParticipantCandidateWriter<P extends ParticipantCandidate,F extends Feature> |
Abstract Xml writer for participant candidate
|
| AbstractXmlParticipantEvidenceWriter |
Abstract class for writer of participant evidences
|
| AbstractXmlParticipantEvidenceWriter |
Abstract class for XML 2.5 writer of participant evidences
|
| AbstractXmlParticipantEvidenceWriter |
Abstract class for XML 3.0 writer of participant evidences
|
| AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
Abstract class for XML Participant pool
|
| AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
Abstract class for XML Participant pool
|
| AbstractXmlParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
Abstract class for XML Participant pool
|
| AbstractXmlParticipantWriter<P extends Participant,F extends Feature> |
Abstract Xml writer for participant
|
| AbstractXmlParticipantWriter |
Xml 2.5 writer for participant
|
| AbstractXmlPosition |
Abstract class for XmlPosition
|
| AbstractXmlPosition |
Abstract class for XmlPosition
|
| AbstractXmlPosition |
Abstract class for XmlPosition
|
| AbstractXmlPositionWriter |
Abstract Xml writer for a range position
|
| AbstractXmlPublicationWriter |
Abstract Xml writer for publications (bibref objects)
|
| AbstractXmlRangeWriter |
Abstract Xml writer for a feature range
|
| AbstractXmlSource |
Desciption of the source of the entry, usually an organisation
|
| AbstractXmlSource |
Desciption of the source of the entry, usually an organisation
|
| AbstractXmlSource |
Desciption of the source of the entry, usually an organisation
|
| AbstractXmlSource.JAXBAttributeWrapper |
|
| AbstractXmlSource.JAXBAttributeWrapper |
|
| AbstractXmlSource.JAXBAttributeWrapper |
|
| AbstractXmlSourceWriter |
Abstract class for writer of a source in an entry.
|
| AbstractXmlVariableParameterValue |
XML implementation of variable parameter value
|
| AbstractXmlWriter<T extends Interaction> |
Abstract class for XML writer of interactions
|
| Alias |
Alias is a synonym.
|
| AliasComparator |
Simple comparator for aliases.
|
| AliasesChangeListener<T> |
A listener for changes to a bioactiveEntity.
|
| AliasesCollectionComparator |
Comparator for collection of aliases
|
| AliasUtils |
Utility class for aliases
|
| AllostericEffector |
The effector that elicits an allosteric response.
|
| AllostericEffectorType |
The types of allosteryEffectors
|
| Allostery<T extends AllostericEffector> |
The allostery cooperative Effect.
|
| AllosteryComparator |
Basic comparator for Allostery
It will first compare basic cooperative effect properties using CooperativeEffectBaseComparator.
|
| Annotation |
An Annotations gives some information about a specific topic.
|
| AnnotationComparator |
Simple comparator for annotations
It compares first the topics and then the value (case insensitive)
- Two annotations which are null are equals
- The annotation which is not null is before null.
|
| AnnotationsChangeListener<T> |
A listener for changes to a bioactiveEntity.
|
| AnnotationsCollectionComparator |
Comparator for collection of Annotations
|
| AnnotationUtils |
Utility class for Annotation
|
| Availability |
A text describing the availability of data, e.g.
|
| Availability |
A text describing the availability of data, e.g.
|
| Availability |
A text describing the availability of data, e.g.
|
| Base64 |
Encodes and decodes to and from Base64 notation.
|
| Base64.InputStream |
A Base64.InputStream will read data from another
java.io.InputStream, given in the constructor,
and encode/decode to/from Base64 notation on the fly. |
| Base64.OutputStream |
A Base64.OutputStream will write data to another
java.io.OutputStream, given in the constructor,
and encode/decode to/from Base64 notation on the fly. |
| BasicChunkLoggerListener |
Listener to chumk operations
|
| BasicEntry |
Basic Entry implementation for JAXB read only.
|
| BasicEntry |
Basic Entry implementation for JAXB read only.
|
| BasicEntry |
Basic Entry implementation for JAXB read only.
|
| BasicEntry.JAXBInteractionsWrapper |
|
| BasicEntry.JAXBInteractionsWrapper |
|
| BasicEntry.JAXBInteractionsWrapper |
|
| BatchDataSourceInitializer |
This class will initialize the batch database using external scripts containing sql commands to create the tables necessary for running Spring batch jobs.
|
| BibRef |
Xml implementation of a Publication
|
| BibRef |
Xml implementation of a Publication
|
| BibRef |
Xml implementation of a Publication
|
| BibRef.JAXBAttributeWrapper |
|
| BibRef.JAXBAttributeWrapper |
|
| BibRef.JAXBAttributeWrapper |
|
| BinaryEvidenceLineParser |
An extension of MitabLineParser that returns binary interactions evidences only.
|
| BinaryInteraction<T extends Participant> |
A Binary interaction is an interaction only composed of two participants.
|
| BinaryInteractionEvidence |
A BinaryInteractionEvidence is an InteractionEvidence with only two participants
|
| BinaryInteractionEvidenceSource |
A dataSource of binary interaction evidences
It gives full access to all the interactions using Iterator or the full collection.
|
| BinaryInteractionEvidenceStream |
A Data source of binary interaction evidences giving only a stream of interactions.
|
| BinaryInteractionEvidenceWrapper |
A wrapper for InteractionEvidence which contains two participants
|
| BinaryInteractionFactory |
An interface for a factory of BinaryInteractions
|
| BinaryInteractionSource<T extends BinaryInteraction> |
A Data source of binary interactions.
|
| BinaryInteractionStream<T extends BinaryInteraction> |
A Data source of binary interactions giving only a stream of interactions.
|
| BinaryInteractionWrapper |
Binary Wrapper for an Interaction
|
| BinaryLineParser |
An extension of MitabLineParser that returns simple binary interactions only.
|
| BindingFeatureGraph<T extends Feature> |
A binding feature graph is a pseudograph of binding features.
|
| BindingFeatures |
Class that wraps a list of linkedFeatures which all bind together
|
| BindingPair<F extends Feature> |
A feature binding pair is an undirected MI edge of features that are linked to each other.
|
| BindingPairFactory<F extends Feature> |
A feature edge factory is an edge factory generating FeatureBindingPairs
The factory can be instantiated with a specific MIComparator if it wants to override the comparison and hashcodes of features A and B
|
| BindingSiteCliqueFinder<I extends Interaction,F extends Feature> |
The BindingSiteClique finder is an extension of BronKerboschCliqueFinder.
|
| BioactiveEntity |
Molecules showing activity in a living system and which can interact with other molecules
|
| BioactiveEntityComparator |
Unambiguous bioactive entity comparator.
|
| BioactiveEntityEnricherListener |
Created with IntelliJ IDEA.
|
| BioactiveEntityEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| BioactiveEntityEnricherLogger |
A logging listener.
|
| BioactiveEntityEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| BioactiveEntityFetcher |
A fetcher for bioactiveEntities
|
| BipartiteExpansion |
The bipartite expansion.
|
| BridgeFailedException |
An error object to signify that a query to an external service has failed.
|
| BuildBindingSitesCliqueGraph |
In this code example, we can build a clique graph of binding sites in an interactions.
|
| CachedChebiFetcher |
A Cached version of the chebi fetcher
|
| CachedEuroPubmedCentralFetcher |
A cached version of the EuroPubmedCentralFetcher.
|
| CachedFetcher |
An interface defining the basic interaction with the cache.
|
| CachedOlsCvTermFetcher |
Created with IntelliJ IDEA.
|
| CachedOlsFetcher<T extends CvTerm> |
Generic implementation for CachedOlsService
|
| CachedOlsOntologyTermFetcher |
Code for the cache based on the CachedOntologyService at uk.ac.ebi.intact.bridges.olslight;
|
| CachedOlsSourceFetcher |
Code for the cache OLS fetcher;
|
| CachedUniprotGeneFetcher |
Created with IntelliJ IDEA.
|
| CachedUniprotProteinFetcher |
Created with IntelliJ IDEA.
|
| CachedUniprotTaxonomyFetcher |
Created with IntelliJ IDEA.
|
| CachedUnisaveClient |
Cached unisave client
|
| CausalRelationship |
These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object term
|
| CausalRelationshipComparator |
Basic comparator for CausalRelationship
It will first compare the relationType using AbstractCvTermComparator.
|
| ChebiFetcher |
Accesses Chebi entries using the WSDL SOAP service.
|
| Checksum |
Checksum is a value for checking consistency of the data and can also be used for identifying objects.
|
| ChecksumComparator |
Simple comparator for checksum.
|
| ChecksumsChangeListener<T> |
Listener for changes in checkusms
|
| ChecksumUtils |
Utility class for Checksums
|
| CollectionComparator<T> |
A comparator for collections.
|
| CommonUtils |
|
| CompactPsiXmlElementWriter<T> |
Interface for a compact XML element writer.
|
| CompactXmlBinaryEvidenceWriter |
Compact PSI-XML writer for binary interaction evidences (full experimental evidences)
|
| CompactXmlBinaryEvidenceWriter |
Compact PSI-XML writer for expanded binary interaction evidences (full experimental evidences)
|
| CompactXmlBinaryWriter |
Compact PSI-XML writer for a mix of binary interactions
|
| CompactXmlBinaryWriter |
Compact PSI-XML writer for a mix of expanded binary interactions
|
| CompactXmlComplexWriter |
Compact PSI-XML writer for named biological complexes (no experimental evidences).
|
| CompactXmlComplexWriter |
Compact PSI-XML writer for biological complexes (no experimental evidences)
|
| CompactXmlEvidenceWriter |
Compact PSI-XML writer for interaction evidences (full experimental evidences)
|
| CompactXmlEvidenceWriter |
Compact PSI-XML writer for expanded interaction evidences (full experimental evidences)
|
| CompactXmlModelledBinaryWriter |
Compact PSI-XML writer for modelled binary interactions (no experimental evidences)
|
| CompactXmlModelledBinaryWriter |
Compact PSI-XML writer for modelled binary interactions (no experimental evidences)
|
| CompactXmlModelledWriter |
Compact PSI-XML writer for abstract interactions (no experimental evidences)
|
| CompactXmlModelledWriter |
Compact PSI-XML writer for abstract interactions (no experimental evidences)
|
| CompactXmlNamedBinaryEvidenceWriter |
Compact PSI-XML writer for named binary interaction evidences (full experimental evidences)
Participants, features and experiments also have expanded names to write
|
| CompactXmlNamedBinaryWriter |
Compact PSI-XML writer for a mix of named binary interactions
|
| CompactXmlNamedEvidenceWriter |
Compact PSI-XML writer for named interaction evidences (full experimental evidences)
Participants, features and experiments also have expanded names to write
|
| CompactXmlNamedModelledBinaryWriter |
Compact PSI-XML writer for named modelled binary interactions (no experimental evidences).
|
| CompactXmlNamedModelledWriter |
Compact PSI-XML writer for named abstract interactions (no experimental evidences).
|
| CompactXmlNamedWriter |
Compact PSI-XML writer for a mix of named interactions
|
| CompactXmlWriter |
Compact PSI-XML writer for a mix of interactions
|
| CompactXmlWriter |
Compact PSI-XML writer for a mix of interactions
|
| ComparatorUtils |
Utility class for Comparator
|
| Complex |
An interactor composed of interacting molecules that can be copurified.
|
| ComplexChangeListener |
Listener for changes in complex
|
| ComplexChangeLogger |
This listener will just complex change events
|
| ComplexComparator |
Basic ComplexComparator.
|
| ComplexComparatorListener |
|
| ComplexComparatorListenerAnalyzer |
|
| ComplexComparatorListenerImpl |
|
| ComplexComparatorObserver |
|
| ComplexComparisonEvent |
|
| ComplexComparisonEvent.EventType |
|
| ComplexEnricher |
The enricher for Interactions which can enrich a single interaction or a collection.
|
| ComplexEnricherListener |
Listener for complex enrichment
|
| ComplexEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| ComplexEnricherLogger |
A logging listener.
|
| ComplexEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| ComplexEntry |
Complex Entry implementation for JAXB read only.
|
| ComplexEntry |
Complex Entry implementation for JAXB read only.
|
| ComplexEntry |
Complex Entry implementation for JAXB read only.
|
| ComplexEntry.JAXBExperimentsWrapper |
|
| ComplexEntry.JAXBExperimentsWrapper |
|
| ComplexEntry.JAXBExperimentsWrapper |
|
| ComplexEntry.JAXBInteractionsWrapper |
|
| ComplexEntry.JAXBInteractionsWrapper |
|
| ComplexEntry.JAXBInteractionsWrapper |
|
| ComplexExpansionException |
Exception for Interactions that cannot be expanded with a specific complex expansion
|
| ComplexExpansionFactory |
An interface for a factory of complex expansion methods
|
| ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction> |
The method by which complex n-ary data is expanded into binary data.
|
| ComplexExpansionType |
Existing complex expansion types that will be recognised by the complex expansion factory
|
| ComplexExpansionWithJami |
In this code example, we wil do spoke, matrix and bipartite expansion to explode n-ary interactions in binary interactions.
|
| ComplexNamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| ComplexNamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| ComplexNamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| ComplexSource |
A Data source of biological complexes.
|
| ComplexStream |
A Data source of biological complexes giving only a stream of complexes.
|
| ComplexType |
The type of complex that can describe this interaction.
|
| ComplexUtils |
|
| CompositeEntityEnricher |
General enricher for entities and participants candidates that can use sub enrichers for enriching specific interactors
|
| CompositeInteractorEnricher |
General enricher for interactors that can use sub enrichers for enriching specific interactors
|
| CompositeModelledParticipantEnricher |
General enricher for entities and participants that can use sub enrichers for enriching specific interactors
|
| CompositeParticipantEnricher |
General enricher for entities and participants that can use sub enrichers for enriching specific interactors
|
| CompositeParticipantEvidenceEnricher |
General enricher for entities and participants that can use sub enrichers for enriching specific interactors
|
| Confidence |
A Confidence gives information about how reliable an object is.
|
| ConfidenceComparator |
Simple Comparator for Confidences.
|
| ConfidencesChangeListener<T> |
A listener for changes to an object having confidences.
|
| ConfidenceUtils |
Utility class for confidences
|
| Constants |
Created by anjali on 23/11/18.
|
| CooperativeEffect |
A cooperative effect an interaction has on a subsequent interaction.
|
| CooperativeEffectBaseComparator |
Basic comparator for CooperativeEffect
It will first compare the outcome using AbstractCvTermComparator.
|
| CooperativeEffectCloner |
Utility class for cloning cooperativity evidences
|
| CooperativeEffectComparator |
Basic cooperative effect comparator
Allostery effects will always come before basic cooperative effects (preassembly)
- It will use AllosteryComparator to compare allostery
- It will use CooperativeEffectBaseComparator to compare basic cooperative effects
|
| CooperativityEvidence |
The experimental method and corresponding publication from which a cooperative effect has been inferred.
|
| CooperativityEvidenceCloner |
Utility class for cloning cooperativity evidences
|
| CooperativityEvidenceCollectionComparator |
Comparator for a collection of CooperativityEvidences
|
| CooperativityEvidenceComparator |
Basic comparator for cooperativityEvidence
It will first compare the publications using AbstractPublicationComparator and then the evidenceMethods using AbstractCvTermComparator
|
| Crc64Generator |
A class to generate Crc64 for protein and nucleic acids sequences
|
| CreateRogidAndRigid |
This code example shows how to compute RIGID/ROGID checksums for proteins and interactions
|
| CrossLinkCsv |
This class is a central access to basic methods to register crosslink csv datasources.
|
| CrossLinkCSVColumns |
Enum listing possible column names
|
| CrosslinkCsvInteraction |
Interaction evidence extension from crosslinking CSV files
|
| CrossLinkCsvOptionFactory |
The factory to populate the map of options for the DataSourceFactory for crosslink csv datasources
|
| CsvBinaryEvidenceSource |
CrossLink CVS source of binary interaction evidences
|
| CsvBinaryEvidenceStreamSource |
CrossLink CVS stream source of binary interaction evidences
|
| CsvBinaryInteractionEvidence |
Crosslink CSV implementation of BinaryInteractionEvidence
|
| CsvBinaryInteractionEvidenceParser |
Binary Interaction evidence crosslink CSV parser
|
| CsvDatasourceOptions |
Options for CSV datasource which extends MIFileDataSource option
|
| CsvEvidenceSource |
CrossLink CVS source of interaction evidences
|
| CsvEvidenceStreamSource |
CrossLink CVS stream source of interaction evidences
|
| CsvExperimentalParticipantCandidate |
Crosslink CSV extension of ExperimentalParticipantCandidate.
|
| CsvExperimentalParticipantPool |
Crosslink CSV extension of ParticipantEvidencePool.
|
| CsvFeatureEvidence |
CrossLink CSV extension for FeatureEvidence
|
| CsvInteractionEvidence |
CSV extension for InteractionEvidence
|
| CsvInteractionEvidenceIterator<T extends InteractionEvidence> |
Crosslink CSV interaction evidence iterator
|
| CsvInteractionEvidenceParser |
Interaction evidence crosslink CSV parser
|
| CsvMixedEvidenceSource |
This class is a source that can build a mix of n-ary interaction evidences/binary from a Crosslink csv file depending on the
bait column to rebuild the original n-ary interaction
|
| CsvNaryEvidenceSource |
This class is a source that can build a n-ary interaction evidence from a full Crosslink csv file
|
| CsvParserListener |
A listener listening to events when parsing a crosslink CSV file
|
| CsvParserLogger |
Logger for CsvParser
|
| CsvParticipantEvidence |
Crosslink CSV extension of ParticipantEvidence.
|
| CsvProtein |
Crosslink CSV extension of Protein.
|
| CsvRange |
Crosslink CSV extension of Range
It contains a FileSourceLocator
|
| CsvSource<I extends InteractionEvidence> |
Interface for Crosslink CSV sources that can parse full CSV files
|
| CsvSourceLocator |
A Crosslink CSV file source context
|
| CsvStreamSource<I extends InteractionEvidence> |
Interface for Crosslink CSV datasources that can stream CSV files
|
| CsvType |
The different types of crosslink CSV input files
- mix: Mix of binary and n-ary interactions which can be distinguished using bait/complex column
- single_nary: the CSV file is reporting one single n-ary interaction
- binary_only: the CSV file only contains binary interactions
|
| CsvUtils |
Crosslink CSV utils class
|
| CsvXref |
CSV extension for Xref.
|
| CuratedInteractionBaseComparator |
Basic comparator for curated interactions.
|
| CuratedModelledInteractionComparator |
Basic CuratedModelledInteraction comparator.
|
| CuratedPublicationComparator |
Simple comparator for curated publications.
|
| CuratedPublicationEnricher |
An enricher for curated publications which can enrich either a single publication or a collection.
|
| CurationDepth |
Flag to determine the curation depth.
|
| CustomizableModelledParticipantComparator<E extends ModelledEntity> |
A ModelledParticipantComparator that can be customized so we can ignore interactors
when comparing modelled participants
|
| CvOboLoader |
Basic implementation of Obo loader
|
| CvTerm |
A controlled vocabulary term defined by an ontology.
|
| CvTermChangeListener |
CvTerm change listener
|
| CvTermChangeLogger |
This listener will just log cvTerm change events
|
| CvTermCloner |
Utility class for cloning CvTerms
|
| CvTermComparator |
comparator for CvTerms :
If one CvTerm does not have any identifiers, it will only compare the short names (case insensitive).
|
| CvTermCompositeFetcherTemplate<T extends CvTerm,F extends CvTermFetcher<T>> |
Template for a CvTermCompositeFetcher which delegates fetching to other fetcher
|
| CvTermEnricher<C extends CvTerm> |
The CvTerm enricher is an enricher which can enrich either single cvTerm or a collection.
|
| CvTermEnricherListener<C extends CvTerm> |
An extension of the CvTermChangeListener
with specific methods related to the process of enriching.
|
| CvTermEnricherListenerManager<C extends CvTerm> |
A manager for listeners which holds a list of listeners.
|
| CvTermEnricherLogger |
A logging listener.
|
| CvTermEnricherStatisticsWriter<C extends CvTerm> |
A statistics logger which records changes made by the enricher.
|
| CvTermFetcher<C extends CvTerm> |
The interface for finding a CvTerm or extension of CvTerm.
|
| CvTermIdentifierComparator |
Cv term comparator that only takes into consideration identifiers.
|
| CvTermNameComparator |
Comparator for CvTerms that only takes into consideration the shortName of ths cv term
|
| CvTermsCollectionComparator |
Comparator for a collection of CvTerms
|
| CvTermStream |
A CV term data source allows to stream the controlled vocabulary terms of a given dataSource
|
| CvTermUtils |
Utility class for CvTerms
|
| CvTermXrefContainer |
Container for both xrefs and identifiers in a CvTerm
|
| CvTermXrefContainer |
Container for both xrefs and identifiers in a CvTerm
|
| CvTermXrefContainer |
Container for both xrefs and identifiers in a CvTerm
|
| DbReferenceType |
Java class for dbReferenceType complex type.
|
| DefaultAlias |
Default implementation of Alias.
|
| DefaultAliasComparator |
Default alias comparator.
|
| DefaultAllostery<T extends AllostericEffector> |
Default implementation for Allostery
Notes: The equals and hashcode methods have NOT been overridden because the Allostery object is a complex object.
|
| DefaultAllosteryComparator |
Default comparator for Allostery
It will first compare basic cooperative effect properties using DefaultCooperativeEffectBaseComparator.
|
| DefaultAnnotation |
Default implementation for Annotation.
|
| DefaultAnnotationComparator |
Default annotation comparator
It compares first the topics and then the value (case insensitive)
- Two annotations which are null are equals
- The annotation which is not null is before null.
|
| DefaultAvailability |
A text describing the availability of data, e.g.
|
| DefaultAvailability |
A text describing the availability of data, e.g.
|
| DefaultAvailability |
A text describing the availability of data, e.g.
|
| DefaultBinaryInteraction |
Default implementation for BinaryInteraction
Note: the methods equals and hashCode have not been overridden.
|
| DefaultBinaryInteractionEvidence |
Default implementation for BinaryInteractionEvidence
|
| DefaultBinaryInteractionFactory |
A factory to create default BinaryInteractions
|
| DefaultBioactiveEntity |
Default implementation for bioactive entity
Notes: The equals and hashcode methods have NOT been overridden because the BioactiveEntity object is a complex object.
|
| DefaultBioactiveEntityComparator |
Default bioactive entity comparator.
|
| DefaultCausalRelationship |
Default implementation for CausalRelationship
Notes: The equals and hashcode methods have NOT been overridden because the CausalRelationship object is a complex object.
|
| DefaultCausalRelationshipComparator |
Default comparator for CausalRelationship
It will first compare the relationType using DefaultCvTermComparator.
|
| DefaultChecksum |
Default implementation for Checksum
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousChecksumComparator
|
| DefaultChecksumComparator |
Default checksum comparator.
|
| DefaultComplex |
Default implementation for complexes
Notes: The equals and hashcode methods have NOT been overridden because the Complex object is a complex object.
|
| DefaultComplexComparator |
Default Complex comparator
It will first look at the default properties of an interactor using DefaultInteractorBaseComparator.
|
| DefaultComplexExpansionFactory |
Default implementation of complex expansion
|
| DefaultConfidence |
Default implementation for Confidence
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousConfidenceComparator
|
| DefaultConfidenceComparator |
Default confidence comparator.
|
| DefaultCooperativeEffect |
Default implementation for CooperativeEffect
Notes: The equals and hashcode methods have NOT been overridden because the CooperativeEffect object is a complex object.
|
| DefaultCooperativeEffectBaseComparator |
Default comparator for CooperativeEffect
It will first compare the outcome using DefaultCvTermComparator.
|
| DefaultCooperativeEffectComparator |
Default cooperative effect comparator
Allostery effects will always come before basic cooperative effects (preassembly)
- It will use DefaultAllosteryComparator to compare allostery
- It will use DefaultCooperativeEffectBaseComparator to compare basic cooperative effects
|
| DefaultCooperativityEvidence |
Default implementation for CooperativityEvidence
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCooperativityEvidenceComparator
|
| DefaultCooperativityEvidenceComparator |
Default comparator for cooperativityEvidence
It will first compare the publications using DefaultPublicationComparator and then the evidenceMethods using DefaultCvTermComparator
|
| DefaultCuratedExperimentComparator |
Default curated experiment comparator.
|
| DefaultCuratedInteractionBaseComparator |
Default comparator for curated interactions.
|
| DefaultCuratedInteractionComparator |
Default curated Generic interaction comparator.
|
| DefaultCuratedInteractionEvidenceComparator |
Default curated InteractionEvidenceComparator.
|
| DefaultCuratedModelledInteractionComparator |
Default curated ModelledInteraction comparator.
|
| DefaultCuratedPublicationComparator |
Default curated AbstractPublicationComparator
It uses a DefaultPublicationComparator to compares the bibliographic details and then will compare first the curation depth, then the source using DefaultCvTermComparator and then the released date.
|
| DefaultCvTerm |
Default implementation for CvTerm
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparator
|
| DefaultCvTermComparator |
Default comparator for CvTerms.
|
| DefaultEntityBaseComparator |
Default entity comparator
It will first compare the interactors using DefaultInteractorComparator.
|
| DefaultEntityComparator |
Generic default entity comparator.
|
| DefaultExactAllosteryComparator |
Default exact comparator for Allostery
It will first compare basic cooperative effect properties using DefaultExactCooperativeEffectBaseComparator.
|
| DefaultExactBioactiveEntityComparator |
default Exact bioactive entity comparator.
|
| DefaultExactCausalRelationshipComparator |
Default exact comparator for CausalRelationship
It will first compare the relationType using DefaultCvTermComparator.
|
| DefaultExactComplexComparator |
Default exact Complex comparator
It will first look at the default properties of an interactor using DefaultExactInteractorBaseComparator.
|
| DefaultExactCooperativeEffectBaseComparator |
Default exact comparator for CooperativeEffect
It will first compare the outcome using DefaultCvTermComparator.
|
| DefaultExactCooperativeEffectComparator |
Default exact cooperative effect comparator
Allostery effects will always come before basic cooperative effects (preassembly)
- It will use DefaultExactAllosteryComparator to compare allostery
- It will use DefaultExactCooperativeEffectBaseComparator to compare basic cooperative effects
|
| DefaultExactCuratedInteractionComparator |
Default exact curated Generic interaction comparator.
|
| DefaultExactCuratedInteractionEvidenceComparator |
Default exact curated InteractionEvidenceComparator.
|
| DefaultExactCuratedModelledInteractionComparator |
Default exact curated ModelledInteraction comparator.
|
| DefaultExactEntityBaseComparator |
Default exact entity comparator
It will first compare the interactors using DefaultExactInteractorComparator.
|
| DefaultExactEntityComparator |
Generic default exact entity comparator.
|
| DefaultExactExperimentalEntityComparator |
Default exact experimental entity comparator.
|
| DefaultExactExperimentalParticipantPoolComparator |
Default exact experimental participant pool comparator.
|
| DefaultExactGeneComparator |
Default exact gene comparator.
|
| DefaultExactInteractionComparator |
Default exact Generic interaction comparator.
|
| DefaultExactInteractionEvidenceComparator |
Default exact InteractionEvidenceComparator.
|
| DefaultExactInteractionInteractorComparator |
Default exact interaction comparator only based on the interactors of an interaction.
|
| DefaultExactInteractorBaseComparator |
Default Interactor base comparator.
|
| DefaultExactInteractorComparator |
Default exact Interactor Comparator.
|
| DefaultExactInteractorPoolComparator |
Default exact InteractorPoolComparator.
|
| DefaultExactModelledEntityComparator |
Default exact biological entity comparator.
|
| DefaultExactModelledInteractionComparator |
Default exact ModelledInteraction comparator.
|
| DefaultExactModelledParticipantComparator |
Default exact biological participant comparator.
|
| DefaultExactModelledParticipantInteractorComparator |
Default biological participant comparator based on the interactor only.
|
| DefaultExactModelledParticipantPoolComparator |
Default exact biological participant pool comparator.
|
| DefaultExactMoleculeEffectorComparator |
Default exact Comparator for MoleculeEffector.
|
| DefaultExactNucleicAcidComparator |
Default exact nucleic acids comparator.
|
| DefaultExactParticipantBaseComparator |
Default exact participant comparator
It will first compare the interactors and stoichiometry using DefaultExactEntityComparator.
|
| DefaultExactParticipantComparator |
Generic default exact participant comparator.
|
| DefaultExactParticipantEvidenceComparator |
Default exact Experimental participant comparator.
|
| DefaultExactParticipantEvidenceInteractorComparator |
Default exact experimental participant comparator based on the interactor only.
|
| DefaultExactParticipantInteractorComparator |
It will compare the interactors using DefaultExactInteractorComparator.
|
| DefaultExactParticipantPoolComparator |
Default exact participant pool comparator
It will first compare the interactors, biological role and stoichiometry using DefaultExactParticipantBaseComparator
it will then compare the participant candidates using DefaultExactEntityBaseComparator.
|
| DefaultExactPolymerComparator |
Default exact polymer comparator.
|
| DefaultExactProteinComparator |
Default exact proteins comparator.
|
| DefaultExperiment |
Default implementation for Experiment
Notes: The equals and hashcode methods have NOT been overridden because the Experiment object is a complex object.
|
| DefaultExperimentalEntityComparator |
Default experimental entity comparator.
|
| DefaultExperimentalParticipantCandidate |
Default implementation of experimental participant candidate
|
| DefaultExperimentalParticipantPool |
Default implementation of ExperimentalParticipantPool
|
| DefaultExperimentalParticipantPoolComparator |
Default experimental participant pool comparator.
|
| DefaultExperimentComparator |
Default experiment comparator.
|
| DefaultExtendedMitabColumnFeeder |
Default Mitab 2.5 extended feeder for interaction.
|
| DefaultExternalIdentifierComparator |
Default comparator for external identifiers (Xref database and id).
|
| DefaultFeature |
Default implementation for feature
Notes: The equals and hashcode methods have NOT been overridden because the Feature object is a complex object.
|
| DefaultFeatureBaseComparator |
Default feature comparator.
|
| DefaultFeatureComparator |
Generic default feature comparator.
|
| DefaultFeatureEvidence |
Default implementation for FeatureEvidence
Notes: The equals and hashcode methods have NOT been overridden because the FeatureEvidence object is a complex object.
|
| DefaultFeatureEvidenceComparator |
Default FeatureEvidence comparator.
|
| DefaultFeatureModificationEffector |
Default implementation for FeatureModificationEffector
Notes: The equals and hashcode methods have NOT been overridden because the FeatureModificationEffector object is a complex object.
|
| DefaultFeatureModificationEffectorComparator |
Default comparator for FeatureModificationEffector.
|
| DefaultFileSourceContext |
A DefaultFileSourceContext is the basic implementation of FileSourceContext and
contains some file location information
|
| DefaultGene |
Default implementation for gene
Notes: The equals and hashcode methods have NOT been overridden because the Gene object is a complex object.
|
| DefaultGeneComparator |
Default gene comparator.
|
| DefaultImexCentralClient |
Default IMEx Central Client.
|
| DefaultInteraction |
Default implementation for interaction
Notes: The equals and hashcode methods have NOT been overridden because the interaction object is a complex object.
|
| DefaultInteractionBaseComparator |
Default Interaction comparator.
|
| DefaultInteractionComparator |
Default Generic interaction comparator.
|
| DefaultInteractionEvidence |
Default implementation for InteractionEvidence
Notes: The equals and hashcode methods have NOT been overridden because the InteractionEvidence object is a complex object.
|
| DefaultInteractionEvidenceComparator |
Default InteractionEvidenceComparator.
|
| DefaultInteractionInteractorComparator |
Default interaction comparator only based on the interactors of an interaction.
|
| DefaultInteractor |
Default implementation for Interactor
Notes: The equals and hashcode methods have NOT been overridden because the Interactor object is a complex object.
|
| DefaultInteractorBaseComparator |
Default interactor comparator.
|
| DefaultInteractorComparator |
Default generic Interactor Comparator.
|
| DefaultInteractorFactory |
This factory allows to create a proper interactor depending on the type
and xrefs
|
| DefaultInteractorPool |
Default implementation for interactor pool
|
| DefaultInteractorPoolComparator |
Default InteractorPoolComparator.
|
| DefaultMitabColumnFeeder |
The default Mitab 2.5 column feeder for interactions
|
| DefaultMitabFeature |
A DefaultMitabFeature is a feature in MITAB with some free text.
|
| DefaultMitabSource |
Abstract class for an InteractionSource coming from a MITAB file.
|
| DefaultMitabStreamSource |
Generic class for Mitab streaming datasource.
|
| DefaultMitabWriter |
Generic writer for MITAB
|
| DefaultModelledBinaryInteraction |
Default implementation for ModelledBinaryInteraction
|
| DefaultModelledConfidence |
Default implementation for ModelledInteraction
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousConfidenceComparator
|
| DefaultModelledEntityComparator |
Default biological entity comparator.
|
| DefaultModelledFeature |
Default implementation for ModelledFeature
Notes: The equals and hashcode methods have NOT been overridden because the ModelledFeature object is a complex object.
|
| DefaultModelledFeatureComparator |
Default ModelledFeature comparator.
|
| DefaultModelledInteraction |
Default implemntation for ModelledInteraction
Notes: The equals and hashcode methods have NOT been overridden because the ModelledInteraction object is a complex object.
|
| DefaultModelledInteractionComparator |
Default ModelledInteraction comparator.
|
| DefaultModelledParameter |
Default implementation for ModelledParameter
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousParameterComparator
|
| DefaultModelledParticipant |
Default implementation for ModelledParticipant
Notes: The equals and hashcode methods have NOT been overridden because the ModelledParticipant object is a complex object.
|
| DefaultModelledParticipantCandidate |
Default implementation of modelled participant candidate
|
| DefaultModelledParticipantComparator |
Default biological participant comparator.
|
| DefaultModelledParticipantInteractorComparator |
Default biological participant comparator based on the interactor only.
|
| DefaultModelledParticipantPool |
Default implementation of ParticipantPool
|
| DefaultModelledParticipantPoolComparator |
Default biological participant pool comparator.
|
| DefaultMolecule |
The default implementation for a molecule
Notes: The equals and hashcode methods have NOT been overridden because the molecule object is a complex object.
|
| DefaultMoleculeEffector |
Default implementation for MoleculeEffector
Notes: The equals and hashcode methods have NOT been overridden because the MoleculeEffector object is a complex object.
|
| DefaultMoleculeEffectorComparator |
Default Comparator for MoleculeEffector.
|
| DefaultNamedBinaryInteraction |
Default implementation of a named binary interaction
|
| DefaultNamedBinaryInteractionEvidence |
Default implementation of a Named binary interaction evidence
|
| DefaultNamedExperiment |
Default implementation for NamedExperiment.
|
| DefaultNamedInteraction |
Default implementation for Named interaction
|
| DefaultNamedInteractionEvidence |
Default implementation for Named InteractionEvidence
|
| DefaultNamedModelledBinaryInteraction |
Default implementation for Named modelled binary interaction
|
| DefaultNamedModelledInteraction |
Default implementation of Named modelled interaction
|
| DefaultNamedModelledParticipant |
Default implementation of Named modelled participant
|
| DefaultNamedParticipant |
Default implementation of named participant.
|
| DefaultNamedParticipantEvidence |
Default implementation of named participant evidence
|
| DefaultNucleicAcid |
Default implementation for NucleicAcid.
|
| DefaultNucleicAcidComparator |
Default nucleic acids comparator.
|
| DefaultOntologyTerm |
Default implementation for ontology term
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparator
|
| DefaultOrganism |
Default implementation for organism
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousOrganismComparator
|
| DefaultOrganismComparator |
Default organism comparator.
|
| DefaultParameter |
Default implementation for Parameter
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousParameterComparator
|
| DefaultParameterComparator |
Default parameter comparator.
|
| DefaultParticipant |
Default implementation for participant
Notes: The equals and hashcode methods have NOT been overridden because the participant object is a complex object.
|
| DefaultParticipantBaseComparator |
Default participant comparator
It will first compare the interactors and stoichiometry using DefaultEntityBaseComparator
it will then compare the biological roles using DefaultCvTermComparator.
|
| DefaultParticipantCandidate |
Default implementation of participant candidate
|
| DefaultParticipantComparator |
Generic default participant comparator.
|
| DefaultParticipantEvidence |
Default implementation for ParticipantEvidence
Notes: The equals and hashcode methods have NOT been overridden because the ParticipantEvidence object is a complex object.
|
| DefaultParticipantEvidenceComparator |
Default Experimental participant comparator.
|
| DefaultParticipantEvidenceInteractorComparator |
Default experimental participant comparator based on the interactor only.
|
| DefaultParticipantInteractorComparator |
It will compare the interactors using DefaultInteractorComparator.
|
| DefaultParticipantPool |
Default implementation of ParticipantPool
|
| DefaultParticipantPoolComparator |
Default participant pool comparator
It will first compare the interactors, biological role and stoichiometry using DefaultParticipantBaseComparator
it will then compare the participant candidates using DefaultEntityBaseComparator.
|
| DefaultPolymer |
Default implementation for Polymer
Notes: The equals and hashcode methods have NOT been overridden because the Polymer object is a complex object.
|
| DefaultPolymerComparator |
Default polymer comparator.
|
| DefaultPosition |
Default implementation for Position
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousPositionComparator
|
| DefaultPositionComparator |
Default PositionComparator.
|
| DefaultPreassemby |
Default implementation for Preassembly
Notes: The equals and hashcode methods have NOT been overridden because the Preassembly object is a complex object.
|
| DefaultProtein |
Default implementation for proteins and peptides
Notes: The equals and hashcode methods have NOT been overridden because the Protein object is a complex object.
|
| DefaultProteinComparator |
Default proteins comparator.
|
| DefaultPsiXmlSource |
Generic class for PSI-XML full datasource.
|
| DefaultPsiXmlStreamSource |
Generic class for PSI-XML streaming datasource.
|
| DefaultPublication |
Default implementation for a Publication
Notes: The equals and hashcode methods have NOT been overridden because the Publication object is a complex object.
|
| DefaultPublicationComparator |
Default publication comparator
It will only look at IMEx identifiers if both are set.
|
| DefaultRange |
Default implementation for Range
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousRangeAndResultingSequenceComparator
|
| DefaultRangeAndResultingSequenceComparator |
Default RangeComparator.
|
| DefaultRangeComparator |
Default RangeComparator.
|
| DefaultResultingSequence |
Default implementation for ResultingSequence
Notes: The equals and hashcode methods have been overridden to be consistent with ResultingSequenceComparator
|
| DefaultSource |
Default implementation for Source
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousCvTermComparator
|
| DefaultStoichiometry |
Default implementation for stoichiometry
Notes: The equals and hashcode methods have been overridden to be consistent with StoichiometryComparator
|
| DefaultVariableParameter |
Default implementation for variableParameters
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousVariableParameterComparator
|
| DefaultVariableParameterComparator |
DefaultVariableParameter comparator
It will first compare the description (case insensitive).
|
| DefaultVariableParameterValue |
Default implementation for variableValue.
|
| DefaultVariableParameterValueSet |
Default implementation for VariableParameterValueSet
Notes: The equals and hashcode methods have been overridden to be consistent with VariableParameterValueSetComparator
|
| DefaultXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| DefaultXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| DefaultXmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| DefaultXmlBasicInteraction |
Xml implementation of interaction
|
| DefaultXmlBasicInteraction |
Xml implementation of interaction
|
| DefaultXmlBasicInteraction |
Xml implementation of interaction
|
| DefaultXmlComplex |
Xml implementation for complex
|
| DefaultXmlComplex |
Xml implementation for complex
|
| DefaultXmlComplex |
Xml implementation for complex
|
| DefaultXmlExperiment |
Xml im
|
| DefaultXmlExperiment |
Xml im
|
| DefaultXmlExperiment |
Xml im
|
| DefaultXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| DefaultXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| DefaultXmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| DefaultXmlInteractor |
The Xml implementation of Interactor
|
| DefaultXmlInteractor |
The Xml implementation of Interactor
|
| DefaultXmlInteractor |
The Xml implementation of Interactor
|
| DefaultXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| DefaultXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| DefaultXmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| DefaultXmlSource |
Desciption of the source of the entry, usually an organisation
|
| DefaultXmlSource |
Desciption of the source of the entry, usually an organisation
|
| DefaultXmlSource |
Desciption of the source of the entry, usually an organisation
|
| DefaultXmlWriter |
Generic writer for PSI-MI XML
|
| DefaultXref |
Default implementation for Xref
Notes: The equals and hashcode methods have been overridden to be consistent with UnambiguousXrefComparator
|
| DefaultXrefComparator |
Default Xref comparator
It compares first the databases and then the ids (case sensitive) but ignores the version.
|
| Diff |
Extension of diff_match_patch.Diff
|
| diff_match_patch |
Class containing the diff, match and patch methods.
|
| diff_match_patch.Diff |
Class representing one diff operation.
|
| diff_match_patch.Operation |
-
The data structure representing a diff is a Linked list of Diff objects:
{Diff(Operation.DELETE, "Hello"), Diff(Operation.INSERT, "Goodbye"),
Diff(Operation.EQUAL, " world.")}
which means: delete "Hello", add "Goodbye" and keep " world."
|
| diff_match_patch.Patch |
Class representing one patch operation.
|
| DiffCalculator |
Compares Strings to find differences.
|
| DiffUtils |
Calculate diffs between strings and other methods to manipulate the differences.
|
| EnricherException |
This exception is thrown when exceptions are induced in the enricher.
|
| EnricherListener<T> |
An enricher listener has enricher specific methods,
fired after the object has been changed and upon completion of the enrichment.
|
| EnricherListenerManager<O,T extends EnricherListener<O>> |
A manager for listeners which holds a list of listeners.
|
| EnricherStatisticsWriter<T> |
Listens to the enrichment, making two lists of elements:
those which have been successfully enriched and those which have failed.
|
| EnricherUtils |
Utilities for enrichers.
|
| EnrichmentStatus |
The possible outcomes upon enriching an entry.
|
| Entity<F extends Feature> |
An entity which gives more information to a specific molecule (such as features, causal relationships)
|
| EntityBaseComparator |
Basic entity comparator.
|
| EntityChangeListener<F extends Entity> |
Listener for changes in an entity
|
| EntityChangeLogger<T extends Entity> |
This listener will just interactor change events
|
| EntityComparator |
Generic entity comparator.
|
| EntityEnricher<P extends Entity,F extends Feature> |
Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
|
| EntityEnricherListener<P extends Entity> |
Entity enricher listener
|
| EntityEnricherListenerManager<P extends Entity> |
A manager for listeners which holds a list of listeners.
|
| EntityEnricherLogger<P extends Entity> |
A logging listener.
|
| EntityEnricherStatisticsWriter<P extends Entity> |
A statistics logger which records changes made by the enricher.
|
| EntityInteractorChangeListener |
Listeners for changes in participant
|
| Entry |
Java class for anonymous complex type.
|
| Entry |
An XML entry is associated with a set of interactions, experiments, source and attributes
|
| Entry |
PSI XML 3.0 Entry implementation for JAXB read only
|
| Entry.JAXBAvailabilitiesWrapper |
|
| Entry.JAXBExperimentsWrapper |
|
| Entry.JAXBInteractionsWrapper |
|
| EntryLocation |
The location of an object with id in an entry
|
| EuroPubmedCentralFetcher |
Uses the EuroPubmedCentral WSDL SOAP service to fetch publication entries.
|
| ExactExternalIdentifierComparator |
Exact comparator for external identifiers (Xref database and id).
|
| ExactInteractorBaseComparator |
Interactor base comparator.
|
| ExactXrefComparator |
Exact comparator for Xrefs.
|
| ExpandedPsiXmlElementWriter<T> |
Interface for an expanded XML element writer.
|
| ExpandedXmlBinaryEvidenceWriter |
Expanded PSI-XML writer for binary interaction evidences (full experimental evidences)
|
| ExpandedXmlBinaryEvidenceWriter |
Expanded PSI-XML writer for expanded binary interaction evidences (full experimental evidences)
|
| ExpandedXmlBinaryWriter |
Expanded PSI-XML writer for a mix of binary interactions
|
| ExpandedXmlBinaryWriter |
Expanded PSI-XML writer for a mix of expanded binary interactions
|
| ExpandedXmlComplexWriter |
Expanded PSI-XML writer for biological complexes (no experimental evidences).
|
| ExpandedXmlComplexWriter |
Expanded PSI-XML writer for biological complexes (no experimental evidences)
|
| ExpandedXmlEvidenceWriter |
Expanded PSI-XML writer for interaction evidences (full experimental evidences)
|
| ExpandedXmlEvidenceWriter |
Expanded PSI-XML writer for expanded interaction evidences (full experimental evidences)
|
| ExpandedXmlModelledBinaryWriter |
Expanded PSI-XML writer for modelled binary interactions (no experimental evidences)
|
| ExpandedXmlModelledBinaryWriter |
Expanded PSI-XML writer for modelled binary interactions (no experimental evidences)
|
| ExpandedXmlModelledWriter |
Expanded PSI-XML writer for abstract interactions (no experimental evidences)
|
| ExpandedXmlModelledWriter |
Expanded PSI-XML writer for abstract interactions (no experimental evidences)
|
| ExpandedXmlNamedBinaryEvidenceWriter |
Expanded PSI-XML writer for named binary interaction evidences (full experimental evidences)
Participants, features and experiments also have expanded names to write
|
| ExpandedXmlNamedBinaryWriter |
Expanded PSI-XML writer for a mix of named binary interactions
|
| ExpandedXmlNamedEvidenceWriter |
Expanded PSI-XML writer for named interaction evidences (full experimental evidences)
Participants, features and experiments also have expanded names to write
|
| ExpandedXmlNamedModelledBinaryWriter |
Expanded PSI-XML writer for named modelled binary interactions (no experimental evidences).
|
| ExpandedXmlNamedModelledWriter |
Expanded PSI-XML writer for named abstract interactions (no experimental evidences).
|
| ExpandedXmlNamedWriter |
Expanded PSI-XML writer for a mix of named interactions
|
| ExpandedXmlWriter |
Expanded PSI-XML writer for a mix of interactions
|
| ExpandedXmlWriter |
Expanded PSI-XML writer for a mix of interactions
|
| Experiment |
Experiment in which some interactions has been determined.
|
| ExperimentalCvTerm |
This elements is controlled by the PSI-MI controlled vocabulary
"experimentalPreparation", root term id MI:0346.
|
| ExperimentalCvTerm |
This elements is controlled by the PSI-MI controlled vocabulary
"experimentalPreparation", root term id MI:0346.
|
| ExperimentalCvTerm |
This elements is controlled by the PSI-MI controlled vocabulary
"experimentalPreparation", root term id MI:0346.
|
| ExperimentalCvTerm.JAXBExperimentRefWrapper |
|
| ExperimentalCvTerm.JAXBExperimentRefWrapper |
|
| ExperimentalCvTerm.JAXBExperimentRefWrapper |
|
| ExperimentalEntity |
An experimental entity with experimental features
|
| ExperimentalEntityComparator |
Basic Experimental entity comparator.
|
| ExperimentalEntry |
Entry implementation for JAXB read only
|
| ExperimentalEntry |
Entry implementation for JAXB read only
|
| ExperimentalEntry |
Entry implementation for JAXB read only
|
| ExperimentalEntry.JAXBAvailabilitiesWrapper |
|
| ExperimentalEntry.JAXBAvailabilitiesWrapper |
|
| ExperimentalEntry.JAXBAvailabilitiesWrapper |
|
| ExperimentalEntry.JAXBExperimentsWrapper |
|
| ExperimentalEntry.JAXBExperimentsWrapper |
|
| ExperimentalEntry.JAXBExperimentsWrapper |
|
| ExperimentalEntry.JAXBInteractionsWrapper |
|
| ExperimentalEntry.JAXBInteractionsWrapper |
|
| ExperimentalEntry.JAXBInteractionsWrapper |
|
| ExperimentalInteractor |
Java class for experimentalInteractor complex type.
|
| ExperimentalInteractor |
Java class for experimentalInteractor complex type.
|
| ExperimentalInteractor |
Java class for experimentalInteractor complex type.
|
| ExperimentalInteractor.JAXBExperimentRefWrapper |
|
| ExperimentalInteractor.JAXBExperimentRefWrapper |
|
| ExperimentalInteractor.JAXBExperimentRefWrapper |
|
| ExperimentalParticipantCandidate |
Interface for experimental participant candidates
|
| ExperimentalParticipantPool |
A pool of experimental participants
|
| ExperimentalParticipantPoolChangeLogger |
This listener will just interactor change events
|
| ExperimentalParticipantPoolComparator |
Basic Experimental participant pool comparator.
|
| ExperimentalParticipantPoolEnricher |
The Participant pool enricher is an enricher which can enrich either single Participant pool or a collection.
|
| ExperimentalParticipantPoolEnricherListener |
Experimental Participant pool enricher listener
|
| ExperimentalParticipantPoolEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| ExperimentalParticipantPoolEnricherLogger |
A logging listener.
|
| ExperimentalParticipantPoolEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| ExperimentChangeListener |
Listener for experiment changes
|
| ExperimentChangeLogger |
This listener will listen to experiment change events
|
| ExperimentCloner |
Utility class for cloning experiments
|
| ExperimentComparator |
Basic experiment comparator.
|
| ExperimentEnricher |
The experimentEnricher can enrich either a single experiment or a collection.
|
| ExperimentEnricherListener |
//An extension of the ExperimentChangeListener
//with specific methods related to the process of enriching.
|
| ExperimentEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| ExperimentEnricherLogger |
A logging listener.
|
| ExperimentEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| ExperimentImexEnricherListener |
An extension of the ExperimentEnricherListener
with specific methods related to the process of enriching.
|
| ExperimentImexEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| ExperimentImexEnricherLogger |
A logging listener.
|
| ExperimentImexEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| ExperimentStream |
An experiment data source allows to stream the experiments of a given dataSource
|
| ExperimentUtils |
Factory for experiment
|
| ExperimentXrefContainer |
Xref container for Experiment
|
| ExperimentXrefContainer |
Xref container for Experiment
|
| ExperimentXrefContainer |
Xref container for Experiment
|
| ExtendedMitabInteractionEvidenceFeeder |
Mitab 2.6 extended feeder for interaction evidence.
|
| ExtendedMitabModelledInteractionFeeder |
Mitab 2.5 extended feeder for Modelled interaction.
|
| ExtendedPsiXmlCausalRelationship |
Extended causal relationship for XML 3.0.
|
| ExtendedPsiXmlEntity<F extends Feature> |
Extended participant for PSI-XML 2,5 standards
|
| ExtendedPsiXmlExperiment |
Extended experiment for PSI-XML 2,5 standards
|
| ExtendedPsiXmlFeature<P extends Entity,F extends Feature> |
Interface for psi25 xml features
|
| ExtendedPsiXmlFeatureEvidence |
PSI-XML extension of a feature evidence
|
| ExtendedPsiXmlInteraction<T extends Participant> |
Extended interaction for PSI-XML 2,5 standards
|
| ExtendedPsiXmlInteractionEvidence |
Extended interaction evidence for PSI-XML 2,5 standards
|
| ExtendedPsiXmlInteractionEvidence |
Extended interaction evidence for PSI-XML 2,5 standards
|
| ExtendedPsiXmlInteractor |
Interface for interactors in PSI-XML standards
|
| ExtendedPsiXmlModelledInteraction |
Extended modelled interaction for PSI-XML 2,5 standards
|
| ExtendedPsiXmlModelledInteraction |
Extended interaction for PSI-XML 2,5 standards
|
| ExtendedPsiXmlParticipant<I extends Interaction,F extends Feature> |
Extended participant for PSI-XML 2,5 standards
|
| ExtendedPsiXmlParticipantEvidence |
Extended participant evidence for PSI-XML 2,5 standards
|
| ExtendedPsiXmlSource |
Extended source for PSI-XML standards
|
| ExtendedPsiXmlXref |
PSI-XML extension of an xref
|
| FailingBioactiveEntityFetcher |
Created with IntelliJ IDEA.
|
| FailingCvTermFetcher |
A mock fetcher for testing exceptions.
|
| FailingGeneFetcher |
A mock fetcher for testing exceptions.
|
| FailingOrganismFetcher |
A mock fetcher for testing exceptions.
|
| FailingProteinFetcher |
A mock fetcher for testing exceptions.
|
| FailingPublicationFetcher |
A mock fetcher for testing exceptions.
|
| FastaSequence |
Fasta sequence
|
| Feature<P extends Entity,F extends Feature> |
Property of a participant that may interfere with the binding of a molecule.
|
| FeatureBaseComparator |
feature comparator.
|
| FeatureChangeListener<F extends Feature> |
Listener to feature change events
|
| FeatureChangeLogger<T extends Feature> |
This listener will just interactor change events
|
| FeatureCloner |
This class will clone/copy properties of a feature
|
| FeatureCollectionComparator<T extends Feature> |
Comparator for collection of Features
|
| FeatureComparator |
Generic feature comparator.
|
| FeatureEnricher<F extends Feature> |
The featureEnricher can enrich either a single feature or a collection.
|
| FeatureEnricherListener<T extends Feature> |
An extension of the FeatureChangeListener
with specific methods related to the process of enriching.
|
| FeatureEnricherListenerManager<T extends Feature> |
A manager for listeners which holds a list of listeners.
|
| FeatureEnricherLogger<T extends Feature> |
A logging listener.
|
| FeatureEnricherStatisticsWriter<T extends Feature> |
A statistics logger which records changes made by the enricher.
|
| FeatureEvidence |
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ
from the sequence described by the identifying accession number.
|
| FeatureEvidenceChangeListener |
Listener which listen to changes in feature evidence
|
| FeatureEvidenceChangeLogger |
This listener will just interactor change events
|
| FeatureEvidenceComparator |
Basic FeatureEvidence comparator.
|
| FeatureEvidenceEnricherListener |
An extension of the FeatureChangeListener
with specific methods related to the process of enriching.
|
| FeatureEvidenceEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| FeatureEvidenceEnricherLogger |
A logging listener.
|
| FeatureEvidenceEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| FeatureGraphBuilder<I extends Interaction,F extends Feature> |
This class will create a graph from one to several interactions.
|
| FeatureModificationEffector |
The modification (feature) that elicits an allosteric response in an allosteric molecule.
|
| FeatureModificationEffectorComparator |
Basic comparator for FeatureModificationEffector.
|
| FeatureUtils |
Utility class for features
|
| FeatureXrefContainer |
Xref container for Feature
|
| FeatureXrefContainer |
Xref container for Feature
|
| FeatureXrefContainer |
Xref container for Feature
|
| FetchDataFromChebi |
In this code example, we fetch some data from Chebi
|
| FileSourceContext |
Some context in a file giving information about object location, etc..
|
| FileSourceLocator |
A source locator of an object in a file
|
| FullBioactiveEntityEnricher |
A full enricher for bioactive entities.
|
| FullBioactiveEntityUpdater |
A full updater for bioactive entities.
|
| FullComplexEnricher |
Full enricher for complexes
|
| FullComplexUpdater |
Full enricher for complexes
|
| FullCuratedPublicationEnricher |
Provides full enrichment of curated Publication.
|
| FullCuratedPublicationUpdater |
Provides full update of Publication.
|
| FullCvTermEnricher<C extends CvTerm> |
Provides full enrichment of cv term.
|
| FullCvTermUpdater<C extends CvTerm> |
Provides full update of cv term.
|
| FullEntityEnricher<P extends Entity,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| FullEntityUpdater<P extends Entity,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| FullExperimentalParticipantPoolEnricher |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| FullExperimentalParticipantPoolUpdater |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| FullExperimentEnricher |
Provides full enrichment of experiment.
|
| FullExperimentUpdater |
Provides full update of experiment.
|
| FullFeatureEnricher<F extends Feature> |
Provides full enrichment of feature.
|
| FullFeatureEvidenceEnricher |
Provides full enrichment of feature evidence.
|
| FullFeatureEvidenceUpdater |
Provides full update of feature evidence.
|
| FullFeatureUpdater<F extends Feature> |
Provides full updater of feature.
|
| FullGeneEnricher |
A full enricher for genes.
|
| FullGeneUpdater |
A full updater for genes.
|
| FullInteractionEnricher<I extends Interaction> |
Full enricher for interactions
|
| FullInteractionEvidenceEnricher |
Full enricher for Interaction evidence
|
| FullInteractionEvidenceUpdater |
Full updater for interaction evidence
|
| FullInteractionUpdater<I extends Interaction> |
Full updater of interaction
|
| FullInteractorBaseEnricher<T extends Interactor> |
Full interactor enricher
|
| FullInteractorBaseUpdater<T extends Interactor> |
Full updater of interactor
|
| FullInteractorPoolEnricher |
A full enricher for interactor pools.
|
| FullInteractorPoolUpdater |
A full updater for interactor pools.
|
| FullModelledInteractionEnricher<I extends ModelledInteraction> |
Full enricher for ModelledInteraction
|
| FullModelledInteractionUpdater<I extends ModelledInteraction> |
Full updater of a modelled interaction
|
| FullOntologyTermEnricher |
Provides full enrichment of ontologYTerm.
|
| FullOntologyTermUpdater |
Provides full update of ontologYTerm.
|
| FullOrganismEnricher |
Provides full enrichment of a Organism.
|
| FullOrganismUpdater |
Provides full update of a Organism.
|
| FullParticipantEnricher<P extends Participant,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| FullParticipantEvidenceEnricher<P extends ParticipantEvidence> |
Created with IntelliJ IDEA.
|
| FullParticipantEvidenceUpdater<P extends ParticipantEvidence> |
Created with IntelliJ IDEA.
|
| FullParticipantPoolEnricher<P extends ParticipantPool,F extends Feature> |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| FullParticipantPoolUpdater<P extends ParticipantPool,F extends Feature> |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| FullParticipantUpdater<P extends Participant,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| FullPolymerEnricher<T extends Polymer> |
Full polymer enricher.
|
| FullPolymerUpdater<T extends Polymer> |
Full updater of polymer
- update all properties of interactor as described in FullInteractorBaseUpdater
- update sequence of polymer.
|
| FullProteinEnricher |
Full enricher of proteins.
|
| FullProteinUpdater |
Full updater of proteins.
|
| FullPsiXmlParser<T extends Interaction> |
Full parser that loads the all entry set.
|
| FullPublicationEnricher |
Provides full enrichment of Publication.
|
| FullPublicationUpdater |
Provides full update of Publication.
|
| FullSourceEnricher |
Provides full enrichment of a Source.
|
| FullSourceUpdater |
Provides full update of a Source.
|
| FullXmlBinaryEvidenceParser |
Full Parser generating basic binary interaction objects and ignoring all experimental details.
|
| FullXmlBinaryParser |
Full Parser generating binary interactions that could be a mix or abstract interactions and interaction evidences.
|
| FullXmlComplexParser |
Full Parser generating biological complex objects and ignore experimental details.
|
| FullXmlEvidenceParser |
Full Parser generating interaction evidence objects and loading all experimental details.
|
| FullXmlModelledBinaryParser |
Full Parser generating binary modelled interaction objects and ignoring all experimental details.
|
| FullXmlModelledParser |
Full Parser generating modelled interaction objects and ignore experimental details.
|
| FullXmlParser |
Full Parser generating interaction objects that could be a mix or abstract interactions and interaction evidences.
|
| Gene |
Interactor for genetic interactions
|
| GeneComparator |
Unambiguous gene comparator.
|
| GeneEnricherListener |
Created with IntelliJ IDEA.
|
| GeneEnricherListenerManager |
Created with IntelliJ IDEA.
|
| GeneEnricherLogger |
Created with IntelliJ IDEA.
|
| GeneEnricherStatisticsWriter |
Created with IntelliJ IDEA.
|
| GeneFetcher |
A fetcher for genes.
|
| HostOrganism |
The experiment/participant host organism
|
| HostOrganism |
The experiment/participant host organism
|
| HostOrganism |
The experiment/participant host organism
|
| HostOrganism.JAXBExperimentRefWrapper |
|
| HostOrganism.JAXBExperimentRefWrapper |
|
| HostOrganism.JAXBExperimentRefWrapper |
|
| HtmlWriterOptions |
Class that lists all possible options for MI HTML writer.
|
| HtmlWriterUtils |
Utility class for writing molecular interactions in html
|
| IdentifiersChangeListener<T> |
A listener for changes to a list of identifiers.
|
| IdentityHashComparator<T> |
The IdentityHashComparator will use the hashcode of each objects to compare the objects.
|
| IInteractorXrefContainer |
|
| IllegalParameterException |
Exception to throw if a Parameter is not valid
|
| IllegalRangeException |
Exception thrown when trying to create an Illegal range
|
| ImexAssigner |
Interface for assigning IMEx id to a publication and updating intact publications, experiments and interactions
|
| ImexAssignerImpl |
This class will assign an IMEx id to a publication using imex central webservice and update experiments and interactions
|
| ImexCentralClient |
IMEx Central publication fetcher.
|
| ImexCentralPublicationRegister |
Interface for registering a publication in IMEx central and collect a publication record in IMEx central
|
| ImexCentralPublicationRegisterImpl |
This class can register a publication in IMEx central and collect a publication record in IMEx central using imex central webservice
|
| ImexCentralUtility |
Created by anjali on 29/11/18.
|
| ImexExperimentUpdater |
This enricher will update an experiment attached to a publication having an IMEx id
|
| ImexInteractionUpdater |
This enricher will update a interaction evidence having a publication with IMEx id
|
| ImexPublication |
Extension of publication for imex central
|
| ImexPublicationAssigner |
This enricher will update a publication having IMEx id and synchronize it with IMEx central
|
| ImexPublicationRegister |
This enricher will update a publication having IMEx id and synchronize it with IMEx central
|
| ImexPublicationUpdater |
This enricher will update a publication having IMEx id and synchronize it with IMEx central
|
| IncrementalIdGenerator |
Id generator that will increment ids
|
| InferredInteraction |
Java class for inferredInteraction complex type.
|
| InferredInteraction |
Java class for inferredInteraction complex type.
|
| InferredInteraction |
Java class for inferredInteraction complex type.
|
| InferredInteraction.JAXBExperimentRefWrapper |
|
| InferredInteraction.JAXBExperimentRefWrapper |
|
| InferredInteraction.JAXBExperimentRefWrapper |
|
| InferredInteractionParticipant |
Participant of the inferred interaction.
|
| InferredInteractionParticipant |
Participant of the inferred interaction.
|
| InferredInteractionParticipant |
Participant of the inferred interaction.
|
| InMemoryIdentityObjectCache |
It keeps a in memory cache of objects having an id.
|
| InMemoryLightIdentityObjectCache |
It keeps a in memory cache of objects having an id.
|
| InMemoryPsiXmlCache |
PsiXmlIdCache that stores objects in memory using a map
|
| IntegerComparator |
Comparator for comparing integers.
|
| Interaction<T extends Participant> |
Interaction involving one to several molecules.
|
| InteractionBaseComparator |
Interaction comparator.
|
| InteractionCategory |
Enum to recognize the object category of an interaction :
- evidence : for InteractionEvidence implementations.
|
| InteractionChangeListener<I extends Interaction> |
Listener for changes in interaction
|
| InteractionChangeLogger<T extends Interaction> |
This listener will just interaction change events
|
| InteractionCloner |
Utility class to clone and copy interaction properties
|
| InteractionComparator |
Generic interaction comparator.
|
| InteractionEnricher<I extends Interaction> |
The enricher for Interactions which can enrich a single interaction or a collection.
|
| InteractionEnricherListener<I extends Interaction> |
Listener for interaction enrichment
|
| InteractionEnricherListenerManager<I extends Interaction> |
A manager for listeners which holds a list of listeners.
|
| InteractionEnricherLogger<I extends Interaction> |
A logging listener.
|
| InteractionEnricherStatisticsWriter<I extends Interaction> |
A statistics logger which records changes made by the enricher.
|
| InteractionEvidence |
Interaction involving one to several molecules supported by experiments.
|
| InteractionEvidenceBipartiteExpansion |
BipartiteExpansion for InteractionEvidence
|
| InteractionEvidenceChangeListener |
Listener for changes in interaction evidence
|
| InteractionEvidenceChangeLogger |
This listener will just interaction evidence change events
|
| InteractionEvidenceComparator |
Basic InteractionEvidenceComparator.
|
| InteractionEvidenceEnricher |
An enricher for interaction evidences.
|
| InteractionEvidenceEnricherListener |
Listener for interaction evidence enrichment
|
| InteractionEvidenceEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| InteractionEvidenceEnricherLogger |
A logging listener.
|
| InteractionEvidenceEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| InteractionEvidenceImexEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| InteractionEvidenceImexEnricherLogger |
A logging listener.
|
| InteractionEvidenceImexEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| InteractionEvidenceLineParser |
An extension of MitabLineParser that returns interactions evidences only.
|
| InteractionEvidenceMatrixExpansion |
Matrix expansion for InteractionEvidence
|
| InteractionEvidenceSource<T extends InteractionEvidence> |
A Data source of interaction evidences.
|
| InteractionEvidenceSpokeExpansion |
Spoke expansion for interaction evidence
|
| InteractionEvidenceStream<T extends InteractionEvidence> |
A Data source of interaction evidences giving only a stream of interactions.
|
| InteractionImexEnricherListener |
An extension of the ExperimentEnricherListener
with specific methods related to the process of enriching.
|
| InteractionInteractorComparator |
Simple interaction comparator only based on the interactors of an interaction.
|
| InteractionLineParser |
An extension of MitabLineParser that returns simple interactions only.
|
| InteractionSource<T extends Interaction> |
A Data source of interactions.
|
| InteractionStream<T extends Interaction> |
A Data source of interactions giving only a stream of interactions.
|
| InteractionUtils |
Factory for experimental interactions
|
| InteractionViewerJson |
This class is a central access to basic methods to register json writer.
|
| InteractionWriter<T extends Interaction> |
The InteractionWriter can write interactions in a datasource (files, database)
|
| InteractionWriterFactory |
A factory for InteractionWriter
|
| InteractionWriterOptions |
Class that lists all possible options for InteractionWriter
|
| InteractionXrefContainer |
Xref container for interactions
|
| InteractionXrefContainer |
Xref container for interactions
|
| InteractionXrefContainer |
Xref container for interactions
|
| Interactor |
Molecule or complex of molecules that interacts with other molecules/complexes
|
| InteractorBaseComparator |
nteractor comparator
It will only compare identifiers if one interactor does have identifiers using UnambiguousIdentifierComparator.
|
| InteractorCategory |
Enum for interactor category
|
| InteractorChangeListener<T extends Interactor> |
A generic listener for an interactor.
|
| InteractorChangeLogger<T extends Interactor> |
This listener will just interactor change events
|
| InteractorCloner |
Cloner for interactors
|
| InteractorComparator |
Generic Interactor Comparator.
|
| InteractorEnricher<T extends Interactor> |
Interface for interactor enrichers.
|
| InteractorEnricherListener<T extends Interactor> |
Interface for interactor enricher listener
|
| InteractorEnricherListenerManager<T extends Interactor> |
Manager of interactor listeners
|
| InteractorEnricherLogger<T extends Interactor> |
Logger of interactor enrichment
|
| InteractorEnricherStatisticsWriter<T extends Interactor> |
TODO comment this
|
| InteractorFactory |
Interface for factories allowing creation of a proper interactor depending on the type
and xrefs
|
| InteractorFetcher<I extends Interactor> |
Fetches the complete records which match an interactor.
|
| InteractorPool |
InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.
|
| InteractorPoolChangeListener |
Listener of changes in interactor pool
|
| InteractorPoolChangeLogger |
This listener will just interactor pool change events
|
| InteractorPoolComparator |
Basic InteractorPoolComparator.
|
| InteractorPoolEnricher |
The Interactor pool enricher is an enricher which can enrich either single interactor pool or a collection.
|
| InteractorPoolEnricherListener |
Interface for interactor pool enricher listener
|
| InteractorPoolEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| InteractorPoolEnricherLogger |
A logging listener.
|
| InteractorPoolEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| InteractorStream<T extends Interactor> |
An interactor data source allows to stream the interactors of a given dataSource
|
| InteractorUtils |
Factory for interactors
|
| InteractorXrefContainer |
Xref container for interactors
|
| InteractorXrefContainer |
Xref container for interactors
|
| InteractorXrefContainer |
Xref container for interactors
|
| IteratorHavingProperties<T> |
Iterator for list having properties
|
| IteratorWrapper<T> |
Iterator for list wrappers
|
| JavaCharStream |
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (with java-like unicode escape processing).
|
| JaxbUnmarshallerFactory |
Factory to initialise JAXB context depending on the version and the interaction object category
|
| JsonElementWriter<T> |
JSON writer for JAMI objects
|
| JsonRangeWriter |
JSON writer for Range objects
|
| LazyCvTerm |
A lazy cvTerm which will only fetch metadata when required.
|
| LazyOntologyTerm |
A lazy ontology term, which only checks for parents of children when required.
|
| LazySource |
A lazy cvTerm which will only fetch metadata when required.
|
| LazyTermLoadingException |
Exception thrown when a Lazy cv term cannot load the lazy data from OLS
|
| LightCompactXmlBinaryWriter |
Compact PSI-XML writer for light binary interactions (no experimental evidences)
|
| LightCompactXmlBinaryWriter |
Compact PSI-XML writer for light binary interactions (no experimental evidences)
|
| LightCompactXmlNamedBinaryWriter |
Compact PSI-XML writer for light binary interactions (no experimental evidences) having names.
|
| LightCompactXmlNamedWriter |
Compact PSI-XML writer for light interactions (no experimental evidences) having names.
|
| LightCompactXmlWriter |
Compact PSI-XML writer for light interactions (no experimental evidences)
|
| LightCompactXmlWriter |
Compact PSI-XML writer for light interactions (no experimental evidences)
|
| LightExpandedXmlBinaryWriter |
Expanded PSI-XML writer for light binary interactions (no experimental evidences)
|
| LightExpandedXmlBinaryWriter |
Expanded PSI-XML writer for light binary interactions (no experimental evidences)
|
| LightExpandedXmlNamedBinaryWriter |
Expanded PSI-XML writer for light binary interactions (no experimental evidences) having names.
|
| LightExpandedXmlNamedWriter |
Expanded PSI-XML writer for light interactions (no experimental evidences) having names.
|
| LightExpandedXmlWriter |
Expanded PSI-XML writer for light interactions (no experimental evidences)
|
| LightExpandedXmlWriter |
Expanded PSI-XML writer for light interactions (no experimental evidences)
|
| LightFullXmlBinaryParser |
Full Parser generating basic binary interaction objects and ignoring all experimental details.
|
| LightFullXmlParser |
Full Parser generating basic interaction objects and ignore experimental details.
|
| LightMIHtmlWriter |
Writer for light interactions
|
| LightMIJsonBinaryWriter |
JSON writer for light interactions
|
| LightMIJsonWriter |
The jsonWriter which writes the light interactions
|
| LightMIJsonWriter |
Abstract JSON writer for interactions (n-ary json format)
|
| LightMitab25BinaryWriter |
Mitab 2.5 writer for light binary interactions (no experimental details)
|
| LightMitab25Writer |
The mitab 2.5 writer for light Interaction (no experimental details)
|
| LightMitab26BinaryWriter |
Mitab 2.6 writer for light binary interactions
|
| LightMitab26Writer |
Mitab 2.6 writer for light interaction
|
| LightMitab27BinaryWriter |
Mitab 2.7 writer for light binary interactions
|
| LightMitab27Writer |
Mitab 2.7 writer for light interaction
|
| LightMitab28BinaryWriter |
Mitab 2.8 writer for light binary interactions
|
| LightMitab28Writer |
Mitab 2.8 writer for light interaction
|
| LightMitabBinarySource |
A mitab datasource that loads very basic binary interactions and ignore experimental details, source, confidence and experimental details.
|
| LightMitabBinaryStreamSource |
A mitab datasource that loads very basic binary interactions and ignore experimental details, source, confidence and experimental details
It only provides an iterator of binary interactions
|
| LightMitabSource |
A mitab datasource that loads very basic interactions and ignore experimental details, source, confidence and experimental details
It will load the full interaction set.
|
| LightMitabStreamSource |
A mitab datasource that loads very basic interactions and ignore experimental details, source, confidence and experimental details
It will only provide an iterator of interactions.
|
| LightXmlBinaryParser |
Xml parser creating light binary interactions and ignoring experimental details
|
| LightXmlBinarySource |
PSI-XML data source that provides light binary interactions (no experimental details).
|
| LightXmlBinaryStreamSource |
Psi-XML binary interaction datasource
|
| LightXmlParser |
Parser generating basic interaction objects and ignore experimental details
|
| LightXmlSource |
PSI-XML data source that provides light interactions (no experimental details).
|
| LightXmlStreamSource |
Datasource for PSI-xml returning basic interactions
|
| ListIteratorHavingProperties<T> |
Iterator for list having properties
|
| ListUtils |
A utility class for lists
|
| LocationType |
Java class for locationType complex type.
|
| MatrixExpansion |
The matrix Expansion method.
|
| MIBatchJobManager |
The psi mi enricher
|
| MIComparator<T> |
A MI comparator is a comparator that can also generate a hashCode of a JAMI object that would be
consistent with the comparison results
|
| MIDataSource |
A data Source in JAMI.
|
| MIDataSourceFactory |
A factory singleton to create data sources.
|
| MIDataSourceOptionFactory |
The factory to populate the map of options for the DataSourceFactory
|
| MIDataSourceOptions |
Class that lists all possible options for MIDataSource
|
| MIEdge<T> |
A MI edge is an edge joining two JAMI objects.
|
| MIEnricher<T> |
General interface for enriching MI objects
|
| MIEvidenceHtmlWriter |
HTML writer for PSI-MI interaction evidences.
|
| MIFileAnalyzer |
The file source analyzer will recognise what kind of molecular interaction source a given file is from.
|
| MIFileDataSource |
Interface for MIDataSource coming from a file.
|
| MIFileDataSourceOptions |
Class that lists all possible options for MIFileDataSource.
|
| MIFileDatasourceUtils |
Utilisty class for MIFileDataSource
|
| MIFileParserCompositeListener<T extends MIFileParserListener> |
This class contains several MI file listeners
|
| MIFileParserListener |
Interface for listening to the parsing of a MI file.
|
| MIFileParserLogger |
Logger for MitabParser
|
| MIFileType |
The MI file source format
|
| MIFileUtils |
Utility class for Molecular interaction datasources
|
| MIHtml |
This class is a central access to basic methods to register html writer.
|
| MIHtmlOptionFactory |
The factory to populate the map of options for the InteractionWriterFactory for html writers
|
| MIHtmlWriter |
MI writer for a mix of interactions
|
| MIIOException |
Exception thrown by a dataSource or a writer when it cannot read/write MI data
|
| MIJsonBinaryEvidenceWriter |
JSON writer for InteractionEvidences
|
| MIJsonBinaryWriter |
JSON writer for mix of modelled and experimental interactions and
|
| MIJsonEvidenceWriter |
The jsonWriter which writes the interaction evidences
|
| MIJsonEvidenceWriter |
Abstract JSON writer for interactions (n-ary json format)
|
| MIJsonModelledBinaryWriter |
JSON writer for ModelledInteractions
|
| MIJsonModelledWriter |
The jsonWriter which writes the modelled interactions
|
| MIJsonModelledWriter |
Abstract JSON writer for interactions (n-ary json format)
|
| MIJsonOptionFactory |
The factory to populate the map of options for the InteractionWriterFactory for json writers
|
| MIJsonType |
Type of json export
binary_only: the JSON writer will always write binary interactions and break n-ary interactions into binary interactions
n_ary_only: the JSON writer will always write the full interaction even if it is n-ary
|
| MIJsonUtils |
Utility class for public properties
|
| MIJsonWriter |
The jsonWriter which writes all interactions
|
| MIJsonWriter |
The jsonWriter which writes the all interactions
|
| MIJsonWriterOptions |
Class that lists all possible options for InteractionViewerJson writers.
|
| MILocalOntology |
JAMI implementation of LocalOntology access
|
| MIModelledHtmlWriter |
Writer for modelled interactions
|
| MinimalBioactiveEntityEnricher |
A basic minimal enricher for bioactive entities.
|
| MinimalBioactiveEntityUpdater |
A basic minimal updater for bioactive entities.
|
| MinimalComplexEnricher |
Minimal enricher for complexes
|
| MinimalComplexUpdater |
Minimal updater for complexes
|
| MinimalCuratedPublicationEnricher |
Provides minimal enrichment of curatedPublication.
|
| MinimalCuratedPublicationUpdater |
Provides minimal update of curated Publication.
|
| MinimalCvTermEnricher<C extends CvTerm> |
Provides minimal enrichment of cv term.
|
| MinimalCvTermUpdater<C extends CvTerm> |
Provides minimal update of cv term.
|
| MinimalEntityEnricher<P extends Entity,F extends Feature> |
The entity enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalEntityUpdater<P extends Entity,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalExperimentalParticipantPoolEnricher |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalExperimentalParticipantPoolUpdater |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalExperimentEnricher |
Provides minimal enrichment of experiment.
|
| MinimalExperimentUpdater |
Provides minimal update of experiment.
|
| MinimalFeatureEnricher<F extends Feature> |
Provides minimal enrichment of feature.
|
| MinimalFeatureEvidenceEnricher |
Provides minimal enrichment of feature evidence.
|
| MinimalFeatureEvidenceUpdater |
Provides minimal update of feature evidence.
|
| MinimalFeatureUpdater<F extends Feature> |
Provides minimal update of feature.
|
| MinimalGeneEnricher |
A basic minimal enricher for genes.
|
| MinimalGeneUpdater |
A basic minimal updater for genes.
|
| MinimalInteractionEnricher<I extends Interaction> |
The enricher for Interactions which can enrich a single interaction or a collection.
|
| MinimalInteractionEvidenceEnricher |
Minimal enricher for interaction evidence
|
| MinimalInteractionEvidenceUpdater |
Minimal updater for interaction evidence
|
| MinimalInteractionUpdater<I extends Interaction> |
The enricher for Interactions which can enrich a single interaction or a collection.
|
| MinimalInteractorBaseEnricher<T extends Interactor> |
A basic minimal enricher for interactors.
|
| MinimalInteractorBaseUpdater<T extends Interactor> |
A basic minimal updater for interactors.
|
| MinimalModelledInteractionEnricher<I extends ModelledInteraction> |
Minimal enricher for modelled interactions
|
| MinimalModelledInteractionUpdater<I extends ModelledInteraction> |
Minimal updater for modelled interaction
|
| MinimalOntologyTermEnricher |
Provides minimal enrichment of ontologYTerm.
|
| MinimalOntologyTermUpdater |
Provides minimal update of ontologYTerm.
|
| MinimalOrganismEnricher |
Provides minimum enrichment of a Organism.
|
| MinimalOrganismUpdater |
Provides minimum update of a Organism.
|
| MinimalParticipantEnricher<P extends Participant,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalParticipantEvidenceEnricher<P extends ParticipantEvidence> |
Created with IntelliJ IDEA.
|
| MinimalParticipantEvidenceUpdater<P extends ParticipantEvidence> |
Created with IntelliJ IDEA.
|
| MinimalParticipantPoolEnricher<P extends ParticipantPool,F extends Feature> |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalParticipantPoolUpdater<P extends ParticipantPool,F extends Feature> |
The participant pool enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalParticipantUpdater<P extends Participant,F extends Feature> |
The participant enricher is an enricher which can enrich either single participant or a collection.
|
| MinimalProteinEnricher |
Enriches a protein to the minimum level.
|
| MinimalProteinUpdater |
Updates a protein to the minimum level.
|
| MinimalPublicationEnricher |
Provides minimal enrichment of Publication.
|
| MinimalPublicationUpdater |
Provides minimal update of Publication.
|
| MinimalSourceEnricher |
Provides minimum enrichment of a Source.
|
| MinimalSourceUpdater |
Provides minimum update of a Source.
|
| MIOlsOntology |
jami extension for OlsOntology
|
| MIOntologyAccess |
Extension of OntologyAcessTemplate for jami
|
| MIOntologyManager |
JAMI extension of the ontologyManager
|
| MIOntologyTermI |
Extension of OntologyTermI for jami
|
| Mitab25BinaryEvidenceWriter |
Extended Mitab 2.5 writer for binary interaction evidences
|
| Mitab25BinaryEvidenceWriter |
Mitab 2.5 writer for binary interaction evidences
|
| Mitab25BinaryWriter |
The basic Mitab 2.5 writer for BinaryInteraction
|
| Mitab25BinaryWriter |
The basic Mitab 2.5 writer for BinaryInteraction
|
| Mitab25EvidenceWriter |
The mitab 2.5 writer for interaction evidence
|
| Mitab25EvidenceWriter |
The mitab 2.5 writer for interaction evidence
|
| Mitab25ModelledBinaryWriter |
Mitab 2.5 writer for modelled binary interactions
|
| Mitab25ModelledBinaryWriter |
Mitab 2.5 writer for modelled binary interactions
|
| Mitab25ModelledWriter |
The mitab 2.5 writer for ModelledInteraction
|
| Mitab25ModelledWriter |
The mitab 2.5 writer for ModelledInteraction
|
| Mitab25Writer |
The simple MITAB 2.5 writer will write interactions using the JAMI interfaces.
|
| Mitab25Writer |
The simple MITAB 2.5 writer will write interactions using the JAMI interfaces.
|
| Mitab26BinaryEvidenceWriter |
Mitab 2.6 writer for binary interaction evidences
|
| Mitab26BinaryEvidenceWriter |
Mitab 2.6 writer for binary interaction evidences
|
| Mitab26BinaryWriter |
The basic Mitab 2.6 writer for BinaryInteraction
|
| Mitab26BinaryWriter |
The basic Mitab 2.6 writer for BinaryInteraction
|
| Mitab26EvidenceWriter |
Mitab 2.6 writer for interaction evidence
|
| Mitab26EvidenceWriter |
Mitab 2.6 writer for interaction evidence
|
| Mitab26ModelledBinaryWriter |
Mitab 2.6 writer for modelled binary interactions
|
| Mitab26ModelledBinaryWriter |
Mitab 2.6 writer for modelled binary interactions
|
| Mitab26ModelledWriter |
Mitab 2.6 writer for Modelled interaction
|
| Mitab26ModelledWriter |
Mitab 2.6 writer for Modelled interaction
|
| Mitab26Writer |
The simple MITAB 2.6 writer will write interactions using the JAMI interfaces.
|
| Mitab26Writer |
The simple MITAB 2.6 writer will write interactions using the JAMI interfaces.
|
| Mitab27BinaryEvidenceWriter |
Mitab 2.7 writer for binary interaction evidences
|
| Mitab27BinaryEvidenceWriter |
Mitab 2.7 writer for binary interaction evidences
|
| Mitab27BinaryWriter |
The basic Mitab 2.7 writer for BinaryInteraction
|
| Mitab27BinaryWriter |
The basic Mitab 2.7 writer for BinaryInteraction
|
| Mitab27EvidenceWriter |
Mitab 2.7 writer for interaction evidence
|
| Mitab27EvidenceWriter |
Mitab 2.7 writer for interaction evidence
|
| Mitab27ModelledBinaryWriter |
Mitab 2.7 writer for modelled binary interactions
|
| Mitab27ModelledBinaryWriter |
Mitab 2.7 writer for modelled binary interactions
|
| Mitab27ModelledWriter |
Mitab 2.7 writer for Modelled interaction
|
| Mitab27ModelledWriter |
Mitab 2.7 writer for Modelled interaction
|
| Mitab27Writer |
The simple MITAB 2.7 writer will write interactions using the JAMI interfaces.
|
| Mitab27Writer |
The simple MITAB 2.7 writer will write interactions using the JAMI interfaces.
|
| Mitab28BinaryEvidenceWriter |
Mitab 2.8 writer for binary interaction evidences
|
| Mitab28BinaryEvidenceWriter |
Mitab 2.8 writer for binary interaction evidences
|
| Mitab28BinaryWriter |
The basic Mitab 2.8 writer for BinaryInteraction
|
| Mitab28BinaryWriter |
The basic Mitab 2.8 writer for BinaryInteraction
|
| Mitab28EvidenceWriter |
Mitab 2.8 writer for interaction evidence
|
| Mitab28EvidenceWriter |
Mitab 2.8 writer for interaction evidence
|
| Mitab28ModelledBinaryWriter |
Mitab 2.8 writer for modelled binary interactions
|
| Mitab28ModelledBinaryWriter |
Mitab 2.8 writer for modelled binary interactions
|
| Mitab28ModelledWriter |
Mitab 2.8 writer for Modelled interaction
|
| Mitab28ModelledWriter |
Mitab 2.8 writer for Modelled interaction
|
| Mitab28Writer |
The simple MITAB 2.8 writer will write interactions using the JAMI interfaces.
|
| Mitab28Writer |
The simple MITAB 2.8 writer will write interactions using the JAMI interfaces.
|
| MitabAlias |
Extended alias in MITAB
|
| MitabAnnotation |
Extension of Annotation for Mitab with a sourceLocator
|
| MitabAuthor |
This class wraps information about the first author found in mitab column 8
|
| MitabBinaryEvidenceIterator |
A MItab iterator of BinaryInteraction evidences
|
| MitabBinaryEvidenceSource |
A mitab datasource that loads interaction evidences (full experimental details).
|
| MitabBinaryEvidenceStreamSource |
A mitab datasource that loads interaction evidences (full experimental details)
It only provides an iterator of the interactions
|
| MitabBinaryInteraction |
A MitabBinaryInteraction is a binaryInteraction with a MitabSourceLocator
|
| MitabBinaryInteractionEvidence |
TODO comment this
|
| MitabBinaryIterator |
A MItab iterator of BinaryInteraction
|
| MitabBioactiveEntity |
Mitab extension for BioactiveEntity.
|
| MitabCausalRelationship |
|
| MitabChecksum |
Mitab extension for Checksum.
|
| MitabColumnFeeder<T extends BinaryInteraction,P extends Participant> |
A MITAB 2.5 column feeder will write the content of MITAB 2.5 columns
|
| MitabColumnName |
Mitab column names
|
| MitabComplex |
Mitab extension for Complex.
|
| MitabConfidence |
A MitabConfidence is a confidence with some text
|
| MitabCvTerm |
Mitab extension for CvTerm.
|
| MitabDataSourceFactory |
Factory for creating a mitab datasource
|
| MitabDataSourceOptions |
Class that lists all possible options for MIFileDataSource reading MITAB files.
|
| MitabDate |
This class wraps a date and a fileSourceLocator
|
| MitabEvidenceSource |
A mitab datasource that loads interaction evidences (full experimental details)
It will load the full interaction dataset
|
| MitabEvidenceStreamSource |
A mitab datasource that loads interaction evidences (full experimental details)
It only provides an iterator of the interactions
|
| MitabExperiment |
Mitab extension for Experiment.
|
| MitabFeature<P extends Entity,F extends Feature> |
Basic interface for Mitab features
|
| MitabFeatureEvidence |
Mitab extension for FeatureEvidence
|
| MitabGene |
Mitab extension for Gene.
|
| MitabInteraction |
Mitab extension for Interaction
It contains a SourceLocator
|
| MitabInteractionEvidence |
Mitab extension for InteractionEvidence
|
| MitabInteractionEvidenceFeeder |
The Mitab 2.5 column feeder for interaction evidences
|
| MitabInteractionEvidenceIterator |
A MItab iterator of BinaryInteraction evidences
|
| MitabInteractionIterator |
A MItab iterator of BinaryInteraction
|
| MitabInteractor |
Mitab extension for interactor.
|
| MitabInteractorFactory |
The MITAB extension of the InteractorFactory
|
| MitabInteractorPool |
The mitab extension for InteractorSet
|
| MitabLineParser<T extends Interaction,P extends Participant,F extends Feature> |
|
| MitabLineParserConstants |
Token literal values and constants.
|
| MitabLineParserTokenManager |
Token Manager.
|
| MitabModelledBinaryInteraction |
A MitabBinaryInteraction is a modelled binaryInteraction with a MitabSourceLocator
|
| MitabModelledBinaryIterator |
A MItab iterator of modelled BinaryInteractions
|
| MitabModelledBinarySource |
A mitab datasource that loads modelled binary interactions and ignore experimental details.
|
| MitabModelledBinaryStreamSource |
A mitab datasource that loads modelled binary interactions and ignore experimental details.
|
| MitabModelledFeature |
Mitab extension of ModelledFeature
|
| MitabModelledInteraction |
Mitab extension for ModelledInteraction.
|
| MitabModelledInteractionFeeder |
The Mitab 2.5 column feeder for Modelled interactions
|
| MitabModelledInteractionIterator |
A MItab iterator of modelled BinaryInteractions
|
| MitabModelledParticipant |
Mitab extension for ModelledParticipant
It contains a FileSourceLocator
|
| MitabModelledSource |
A mitab datasource that loads modelled interactions and ignore experimental details
It will load the full interaction dataset.
|
| MitabModelledStreamSource |
A mitab datasource that loads modelled interactions and ignore experimental details
It only provides an iterator of modelled interactions
|
| MitabMolecule |
Mitab extension for Molecule
|
| MitabNucleicAcid |
Mitab extension for NucleicAcid
It will contain a FileSourceLocator
|
| MitabOrganism |
Mitab extension of Organism.
|
| MitabParameter |
Mitab extension of Parameter
|
| MitabParserCompositeListener |
This class contains several MI file listeners
|
| MitabParserListener |
A listener listening to events when parsing a mitab file
|
| MitabParserLogger |
Logger for MitabParser
|
| MitabParticipant |
Mitab extension for Participant.
|
| MitabParticipantEvidence |
Mitab extension of ParticipantEvidence.
|
| MitabPolymer |
Mitab extension of Polymer.
|
| MitabProtein |
Mitab extension of Protein.
|
| MitabPublication |
Mitab extension of Publication.
|
| MitabRange |
Mitab extension of Range
It contains a FileSourceLocator
|
| MitabSource<I extends Interaction> |
Interface for MITAB sources that can parse full MITAB files
|
| MitabSource |
Mitab extension of DefaultMitabSource
It contains a FileSourceLocator
|
| MitabSourceLocator |
A MITAB file source context
|
| MitabStoichiometry |
Mitab extension for Stoichiometry.
|
| MitabStreamSource<I extends Interaction> |
Interface for MITAB datasources that can stream MITAB files
|
| MitabUtils |
Utilisty class for MitabWriter
|
| MitabVersion |
The mitab versions
|
| MitabWriterFactory |
Factory for creating a mitab writer
|
| MitabWriterOptions |
Class that lists all the options for a Mitab writer.
|
| MitabXref |
Mitab extension for Xref.
|
| MIWriterOptionFactory |
The factory to get options for the InteractionWriter
|
| MockBioactiveEntityFetcher |
Created with IntelliJ IDEA.
|
| MockCvTermFetcher |
A mock fetcher for testing.
|
| MockFetcher<T> |
Created with IntelliJ IDEA.
|
| MockGeneFetcher |
A mock fetcher for testing.
|
| MockImexCentralClient |
Dummy service that one can use to write test against.
|
| MockOntologyTermFetcher |
A mock fetcher for testing.
|
| MockOrganismFetcher |
A mock fetcher for testing.
|
| MockProteinFetcher |
A mock fetcher for testing.
|
| MockProteinMapper |
Created with IntelliJ IDEA.
|
| MockPublicationFetcher |
A mock fetcher for testing.
|
| MockSourceFetcher |
A mock fetcher for testing.
|
| ModelledBinaryInteraction |
A ModelledBinary interaction is a ModelledInteraction with only two participants
|
| ModelledBinaryInteractionSource |
A Data source of modelled binary interactions.
|
| ModelledBinaryInteractionStream |
A Data source of modelled binary interactions giving only a stream of interactions.
|
| ModelledBinaryInteractionWrapper |
A wrapper for ModelledInteraction which contains two participants
|
| ModelledBinaryLineParser |
An extension of MitabLineParser which parses only ModelledBinaryInteraction
|
| ModelledComparableParticipant |
|
| ModelledComparableParticipantComparator |
|
| ModelledConfidence |
A modelled confidence is a confidence for a modelled interaction.
|
| ModelledEntity |
An modelled entity with modelled features
|
| ModelledEntityComparator |
Basic biological entity comparator.
|
| ModelledEntry |
Modelled Entry implementation for JAXB read only.
|
| ModelledEntry |
Modelled Entry implementation for JAXB read only.
|
| ModelledEntry |
Modelled Entry implementation for JAXB read only.
|
| ModelledEntry.JAXBExperimentsWrapper |
|
| ModelledEntry.JAXBExperimentsWrapper |
|
| ModelledEntry.JAXBExperimentsWrapper |
|
| ModelledEntry.JAXBInteractionsWrapper |
|
| ModelledEntry.JAXBInteractionsWrapper |
|
| ModelledEntry.JAXBInteractionsWrapper |
|
| ModelledFeature |
Biological property of a participant that may be involved with or interfere with the binding of a molecule.
|
| ModelledFeatureComparator |
Basic ModelledFeature comparator.
|
| ModelledInteraction |
An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...
|
| ModelledInteractionBipartiteExpansion |
Bipartite expansion for ModelledInteraction
|
| ModelledInteractionChangeListener<I extends ModelledInteraction> |
Listener for changes in modelled interaction
|
| ModelledInteractionChangeLogger<I extends ModelledInteraction> |
This listener will just modelledInteraction change events
|
| ModelledInteractionCollectionComparator |
Comparator for collection of modelled interactions
|
| ModelledInteractionComparator |
Basic ModelledInteraction comparator.
|
| ModelledInteractionEnricher<I extends ModelledInteraction> |
The enricher for Interactions which can enrich a single interaction or a collection.
|
| ModelledInteractionEnricherListener<I extends ModelledInteraction> |
Listener for modelled interaction enrichment
|
| ModelledInteractionEnricherListenerManager<I extends ModelledInteraction> |
A manager for listeners which holds a list of listeners.
|
| ModelledInteractionEnricherLogger<I extends ModelledInteraction> |
A logging listener.
|
| ModelledInteractionEnricherStatisticsWriter<I extends ModelledInteraction> |
A statistics logger which records changes made by the enricher.
|
| ModelledInteractionLineParser |
An extension of MitabLineParser which parses only ModelledInteraction
|
| ModelledInteractionMatrixExpansion |
Matrix expansion for ModelledInteraction
|
| ModelledInteractionSource<T extends ModelledInteraction> |
A Data source of modelled interactions.
|
| ModelledInteractionSpokeExpansion |
Spoke expansion for ModelledInteraction
|
| ModelledInteractionStream<T extends ModelledInteraction> |
A Data source of modelled interaction giving only a stream of interactions.
|
| ModelledParameter |
A modelled parameter is a parameter for a modelled interaction.
|
| ModelledParticipant |
Participant of a modelled interaction.
|
| ModelledParticipantCandidate |
Interface for modelled participant candidates
|
| ModelledParticipantCollectionComparator |
Comparator for collection of biological participants
|
| ModelledParticipantComparator |
Basic biological participant comparator.
|
| ModelledParticipantPool |
A pool of modelled participant candidates
|
| ModelledParticipantPoolComparator |
Basic biological participant pool comparator.
|
| Molecule |
This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes
complexes and interactorSet
|
| MoleculeEffector |
The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.
|
| MoleculeEffectorComparator |
Basic Comparator for MoleculeEffector.
|
| NamedExperiment |
A named experiment is an experiment with a shortname, fullname and aliases
|
| NamedInteraction<T extends Participant> |
A named interaction is an interaction having a fullname and aliases in addition to a shortname.
|
| NamedParticipant<I extends Interaction,F extends Feature> |
A named entity is an entity having a short name and a fullname in addition to aliases.
|
| NamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| NamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| NamesContainer |
A container for aliases, shortname and fullname
The JAXB binding is designed to be read-only and is not designed for writing
|
| NonCloseableInputStreamWrapper |
Wrapper of inputStream
|
| NucleicAcid |
Polymers of nucleotides which can interact with other molecules
|
| NucleicAcidComparator |
Unambiguous nucleic acids comparator.
|
| ObjectFactory |
This object contains factory methods for each
Java content interface and Java element interface
generated in the psidev.psi.mi.jami.bridges.uniprot.rest.response.model.jaxb package.
|
| OboCvTermFetcher |
Simple fetcher based on OBO files
|
| OboFetcherTemplate<T extends CvTerm> |
Template fetcher for OBO files
|
| OboOntologyTermFetcher |
The ontology fetcher based on OBO file
|
| OboSourceFetcher |
Simple fetcher based on OBO files
|
| OlsCvTermFetcher |
Created with IntelliJ IDEA.
|
| OlsOntologyTermFetcher |
Finds ontology terms in the Ontology Lookup Service
as well as having options to recursively find parents and or children.
|
| OlsSourceFetcher |
Created with IntelliJ IDEA.
|
| OlsUtils |
Utility class which contains global variables
|
| OntologyOboLoader |
The ontologyOboLoader is a loader of OntologyTerm with parents and children
|
| OntologyTerm |
Ontology term with definition, parents and children
|
| OntologyTermChangeListener |
OntologyTerm change listener
|
| OntologyTermChangeLogger |
This listener will just log ontologyTerm change events
|
| OntologyTermCompositeFetcher |
Ontology fetcher that delegates to different ontologyTermFetchers
|
| OntologyTermEnricherListener |
An extension of the OntologyTermChangeListener
with specific methods related to the process of enriching.
|
| OntologyTermEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| OntologyTermEnricherLogger |
A logging listener.
|
| OntologyTermEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| OntologyTermFetcher |
Finds ontology terms in the Ontology Lookup Service
as well as having options to recursively find parents and or children.
|
| OntologyTermUtils |
Utility class for OntologyTerm
|
| OntologyTermWrapper |
Ontology term for PSI-MI JAMI
|
| OpenedInputStream |
The openedInputStream contains a PushbackReader reader that can read the opened input stream
and the type of dataSourceFile it represents.
|
| Operation |
Operations supported for some of the web service update methods.
|
| Operation |
-
The data structure representing a diff is a Linked list of Diff objects:
{Diff(Operation.DELETE, "Hello"), Diff(Operation.INSERT, "Goodbye"),
Diff(Operation.EQUAL, " world.")}
which means: delete "Hello", add "Goodbye" and keep " world."
|
| Organism |
The organism is defined by a taxonomy identifier.
|
| OrganismChangeListener |
This listener listen to Organism changes
|
| OrganismChangeLogger |
This listener will just log organism change events
|
| OrganismCloner |
Utility class for cloning organisms
|
| OrganismComparator |
Basic organism comparator.
|
| OrganismEnricher |
An organism enricher which can enrich either a single organism or a collection.
|
| OrganismEnricherListener |
Created with IntelliJ IDEA.
|
| OrganismEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| OrganismEnricherLogger |
A logging listener.
|
| OrganismEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| OrganismFetcher |
Interface for fetching an organism from an external service.
|
| OrganismStream |
An organism data source allows to stream the organisms of a given dataSource
|
| OrganismTaxIdComparator |
Simple organism comparator based on the taxIds.
|
| OrganismUtils |
Created with IntelliJ IDEA.
|
| Parameter |
A numeric parameter e.g.
|
| ParameterCollectionComparator |
Comparator for collection of parameters
|
| ParameterComparator |
Simple comparator for Parameter
It first compares parameter types, then parameter units and then it uses ParameterValueComparator for comparing parameter values
It will also compare the uncertainty.
|
| ParametersChangeListener<T> |
A listener for changes to an object parameters list.
|
| ParameterUtils |
Utility class for parameters
|
| ParameterValue |
A parameter numeric value.
|
| ParameterValueComparator |
Comparator for ParameterValue.
|
| ParseException |
This exception is thrown when parse errors are encountered.
|
| Participant<I extends Interaction,F extends Feature> |
Participant identified in an interaction
|
| ParticipantBaseComparator |
Basic participant comparator.
|
| ParticipantCandidate<P extends ParticipantPool,F extends Feature> |
A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as
features and causal relationships
|
| ParticipantCandidateCloner |
Utility class for cloning a participant candidate
|
| ParticipantChangeListener<F extends Participant> |
Listener for changes in a participant
|
| ParticipantChangeLogger<T extends Participant> |
This listener will just interactor change events
|
| ParticipantCloner |
Utility class for cloning a participant
|
| ParticipantCollectionComparator<T extends Entity> |
Comparator for collection of participants
|
| ParticipantComparator |
Generic participant comparator.
|
| ParticipantEnricher<P extends Participant,F extends Feature> |
Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
|
| ParticipantEnricherListener<P extends Participant> |
Created with IntelliJ IDEA.
|
| ParticipantEnricherListenerManager<P extends Participant> |
A manager for listeners which holds a list of listeners.
|
| ParticipantEnricherLogger<P extends Participant> |
A logging listener.
|
| ParticipantEnricherStatisticsWriter<P extends Participant> |
A statistics logger which records changes made by the enricher.
|
| ParticipantEvidence |
Participant of an interaction which is supported by experimental evidences
|
| ParticipantEvidenceChangeListener<F extends ParticipantEvidence> |
Listener for changes in an experimental entity
|
| ParticipantEvidenceChangeLogger<T extends ParticipantEvidence> |
This listener will just interactor change events
|
| ParticipantEvidenceComparator |
Basic Experimental participant comparator.
|
| ParticipantEvidenceEnricher<T extends ParticipantEvidence> |
The Participant pool enricher is an enricher which can enrich either single Participant pool or a collection.
|
| ParticipantEvidenceEnricherListener<P extends ParticipantEvidence> |
Created with IntelliJ IDEA.
|
| ParticipantEvidenceEnricherListenerManager<P extends ParticipantEvidence> |
A manager for listeners which holds a list of listeners.
|
| ParticipantEvidenceEnricherLogger<P extends ParticipantEvidence> |
A logging listener.
|
| ParticipantEvidenceEnricherStatisticsWriter<P extends ParticipantEvidence> |
A statistics logger which records changes made by the enricher.
|
| ParticipantInteractorComparator<T extends Entity> |
Participant comparator only based on the interactor.
|
| ParticipantPool<I extends Interaction,F extends Feature,P extends ParticipantCandidate> |
A pool of participants that can be grouped together as a single participant as they are interchangeable
|
| ParticipantPoolChangeListener<F extends ParticipantPool> |
Listener for changes in a participant pool
|
| ParticipantPoolChangeLogger<T extends ParticipantPool> |
This listener will just interactor change events
|
| ParticipantPoolComparator |
Basic participant pool comparator.
|
| ParticipantPoolEnricher<P extends ParticipantPool,F extends Feature> |
Sub enrichers: Protein, CvTerm, Feature, Bioactive3Entity
|
| ParticipantPoolEnricherListener<P extends ParticipantPool> |
Participant pool enricher listener
|
| ParticipantPoolEnricherListenerManager<P extends ParticipantPool> |
A manager for listeners which holds a list of listeners.
|
| ParticipantPoolEnricherLogger<P extends ParticipantPool> |
A logging listener.
|
| ParticipantPoolEnricherStatisticsWriter<P extends ParticipantPool> |
A statistics logger which records changes made by the enricher.
|
| ParticipantUtils |
Factory for participants
|
| Polymer |
A polymer is an interactor with a sequence
|
| PolymerChangeListener<P extends Polymer> |
Listener for changes in polymer
|
| PolymerChangeLogger<P extends Polymer> |
This listener will just protein change events
|
| PolymerComparator |
polymer comparator.
|
| PolymerEnricherListener<T extends Polymer> |
Interface for polymer enricher listener
|
| PolymerEnricherListenerManager<P extends Polymer> |
A manager for listeners which holds a list of listeners.
|
| PolymerEnricherLogger<P extends Polymer> |
A logging listener.
|
| PolymerEnricherStatisticsWriter<P extends Polymer> |
A statistics logger which records changes made by the enricher.
|
| Position |
The position of a feature in the interactor sequence
|
| PositionComparator |
Simple Position comparator.
|
| PositionUtils |
Utility class for Positions
|
| Preassembly |
The pre-assembly cooperative effect.
|
| PropertyType |
Java class for propertyType complex type.
|
| Protein |
Polymer of amino acids which can interact with other molecules.
|
| ProteinChangeListener |
This listener listen to Protein changes
|
| ProteinChangeLogger |
This listener will just protein change events
|
| ProteinComparator |
proteins comparator.
|
| ProteinEnricher |
The Protein enricher is an enricher which can enrich either single protein or a collection.
|
| ProteinEnricherListener |
Created with IntelliJ IDEA.
|
| ProteinEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| ProteinEnricherLogger |
A logging listener.
|
| ProteinEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| ProteinFetcher |
Fetches the complete records which match a protein.
|
| ProteinListeningFeatureEnricher<F extends Feature> |
An extension to the feature enricher, the protein listening form also updates ranges.
|
| ProteinMapper |
Created with IntelliJ IDEA.
|
| ProteinMapperListener |
Created with IntelliJ IDEA.
|
| ProteinMappingLogger |
Created with IntelliJ IDEA.
|
| ProteinMappingStatisticsWriter |
Created with IntelliJ IDEA.
|
| PsiJami |
This class is a central access to basic methods in psi-jami.
|
| PsiXmlCausalRelationshipWriter |
Interface for writers of PSI-XML causal relationships elements
It asks for the participant source in addition to the causal relationship
|
| PsiXmlDataSourceFactory |
Factory for creating a Psi-XML datasource
|
| PsiXmlDataSourceOptions |
Class that lists all possible options for PsiXml DataSource.
|
| PsiXmlElementWriter<T> |
Interface for writers of PSI-XML elements
|
| PsiXmlElementWriterFactory |
Factory to initialise PSI-XML element writers depending on the version and the interaction object category
|
| PsiXmlExperimentWriter |
PsiXml Experiment Writer
|
| PsiXmlExtendedInteractionWriter<T extends Interaction> |
Interface for interaction writers writing extensions
|
| PsiXmlFileIndexCache |
Cache using a file and a weak map to cache the objects
|
| PsiXmlIdCache |
Index that can retrieve a MI object given its id
|
| PsiXmlInteraction<T extends Participant> |
Interaction for PSI-XML which contains the entry
|
| PsiXmlInteractionWriter<T extends Interaction> |
Interface for PSI-XML interaction writers that have to write an experiment in XML even if the interaction
does not have any experimental details
|
| PsiXmlLocator |
Psi-XML source locator
|
| PsiXmlObjectCache |
Index that can assign/retrieve an id for a given MI object in a compact XML environment
|
| PsiXmlParameterWriter |
Psi XML writer for parameters.
|
| PsiXmlParser<T extends Interaction> |
Interface for PsiXmlParser
|
| PsiXmlParserCompositeListener |
This class contains several MI file listeners
|
| PsiXmlParserException |
An exception to be thrown when a XML file is invalid and cannot be parsed properly
|
| PsiXmlParserListener |
A listener listening to events when parsing a mitab file
|
| PsiXmlParserLogger |
Logger for MitabParser
|
| PsiXmlParticipantWriter<T extends Participant> |
Interface for PSI-XML participant writers.
|
| PsiXmlPublicationWriter |
Interface for XmlPublicationWriter.
|
| PsiXmlSource<I extends Interaction> |
Interface for PSI-MI XML sources that can parse full PSI-MI XML files
|
| PsiXmlSourceWriter |
Interface for PSI-XML source writers
|
| PsiXmlStreamSource<I extends Interaction> |
Interface for PSI-MI XML datasources that can stream PSI-MI XML files
|
| PsiXmlType |
The type of PSI-XML.
|
| PsiXmlUtils |
Utility class for psixml
|
| PsiXmlVariableNameWriter<T> |
Interface for writers of PSI-XML object elements that do have a variable node name but otherwise are the same element type.
|
| PsiXmlVersion |
Existing PSI-MI xml versions
|
| PsiXmlWriterFactory |
Factory for creating a PSI-XML writer
|
| PsiXmlWriterOptions |
Class that lists all possible options for PsiXml Writer.
|
| PsiXmlXrefWriter |
Interface for PSI-XML Xref writers
|
| Publication |
A scientific publication which has been curated by an interaction database.
|
| PublicationAdminGroupSynchronizer |
Interface for synchronizing admin group of a publication in IMEx central
|
| PublicationAdminGroupSynchronizerImpl |
This class is for synchronizing the admin group of a publication in imex central
|
| PublicationChangeListener |
Listener to publication changes
|
| PublicationChangeLogger |
This listener will listen to publication change events
|
| PublicationCloner |
Utility class for cloning publications
|
| PublicationComparator |
publication comparator.
|
| PublicationEnricher |
An enricher for publications which can enrich either a single publication or a collection.
|
| PublicationEnricherListener |
An extension of the PublicationChangeListener
with specific methods related to the process of enriching.
|
| PublicationEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| PublicationEnricherLogger |
A logging listener.
|
| PublicationEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| PublicationFetcher |
The interface for fetching a publication record.
|
| PublicationIdentifierSynchronizer |
Interface for synchronizing publication identifiers with IMEx central
|
| PublicationIdentifierSynchronizerImpl |
Class which update identifiers in IMEx central if a submitted publication has been published in PubMed
|
| PublicationImexEnricherListener |
An extension of the PublicationEnricherListener
with specific methods related to the process of enriching.
|
| PublicationImexEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| PublicationImexEnricherLogger |
A logging listener.
|
| PublicationImexEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| PublicationStatus |
Various statuses an IMEx publication can have.
|
| PublicationStatusSynchronizer |
interface for synchronizing publication status with IMEx central
|
| PublicationStatusSynchronizerImpl |
It updates and synchronize the publications status if it is released (has a released date)
|
| PublicationStream |
A publication data source allows to stream the publications of a given dataSource
|
| PublicationUtils |
Factory for publications
|
| PublicationXrefContainer |
Xref container for a Publication
|
| PublicationXrefContainer |
Xref container for a Publication
|
| PublicationXrefContainer |
Xref container for a Publication
|
| Range |
A feature range indicates the positions of a feature in the interactor sequence
|
| RangeAndResultingSequenceComparator |
Simple range comparator that will also compare resulting sequences..
|
| RangeCloner |
Utility class for cloning ranges
|
| RangeCollectionComparator |
Comparator for collection of Ranges
|
| RangeComparator |
Simple range comparator.
|
| RangeUtils |
Utility methods for Ranges
|
| ReadWriteCrosslinkCsvWithJami |
This class shows how to read MITAB/PSI-MI XML (and other sources) and how to write JAMI objects in MITAB/PSI-MI XML
(or other JAMI interaction writers)
|
| ReadWriteHtmlWithJami |
This class shows how to read MITAB/PSI-MI XML (and other sources) and how to write JAMI objects in MITAB/PSI-MI XML
(or other JAMI interaction writers)
|
| ReadWriteJsonWithJami |
This class shows how to read MITAB/PSI-MI XML (and other sources) and how to write JAMI objects in MITAB/PSI-MI XML
(or other JAMI interaction writers)
|
| ReadWriteWithJami |
This class shows how to read MITAB/PSI-MI XML (and other sources) and how to write JAMI objects in MITAB/PSI-MI XML
(or other JAMI interaction writers)
|
| ResultingSequence |
This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)
|
| ResultingSequenceComparator |
Simple resultingSequence comparator
It will first compare the original sequence and then if the original sequences are the same, it will compare the
new sequences (case insensitive).
|
| RigidGenerator |
Rigid generator
|
| RogidGenerator |
Rogid generator
|
| SearchDatabase |
TODO: Work in progress to adapt the databases
|
| SeguidException |
Custom Exception class to handle exceptions from this module
|
| SeqFeatureGroupType |
Java class for seqFeatureGroupType complex type.
|
| SeqFeatureType |
Java class for seqFeatureType complex type.
|
| Sequence |
Java class for anonymous complex type.
|
| SequenceVersion |
Represent a sequence version: fasta + sequence version number.
|
| SequenceVersionFetcher |
A fetcher that fetches a sequence from a specific version and/or a version from a specific sequence
|
| SimpleCharStream |
An implementation of interface CharStream, where the stream is assumed to
contain only ASCII characters (without unicode processing).
|
| SimpleJobListener |
Enricher job listener
|
| SimpleJobRegistry |
Job registry for MIBatchJobManager
|
| SimpleJsonAnnotationWriter |
Json writer for annotations
|
| SimpleJsonBinaryInteractionEvidenceWriter |
Json writer for interaction evidences
|
| SimpleJsonBinaryInteractionWriter<I extends BinaryInteraction> |
Json writer for interactions
|
| SimpleJsonConfidenceWriter |
Json writer for confidences
|
| SimpleJsonCvTermWriter |
Json writer for cv terms
|
| SimpleJsonExperimentWriter |
Json writer which will only write experimental details of an interaction evidence
|
| SimpleJsonFeatureEvidenceWriter |
Json writer for modelled features
|
| SimpleJsonFeatureWriter<F extends Feature> |
Json writer for features
|
| SimpleJsonHostOrganismWriter |
Json writer for Host organisms.
|
| SimpleJsonIdentifierWriter |
Json writer for identifiers
|
| SimpleJsonInteractionEvidenceWriter<I extends InteractionEvidence> |
Json writer for interaction evidences
|
| SimpleJsonInteractionWriter<I extends Interaction> |
Json writer for interactions
|
| SimpleJsonInteractorWriter |
Json writer for participants
|
| SimpleJsonModelledBinaryInteractionWriter |
Json writer for modelled interactions
|
| SimpleJsonModelledFeatureWriter |
Json writer for modelled features
|
| SimpleJsonModelledInteractionWriter<I extends ModelledInteraction> |
Json writer for modelled interactions
|
| SimpleJsonModelledParticipantWriter |
Json writer for modelled participants
|
| SimpleJsonOrganismWriter |
Json writer for organisms.
|
| SimpleJsonParameterWriter |
Json writer for parameters
|
| SimpleJsonParticipantEvidenceWriter |
Json writer for participant evidences
|
| SimpleJsonParticipantWriter<P extends Participant> |
Json writer for participants
|
| SimpleJsonPublicationWriter |
Json writer for publications
|
| SimpleJsonRangeWriter |
Json writer for ranges
|
| SimpleJsonStoichiometryWriter |
Json writer for stoichiometry
|
| Source |
Source of the data.
|
| SourceCategory |
Enum to used to label a given String as URL, file_URI or file
|
| SourceChangeListener |
Source change listener
|
| SourceChangeLogger |
This listener will just log Source change events
|
| SourceCompositeFetcher |
Source fetcher that delegates to different sourceFetchers
|
| SourceEnricher |
The source enricher is an enricher which can enrich either single source or a collection.
|
| SourceEnricherListener |
An extension of the SourceChangeListener
with specific methods related to the process of enriching.
|
| SourceEnricherListenerManager |
A manager for listeners which holds a list of listeners.
|
| SourceEnricherLogger |
A logging listener.
|
| SourceEnricherStatisticsWriter |
A statistics logger which records changes made by the enricher.
|
| SourceFetcher |
Finds source
Extends CvTermFetcher with source objects.
|
| SourceOboLoader |
Implementation of Obo loader for sources
|
| SpokeExpansion |
The spoke expansion
Complex n-ary data has been expanded to binary using the spoke model.
|
| Stoichiometry |
The stoichiometry of a participant
|
| StoichiometryComparator |
Simple stoichiometry comparator.
|
| Token |
Describes the input token stream.
|
| TokenKind |
Enum which lists all possible enums
|
| TokenMgrError |
Token Manager Error.
|
| UnambiguousAliasComparator |
Unambiguous alias comparator.
|
| UnambiguousAllosteryComparator |
Unambiguous comparator for Allostery
It will first compare basic cooperative effect properties using UnambiguousCooperativeEffectBaseComparator.
|
| UnambiguousAnnotationComparator |
Strict annotation comparator
It compares first the topics and then the value (case insensitive)
- Two annotations which are null are equals
- The annotation which is not null is before null.
|
| UnambiguousBioactiveEntityComparator |
Unambiguous bioactive entity comparator.
|
| UnambiguousCausalRelationshipComparator |
Unambiguous comparator for CausalRelationship
It will first compare the relationType using UnambiguousCvTermComparator.
|
| UnambiguousChecksumComparator |
Unambiguous checksum comparator.
|
| UnambiguousComplexComparator |
Unambiguous Complex comparator
|
| UnambiguousConfidenceComparator |
Unambiguous confidence comparator.
|
| UnambiguousCooperativeEffectBaseComparator |
Unambiguous comparator for CooperativeEffect
It will first compare the outcome using UnambiguousCvTermComparator.
|
| UnambiguousCooperativeEffectComparator |
Unambiguous cooperative effect comparator
Allostery effects will always come before basic cooperative effects (preassembly)
- It will use UnambiguousAllosteryComparator to compare allostery
- It will use UnambiguousCooperativeEffectBaseComparator to compare basic cooperative effects
|
| UnambiguousCooperativityEvidenceComparator |
Unambiguous comparator for cooperativityEvidence
It will first compare the publications using UnambiguousPublicationComparator and then the evidenceMethods using UnambiguousCvTermComparator
|
| UnambiguousCuratedExperimentComparator |
Unambiguous curated experiments comparator
It will look first at the publications using a UnambiguousCuratedPublicationComparator.
|
| UnambiguousCuratedInteractionBaseComparator |
Unambiguous comparator for curated interactions.
|
| UnambiguousCuratedInteractionComparator |
Unambiguous curated Generic interaction comparator.
|
| UnambiguousCuratedInteractionEvidenceComparator |
Unambiguous curated InteractionEvidenceComparator.
|
| UnambiguousCuratedModelledInteractionComparator |
Unambiguous curated ModelledInteraction comparator.
|
| UnambiguousCuratedPublicationComparator |
Unambiguous curated publication comparator.
|
| UnambiguousCvTermComparator |
Unambiguous comparator for CvTerms :
If one CvTerm does not have any identifiers, it will only compare the short names (case insensitive).
|
| UnambiguousEntityBaseComparator |
Unambiguous entity comparator
It will first compare the interactors using UnambiguousInteractorComparator.
|
| UnambiguousEntityComparator |
Unambiguous generic entity comparator
Modelled participants come first and then experimental participants.
|
| UnambiguousExactAllosteryComparator |
Unambiguous exact comparator for Allostery
It will first compare basic cooperative effect properties using UnambiguousExactCooperativeEffectBaseComparator.
|
| UnambiguousExactBioactiveEntityComparator |
unambiguous Exact bioactive entity comparator.
|
| UnambiguousExactCausalRelationshipComparator |
Unambiguous exact comparator for CausalRelationship
It will first compare the relationType using UnambiguousCvTermComparator.
|
| UnambiguousExactComplexComparator |
Unambiguous exact Complex comparator
|
| UnambiguousExactCooperativeEffectBaseComparator |
Unambiguous exact comparator for CooperativeEffect
It will first compare the outcome using UnambiguousCvTermComparator.
|
| UnambiguousExactCooperativeEffectComparator |
Unambiguous exact cooperative effect comparator
Allostery effects will always come before basic cooperative effects (preassembly)
- It will use UnambiguousExactAllosteryComparator to compare allostery
- It will use UnambiguousExactCooperativeEffectBaseComparator to compare basic cooperative effects
|
| UnambiguousExactCuratedInteractionComparator |
Unambiguous exact curated Generic interaction comparator.
|
| UnambiguousExactCuratedInteractionEvidenceComparator |
Unambiguous exact curated InteractionEvidenceComparator.
|
| UnambiguousExactCuratedModelledInteractionComparator |
Unambiguous exact curated ModelledInteraction comparator.
|
| UnambiguousExactEntityBaseComparator |
Unambiguous exact entity comparator
It will first compare the interactors using UnambiguousExactInteractorComparator.
|
| UnambiguousExactEntityComparator |
Unambiguous exact generic entity comparator
Modelled participants come first and then experimental participants.
|
| UnambiguousExactExperimentalEntityComparator |
Unambiguous exact Experimental entity comparator.
|
| UnambiguousExactExperimentalParticipantPoolComparator |
Unambiguous exact Experimental participant pool comparator.
|
| UnambiguousExactGeneComparator |
Unambiguous exact gene comparator.
|
| UnambiguousExactInteractionComparator |
Unambiguous exact Generic interaction comparator.
|
| UnambiguousExactInteractionEvidenceComparator |
Unambiguous exact InteractionEvidenceComparator.
|
| UnambiguousExactInteractionInteractorComparator |
Unambiguous exact interaction comparator only based on the interactors of an interaction.
|
| UnambiguousExactInteractorBaseComparator |
Unambiguous Interactor base comparator.
|
| UnambiguousExactInteractorComparator |
Unambiguous exact Interactor Comparator.
|
| UnambiguousExactInteractorPoolComparator |
Unambiguous exact InteractorPoolComparator.
|
| UnambiguousExactModelledEntityComparator |
unambiguous exact biological entity comparator.
|
| UnambiguousExactModelledInteractionComparator |
Unambiguous exact ModelledInteraction comparator.
|
| UnambiguousExactModelledParticipantComparator |
unambiguous exact biological participant comparator.
|
| UnambiguousExactModelledParticipantInteractorComparator |
Unambiguous exact biological participant comparator based on the interactor only.
|
| UnambiguousExactModelledParticipantPoolComparator |
unambiguous exact biological participant pool comparator.
|
| UnambiguousExactMoleculeEffectorComparator |
Unambiguous exact Comparator for MoleculeEffector.
|
| UnambiguousExactNucleicAcidComparator |
Unambiguous exact nucleic acids comparator.
|
| UnambiguousExactParticipantBaseComparator |
Unambiguous exact participant comparator
It will first compare the interactors using UnambiguousExactEntityBaseComparator.
|
| UnambiguousExactParticipantComparator |
Unambiguous exact generic Participant comparator
Modelled participants come first and then experimental participants.
|
| UnambiguousExactParticipantEvidenceComparator |
Unambiguous exact Experimental participant comparator.
|
| UnambiguousExactParticipantEvidenceInteractorComparator |
Unambiguous exact experimental participant comparator based on the interactor only.
|
| UnambiguousExactParticipantInteractorComparator |
It will compare the interactors using UnambiguousExactInteractorComparator.
|
| UnambiguousExactParticipantPoolComparator |
Unambiguous exact participant pool comparator
It will first compares basic participant properties using UnambiguousExactParticipantBaseComparator, then it will compare participant pool type using cv term comparator and then it will compare
each participant candidate using UnambiguousExactEntityBaseComparator
|
| UnambiguousExactPolymerComparator |
Unambiguous exact polymer comparator.
|
| UnambiguousExactProteinComparator |
Unambiguous exact proteins comparator.
|
| UnambiguousExperimentalEntityComparator |
Unambiguous Experimental entity comparator.
|
| UnambiguousExperimentalParticipantPoolComparator |
Unambiguous Experimental participant pool comparator.
|
| UnambiguousExperimentComparator |
Unambiguous experiments comparator
It will look first at the publications using a UnambiguousPublicationComparator.
|
| UnambiguousExternalIdentifierComparator |
Unambiguous comparator for external identifiers (Xref database and id).
|
| UnambiguousFeatureBaseComparator |
Unambiguous feature comparator.
|
| UnambiguousFeatureComparator |
Generic unambiguous feature comparator.
|
| UnambiguousFeatureEvidenceComparator |
Unambiguous FeatureEvidence comparator.
|
| UnambiguousFeatureModificationEffectorComparator |
Unambiguous comparator for FeatureModificationEffector.
|
| UnambiguousGeneComparator |
Unambiguous gene comparator.
|
| UnambiguousInteractionBaseComparator |
Unambiguous Interaction comparator.
|
| UnambiguousInteractionComparator |
Unambiguous Generic interaction comparator.
|
| UnambiguousInteractionEvidenceComparator |
Unambiguous InteractionEvidenceComparator.
|
| UnambiguousInteractionInteractorComparator |
Unambiguous interaction comparator only based on the interactors of an interaction.
|
| UnambiguousInteractorBaseComparator |
Unambiguous interactor comparator
It will only compare identifiers if one interactor does have identifiers using UnambiguousIdentifierComparator.
|
| UnambiguousInteractorComparator |
Unambiguous generic Interactor Comparator.
|
| UnambiguousInteractorPoolComparator |
Unambiguous InteractorPoolComparator.
|
| UnambiguousModelledEntityComparator |
unambiguous biological entity comparator.
|
| UnambiguousModelledFeaturecomparator |
Unambiguous ModelledFeature comparator.
|
| UnambiguousModelledInteractionComparator |
Unambiguous ModelledInteraction comparator.
|
| UnambiguousModelledParticipantComparator |
Unambiguous biological participant comparator.
|
| UnambiguousModelledParticipantInteractorComparator |
Unambiguous biological participant comparator based on the interactor only.
|
| UnambiguousModelledParticipantPoolComparator |
unambiguous biological participant pool comparator.
|
| UnambiguousMoleculeEffectorComparator |
Unambiguous Comparator for MoleculeEffector.
|
| UnambiguousNucleicAcidComparator |
Unambiguous nucleic acids comparator.
|
| UnambiguousOrganismComparator |
Unambiguous organism comparator.
|
| UnambiguousParameterComparator |
Unambiguous parameter comparator.
|
| UnambiguousParticipantBaseComparator |
Unambiguous participant comparator
It will first compare the interactors and stoichiometry using UnambiguousEntityComparator.
|
| UnambiguousParticipantComparator |
Unambiguous generic Participant comparator
Modelled participants come first and then experimental participants.
|
| UnambiguousParticipantEvidenceComparator |
Unambiguous Experimental participant comparator.
|
| UnambiguousParticipantEvidenceInteractorComparator |
Unambiguous experimental participant comparator based on the interactor only.
|
| UnambiguousParticipantInteractorComparator |
It will compare the interactors using UnambiguousInteractorComparator.
|
| UnambiguousParticipantPoolComparator |
Unambiguous participant pool comparator
It will first compares basic participant properties using UnambiguousParticipantBaseComparator, then it will compare participant pool type using cv term comparator and then it will compare
each participant candidate using UnambiguousEntityBaseComparator
|
| UnambiguousPolymerComparator |
Unambiguous polymer comparator.
|
| UnambiguousPositionComparator |
Strict PositionComparator.
|
| UnambiguousProteinComparator |
Unambiguous proteins comparator.
|
| UnambiguousPublicationComparator |
Unambiguous publication comparator.
|
| UnambiguousRangeAndResultingSequenceComparator |
Unambiguous RangeComparator.
|
| UnambiguousRangeComparator |
Unambiguous RangeComparator.
|
| UnambiguousVariableParameterComparator |
Unambiguous VariableParameter comparator
It will first compare the description (case insensitive).
|
| UnambiguousXrefComparator |
Strict Xref comparator
It compares first the databases and then the ids (case sensitive) but ignores the version.
|
| Uniparc |
Java class for anonymous complex type.
|
| UniprotGeneFetcher |
Created with IntelliJ IDEA.
|
| UniprotProteinAPIClient |
Client for the Uniprot Protein API
|
| UniprotProteinAPIClientException |
|
| UniprotProteinFetcher |
Created with IntelliJ IDEA.
|
| UniprotTaxonomyFetcher |
Created with IntelliJ IDEA.
|
| UniprotUtils |
Uniprot utils
|
| UnisaveClient |
Client to query unisave and collect sequence versions or sequence from a particular version
|
| VariableParameter |
A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used
and that affects some interactions (dynamic interactions).
|
| VariableParameterCloner |
Utility class for cloning VariableParameters
|
| VariableParameterCollectionComparator |
Comparator for a collection of variableParameters
|
| VariableParameterComparator |
Basic comparator for VariableParameterComparator
It will first compare the description (case insensitive).
|
| VariableParameterValue |
A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.
|
| VariableParameterValueCollectionComparator |
Comparator for a collection of variableParameterValues
|
| VariableParameterValueComparator |
Simple Comparator for VariableParameterValue
It will first compare the value (case insensitive) and then the order.
|
| VariableParameterValueSet |
Set of variable parameter values applied together in a same experiment
|
| VariableParameterValueSetCollectionComparator |
Comparator for a collection of variableParameterValueSet
|
| VariableParameterValueSetComparator |
Simple comparator for VariableParameterValueSet
It will use VariableParameterValueComparator to compare each variableParameterValue independently from the order.
|
| Xml253BasicEntrySet |
Basic EntrySet implementation for JAXB read only .
|
| Xml253ComplexEntrySet |
Modelled EntrySet implementation for JAXB read only
Ignore all experimental details
|
| Xml253ExperimentalEntrySet |
Xml253ExperimentalEntrySet implementation for JAXB read only
|
| Xml253ModelledEntrySet |
Modelled EntrySet implementation for JAXB read only
Ignore all experimental details
|
| Xml254BasicEntrySet |
Basic EntrySet implementation for JAXB read only .
|
| Xml254ComplexEntrySet |
Modelled EntrySet implementation for JAXB read only
Ignore all experimental details
|
| Xml254ExperimentalEntrySet |
Xml254ExperimentalEntrySet implementation for JAXB read only
|
| Xml254ModelledEntrySet |
Modelled EntrySet implementation for JAXB read only
Ignore all experimental details
|
| Xml300EntrySet |
Xml300EntrySet implementation for JAXB read only
|
| XmlAlias |
Xml implementation of an Alias.
|
| XmlAlias |
Xml implementation of an Alias.
|
| XmlAlias |
Xml implementation of an Alias.
|
| XmlAliasWriter |
XML25 writer for aliases
|
| XmlAllostery<T extends AllostericEffector> |
XML implementation of Allostery
|
| XmlAllostery<T extends AllostericEffector> |
XML implementation of Allostery
|
| XmlAllostery |
XML 3.0 implementation of Allostery
|
| XmlAllosteryWriter |
Xml 3.0 writer for allostery
|
| XmlAllosteryWriter |
Xml 3.0 writer for allostery
|
| XmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlAnnotation |
Xml implementation of an Annotation
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlAnnotationWriter |
XML writer for attributes
|
| XmlAvailabilityWriter |
XML availability writer
|
| XmlBasicBinaryInteractionWriter |
Compact XML 2.5 writer for a basic binary interaction (ignore experimental details)
|
| XmlBasicBinaryInteractionWriter |
Expanded XML 2.5 writer for a basic binary interaction (ignore experimental details)
|
| XmlBasicBinaryInteractionWriter |
Compact XML 2.5 writer for a basic binary interaction (ignore experimental details) which has a fullname
and aliases in addition to a shortname
|
| XmlBasicBinaryInteractionWriter |
Expanded XML 2.5 writer for a basic binary interaction (ignore experimental details).
|
| XmlBasicInteraction |
Xml implementation of interaction
|
| XmlBasicInteraction |
Xml implementation of interaction
|
| XmlBasicInteraction |
Xml implementation of interaction
|
| XmlBasicInteractionComplexWrapper |
Wrapper of basic interactions
If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the
wrapped interaction.
|
| XmlBasicInteractionComplexWrapper |
Wrapper of basic interactions
If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the
wrapped interaction.
|
| XmlBasicInteractionComplexWrapper |
Wrapper of basic interactions
If we add new modelled participants/remove participants, they will be added/removed from the list of participants of the
wrapped interaction.
|
| XmlBasicInteractionWriter |
Compact XML 2.5 writer for a basic interaction (ignore experimental details)
|
| XmlBasicInteractionWriter |
Expanded XML 2.5 writer for a basic interaction (ignore experimental details)
|
| XmlBasicInteractionWriter |
Compact XML 2.5 writer for a basic interaction (ignore experimental details) which has a fullname
and aliases in addition to a shortname
|
| XmlBasicInteractionWriter |
Expanded XML 2.5 writer for a basic interaction (ignore experimental details).
|
| XmlBeginPositionWriter |
XML writer for the begin position of a range
|
| XmlBeginPositionWriter |
XML writer for the begin position of a range
|
| XmlBinaryEvidenceParser |
Xml parser creating binary interaction evidences
|
| XmlBinaryEvidenceSource |
PSI-XML data source that provides binary interactions evidence (full experimental details).
|
| XmlBinaryEvidenceStreamSource |
PsiXml datasource for binaryInteractionEvidence
|
| XmlBinaryInteraction |
Xml implementation of binary interaction
|
| XmlBinaryInteractionEvidence |
Xml implementation of BinaryInteractionEvidence
|
| XmlBinaryInteractionEvidence |
Xml implementation of BinaryInteractionEvidence
|
| XmlBinaryInteractionEvidence |
Xml implementation of BinaryInteractionEvidence
|
| XmlBinaryInteractionEvidenceIterator |
Xml binary interaction evidence iterator
|
| XmlBinaryInteractionEvidenceWrapper |
Xml implementation of BinaryInteractionWrapper with a source locator
|
| XmlBinaryInteractionEvidenceWrapper |
Xml implementation of BinaryInteractionWrapper with a source locator
|
| XmlBinaryInteractionEvidenceWriter |
Compact XML 2.5 writer for a binary interaction evidence (with full experimental details).
|
| XmlBinaryInteractionEvidenceWriter |
Compact XML 3.0 writer for a binary interaction evidence (with full experimental details).
|
| XmlBinaryInteractionEvidenceWriter |
Expanded XML 2.5 writer for a binary interaction evidence (with full experimental details).
|
| XmlBinaryInteractionEvidenceWriter |
Expanded XML 3.0 writer for a binary interaction evidence (with full experimental details).
|
| XmlBinaryInteractionEvidenceWriter |
Compact XML 2.5 writer for an expanded binary interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlBinaryInteractionEvidenceWriter |
Compact XML 3.0 writer for an expanded binary interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlBinaryInteractionEvidenceWriter |
Expanded XML 2.5 writer for an expanded binary interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlBinaryInteractionEvidenceWriter |
Expanded XML 3.0 writer for an expanded binary interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlBinaryInteractionFactory |
Xml extension of BinaryInteractionFactory for XML 2.5
|
| XmlBinaryInteractionFactory |
Xml extension of BinaryInteractionFactory for XML 3.0
|
| XmlBinaryInteractionIterator |
Xml basic binary interaction iterator
|
| XmlBinaryInteractionWrapper |
Wrapper for ModelledBinaryInteraction
|
| XmlBinaryParser |
Xml parser creating binary interactions that can be a mix of interaction evidences and abstract interactions
|
| XmlBinarySource |
PSI-XML data source that provides binary interactions (mixed of abstract interactions and interaction evidences).
|
| XmlBinaryStreamSource |
Psi-XML mixed binary interaction datasource
|
| XmlBindingFeaturesWriter |
XML 3.0 writer for binding features
|
| XmlBioactiveEntity |
Xml implementation of BioactiveEntity
|
| XmlBioactiveEntity |
Xml implementation of BioactiveEntity
|
| XmlBioactiveEntity |
Xml implementation of BioactiveEntity
|
| XmlCausalRelationship |
XML 3.0 implementation of causal relationship
|
| XmlCausalRelationshipWriter |
XML 3.0 writer for causal relationship
|
| XmlCausalRelationshipWriter |
XML 3.0 writer for causalRelationship
|
| XmlChecksum |
Xml implementation of a checksum
|
| XmlChecksumWriter |
Xml writer of checksums
|
| XmlComplex |
Xml implementation of ModelledInteraction
|
| XmlComplex |
Xml implementation of ModelledInteraction
|
| XmlComplex |
Xml implementation of ModelledInteraction
|
| XmlComplexIterator |
Xml complex iterator
|
| XmlComplexParser |
Parser generating biological complex objects and ignore experimental details
|
| XmlComplexSource |
PSI-XML data source that provides abstract interactions (ignore full experimental details).
|
| XmlComplexStreamSource |
Datasource for Psi-XML abstract interactions
|
| XmlComplexWriter |
Compact XML 2.5 writer for a biological complex (ignore experimental details).
|
| XmlComplexWriter |
Expanded XML 2.5 writer for a biological complex (ignore experimental details).
|
| XmlComplexWriter |
Compact XML 2.5 writer for an expanded biological complex (ignore experimental details).
|
| XmlComplexWriter |
Expanded XML 2.5 writer for an expanded biological complexes (ignore experimental details).
|
| XmlConfidence |
Xml implementation of confidence
|
| XmlConfidence |
Xml implementation of confidence
|
| XmlConfidence |
Xml implementation of confidence
|
| XmlConfidence.JAXBExperimentRefWrapper |
|
| XmlConfidence.JAXBExperimentRefWrapper |
|
| XmlConfidence.JAXBExperimentRefWrapper |
|
| XmlConfidenceWrapper |
A wrapper for confidences
|
| XmlConfidenceWrapper |
A wrapper for confidences
|
| XmlConfidenceWrapper |
A wrapper for confidences
|
| XmlConfidenceWriter |
Extended Xml25 writer for confidences.
|
| XmlConfidenceWriter |
Extended Xml25 writer for confidences.
|
| XmlConfidenceWriter |
Extended Xml30 writer for confidences.
|
| XmlConfidenceWriter |
Xml25 writer for confidences
|
| XmlCooperativityEvidence |
Xml implementation for cooperativity evidence
|
| XmlCooperativityEvidence |
Xml implementation for cooperativity evidence
|
| XmlCooperativityEvidence |
Xml 3.0 implementation for cooperativity evidence
|
| XmlCooperativityEvidence.JAXBEvidenceMethodWrapper |
|
| XmlCooperativityEvidenceWriter |
Xml 3.0 writer for cooperativity evidence
|
| XmlCooperativityEvidenceWriter |
Xml 3.0 writer for cooperativity evidence
|
| XmlCvTerm |
Xml implementation of CvTerm.
|
| XmlCvTerm |
Xml implementation of CvTerm.
|
| XmlCvTerm |
Xml implementation of CvTerm.
|
| XmlCvTermWriter |
CvTerm writers for cvs without attributes
|
| XmlCvTermWriter |
CvTerm writers for cvs without attributes
|
| XmlDbXrefWriter |
XML writer for an expanded PSI25Xref having secondary and annotations
|
| XmlDbXrefWriter |
Xml Writer for Xref object
|
| XmlEndPositionWriter |
XML writer for the end position of a range
|
| XmlEndPositionWriter |
XML writer for the end position of a range
|
| XmlEntryContext |
The xml entry context is a context threadlocal that will be valid for the whole xml entry
but will be cleared after each entry in the entrySet
|
| XmlEvidenceParser |
Parser generating interaction evidence objects with all experimental details
|
| XmlEvidenceSource |
PSI-XML data source that provides interaction evidences (with full experimental details).
|
| XmlEvidenceStreamSource |
Datasource for Psi-xml interaction evidence
|
| XmlExperiment |
Xml im
|
| XmlExperiment |
Xml im
|
| XmlExperiment |
Xml 3.0 implementation of experiment
|
| XmlExperimentalCvTermWriter |
XML writer for experimental cv terms
|
| XmlExperimentalCvTermWriter |
XML writer for experimental cv terms
|
| XmlExperimentalCvTermWriter |
XML writer for experimental cv terms
|
| XmlExperimentalInteractorWriter |
Compact XML writer of experimental interactors
|
| XmlExperimentalInteractorWriter |
Expanded XML writer of experimental interactors
|
| XmlExperimentalParticipantCandidate |
Xml implementation of ParticipantEvidence
|
| XmlExperimentalParticipantCandidate |
Xml implementation of ParticipantEvidence
|
| XmlExperimentalParticipantCandidate |
Xml implementation of ParticipantEvidence
|
| XmlExperimentalParticipantCandidate.JAXBFeatureWrapper |
|
| XmlExperimentalParticipantCandidate.JAXBFeatureWrapper |
|
| XmlExperimentalParticipantCandidate.JAXBFeatureWrapper |
|
| XmlExperimentalParticipantCandidateWrapper |
Wrapper for Xml participants candidates
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentalParticipantCandidateWrapper |
Wrapper for Xml participants candidates
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentalParticipantCandidateWrapper |
Wrapper for Xml participants candidates
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentalParticipantCandidateWriter |
Compact XML 3.0 writer for a participant evidence with full experimental details
|
| XmlExperimentalParticipantCandidateWriter |
Expanded XML 3.0 writer for a participant evidence with full experimental details
|
| XmlExperimentalParticipantCandidateWriter |
Compact XML 3.0 writer for a participant evidence with full experimental details
|
| XmlExperimentalParticipantCandidateWriter |
Expanded XML 3.0 writer for a participant evidence with full experimental details
|
| XmlExperimentalParticipantPool |
Xml implementation of participant pool
|
| XmlExperimentalParticipantPool |
Xml implementation of participant pool
|
| XmlExperimentalParticipantPool |
Xml implementation of participant pool
|
| XmlExperimentalParticipantPoolWrapper |
Wrapper for Xml participants pools
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentalParticipantPoolWrapper |
Wrapper for Xml participants pools
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentalParticipantPoolWrapper |
Wrapper for Xml participants pools
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlExperimentWriter |
XML 2.5 writer for expanded experiments having participant identification method,
feature detection method and a list of host organisms
|
| XmlExperimentWriter |
XML 3.0 writer for expanded experiments having participant identification method,
feature detection method and a list of host organisms
|
| XmlExperimentWriter |
PSI-XML 2.5 experiment writer
|
| XmlExperimentWriter |
PSI-XML 3.0.0 experiment writer
|
| XmlFeature |
Simple Xml implementation of a Feature
|
| XmlFeature |
Simple Xml implementation of a Feature
|
| XmlFeature |
Simple Xml implementation of a Feature
|
| XmlFeatureEvidence |
Xml implementation of a Feature
|
| XmlFeatureEvidence |
Xml implementation of a Feature
|
| XmlFeatureEvidence |
Xml implementation of a Feature
|
| XmlFeatureEvidence.JAXBExperimentRefWrapper |
|
| XmlFeatureEvidence.JAXBExperimentRefWrapper |
|
| XmlFeatureEvidence.JAXBExperimentRefWrapper |
|
| XmlFeatureEvidence.JAXBParameterWrapper |
|
| XmlFeatureEvidence.JAXBParameterWrapper |
|
| XmlFeatureEvidence.JAXBParameterWrapper |
|
| XmlFeatureEvidenceWrapper |
Xml wrapper for feature evidences.
|
| XmlFeatureEvidenceWrapper |
Xml wrapper for feature evidences.
|
| XmlFeatureEvidenceWrapper |
Xml wrapper for feature evidences.
|
| XmlFeatureEvidenceWriter |
Writer for expanded feature evidence having experiment references
|
| XmlFeatureEvidenceWriter |
Writer for expanded feature evidence having experiment references
|
| XmlFeatureEvidenceWriter |
XML 2.5 writer for a feature evidence (with feature detection method)
|
| XmlFeatureEvidenceWriter |
XML 3.0 writer for a feature evidence (with feature detection method)
|
| XmlFeatureModificationEffector |
Xml implementation of feature modification effector
|
| XmlFeatureModificationEffector |
Xml implementation of feature modification effector
|
| XmlFeatureModificationEffector |
Xml implementation of feature modification effector
|
| XmlFeatureWrapper |
Xml wrapper for basic features
|
| XmlFeatureWrapper |
Xml wrapper for basic features
|
| XmlFeatureWrapper |
Xml wrapper for basic features
|
| XmlFeatureWriter |
XML 2.5 writer for a basic feature (ignore experimental details)
|
| XmlFeatureWriter |
XML 2.5 writer for a basic feature (ignore experimental details)
|
| XmlGene |
Xml implementation of a Gene
|
| XmlGene |
Xml implementation of a Gene
|
| XmlGene |
Xml implementation of a Gene
|
| XmlHostOrganismWriter |
XML 2.5 writer for an expanded host organism having experiment references
|
| XmlHostOrganismWriter |
XML 2.5 writer for an expanded host organism having experiment references
|
| XmlHostOrganismWriter |
XML 3.0 writer for an expanded host organism having experiment references
|
| XmlHostOrganismWriter |
PSI-XML writer for host organism
|
| XmlIdReference |
A XML reference to an parent having an id
|
| XmlInferredInteractionWriter |
XML writer for an expanded inferred interaction
|
| XmlInferredInteractionWriter |
XML writer for Inferred interactions
|
| XmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| XmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| XmlInteractionEvidence |
Xml implementation of InteractionEvidence
|
| XmlInteractionEvidence.JAXBCausalRelationshipWrapper |
|
| XmlInteractionEvidence.JAXBExperimentWrapper |
|
| XmlInteractionEvidence.JAXBVariableParameterValueSetWrapper |
|
| XmlInteractionEvidenceComplexWrapper |
Xml wrapper for interaction evidences used as complex
|
| XmlInteractionEvidenceComplexWrapper |
Xml wrapper for interaction evidences used as complex
|
| XmlInteractionEvidenceComplexWrapper |
Xml wrapper for interaction evidences used as complex
|
| XmlInteractionEvidenceIterator |
Xml interaction evidence iterator
|
| XmlInteractionEvidenceWriter |
Compact XML 2.5 writer for an interaction evidence (with full experimental details).
|
| XmlInteractionEvidenceWriter |
Compact XML 3.0 writer for an interaction evidence (with full experimental details).
|
| XmlInteractionEvidenceWriter |
Expanded XML 2.5 writer for an interaction evidence (with full experimental details).
|
| XmlInteractionEvidenceWriter |
Expanded XML 3.0 writer for an interaction evidence (with full experimental details).
|
| XmlInteractionEvidenceWriter |
Compact XML 2.5 writer for an expanded interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlInteractionEvidenceWriter |
Compact XML 3.0 writer for an expanded interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlInteractionEvidenceWriter |
Expanded XML 2.5 writer for an expanded interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlInteractionEvidenceWriter |
Expanded XML 3.0 writer for an expanded interaction evidence (having modelled, intramolecular properties, list
of experiments, list of interaction types, etc.).
|
| XmlInteractionIterator |
Xml basic interaction iterator
|
| XmlInteractor |
The Xml implementation of Interactor
|
| XmlInteractor |
The Xml implementation of Interactor
|
| XmlInteractor |
The Xml implementation of Interactor
|
| XmlInteractorFactory |
Interactor factory for XML interactors
|
| XmlInteractorPool |
Xml implementation for InteractorSet
|
| XmlInteractorPool |
Xml implementation for InteractorSet
|
| XmlInteractorPool |
Xml implementation for InteractorSet
|
| XmlInteractorWriter |
Xml interactor writer
|
| XmlInteractorWriter |
Xml interactor writer
|
| XmlInterval |
Xml implementation of a position which is an interval
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlInterval |
Xml implementation of a position which is an interval
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlInterval |
Xml implementation of a position which is an interval
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlModelledBinaryInteraction |
Xml implementation of ModelledInteraction
|
| XmlModelledBinaryInteraction |
Xml implementation of ModelledInteraction
|
| XmlModelledBinaryInteractionIterator |
Xml modelled binary interaction iterator
|
| XmlModelledBinaryInteractionWrapper |
Wrapper for Xml binary interactions
|
| XmlModelledBinaryInteractionWrapper |
Wrapper for Xml binary interactions
|
| XmlModelledBinaryInteractionWriter |
Compact XML 2.5 writer for a modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Compact XML 3.0 writer for a modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Expanded XML 2.5 writer for a modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Expanded XML 3.0 writer for a modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Compact XML 2.5 writer for an expanded modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Compact XML 3.0 writer for an expanded modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Expanded XML 2.5 writer for an expanded modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryInteractionWriter |
Expanded XML 3.0 writer for an expanded modelled binary interaction (ignore experimental details).
|
| XmlModelledBinaryParser |
Xml parser creating modelled binary interaction
|
| XmlModelledBinarySource |
PSI-XML data source that provides modelled binary interactions (ignore experimental details).
|
| XmlModelledBinaryStreamSource |
Psi-xml datasource for modelled binary interactions
|
| XmlModelledConfidence |
Xml implementation of ModelledConfidence
|
| XmlModelledConfidence |
Xml implementation of ModelledConfidence
|
| XmlModelledConfidence |
Xml 3.0 implementation of ModelledConfidence
|
| XmlModelledConfidenceWriter |
Xml30 writer for modelled confidences
|
| XmlModelledConfidenceWriter |
Xml30 writer for modelled confidences
|
| XmlModelledFeature |
The xml implementation of a modelledFeature
|
| XmlModelledFeature |
The xml implementation of a modelledFeature
|
| XmlModelledFeature |
The xml implementation of a modelledFeature
|
| XmlModelledFeatureWriter |
XML 2.5 writer for a modelled feature (ignore experimental details)
|
| XmlModelledFeatureWriter |
XML 3.0 writer for a modelled feature (ignore experimental details)
|
| XmlModelledFeatureWriter |
XML 2.5 writer for a modelled feature (ignore experimental details)
|
| XmlModelledFeatureWriter |
XML 3.0 writer for a modelled feature (ignore experimental details)
|
| XmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| XmlModelledInteraction |
Xml implementation of ModelledInteraction
|
| XmlModelledInteraction |
Xml 3.0.0 implementation of ModelledInteraction
|
| XmlModelledInteraction.JAXBAttributeWrapper |
|
| XmlModelledInteraction.JAXBBindingFeaturesWrapper |
|
| XmlModelledInteraction.JAXBCausalRelationshipWrapper |
|
| XmlModelledInteraction.JAXBConfidenceWrapper |
|
| XmlModelledInteraction.JAXBCooperativeEffectWrapper |
|
| XmlModelledInteraction.JAXBParameterWrapper |
|
| XmlModelledInteraction.JAXBParticipantWrapper |
|
| XmlModelledInteractionComplexWrapper |
Wrapper for complexes that were loaded as abstract interactions
|
| XmlModelledInteractionComplexWrapper |
Wrapper for complexes that were loaded as abstract interactions
|
| XmlModelledInteractionComplexWrapper |
Wrapper for complexes that were loaded as abstract interactions
|
| XmlModelledInteractionIterator |
Xml modelled interaction iterator
|
| XmlModelledInteractionWriter |
Compact XML 2.5 writer for a modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Compact XML 3.0 writer for a modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Expanded XML 2.5 writer for a modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Expanded XML 3.0 writer for a modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Compact XML 2.5 writer for an expanded modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Compact XML 3.0 writer for an expanded modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Expanded XML 2.5 writer for an expanded modelled interaction (ignore experimental details).
|
| XmlModelledInteractionWriter |
Expanded XML 3.0 writer for an expanded modelled interaction (ignore experimental details).
|
| XmlModelledParameter |
Xml implementation of ModelledParameter
|
| XmlModelledParameter |
Xml implementation of ModelledParameter
|
| XmlModelledParameter |
Xml 3.0 implementation of ModelledParameter
|
| XmlModelledParameterWriter |
XML 3.0 writer of a modelled parameter
|
| XmlModelledParameterWriter |
XML 3.0 writer of a modelled parameter
|
| XmlModelledParser |
Parser generating modelled interaction objects and ignore experimental details
|
| XmlModelledParticipant |
XML implementation of ModelledParticipant
|
| XmlModelledParticipant |
XML implementation of ModelledParticipant
|
| XmlModelledParticipant |
XML implementation of ModelledParticipant
|
| XmlModelledParticipant.JAXBFeatureWrapper |
|
| XmlModelledParticipant.JAXBFeatureWrapper |
|
| XmlModelledParticipant.JAXBFeatureWrapper |
|
| XmlModelledParticipant.JAXBInteractorCandidatesWrapper |
|
| XmlModelledParticipant.JAXBInteractorCandidatesWrapper |
|
| XmlModelledParticipant.JAXBInteractorCandidatesWrapper |
|
| XmlModelledParticipantCandidate |
XML implementation of ModelledParticipantCandidate
|
| XmlModelledParticipantCandidate |
XML implementation of ModelledParticipantCandidate
|
| XmlModelledParticipantCandidate |
XML implementation of ModelledParticipantCandidate
|
| XmlModelledParticipantCandidate.JAXBFeatureWrapper |
|
| XmlModelledParticipantCandidate.JAXBFeatureWrapper |
|
| XmlModelledParticipantCandidate.JAXBFeatureWrapper |
|
| XmlModelledParticipantCandidateWriter |
Compact XML 3.0 writer for a participant evidence with full experimental details
|
| XmlModelledParticipantCandidateWriter |
Expanded XML 3.0 writer for a participant evidence with full experimental details
|
| XmlModelledParticipantCandidateWriter |
Compact XML 3.0 writer for a participant evidence with full experimental details
|
| XmlModelledParticipantCandidateWriter |
Expanded XML 3.0 writer for a participant evidence with full experimental details
|
| XmlModelledParticipantPool |
Xml implementation of participant pool
|
| XmlModelledParticipantPool |
Xml implementation of participant pool
|
| XmlModelledParticipantPool |
Xml implementation of participant pool
|
| XmlModelledParticipantWriter |
Compact XML 2.5 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Compact XML 3.0 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Expanded XML 2.5 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Expanded XML 3.0 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Compact XML 2.5 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Compact XML 3.0 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Expanded XML 2.5 writer for a modelled participant.
|
| XmlModelledParticipantWriter |
Compact XML 3.0 writer for a modelled participant.
|
| XmlModelledSource |
PSI-XML data source that provides abstract interactions (ignore full experimental details).
|
| XmlModelledStreamSource |
Datasource for Psi-XML abstract interactions
|
| XmlMolecule |
Xml implementation of molecule
|
| XmlMolecule |
Xml implementation of molecule
|
| XmlMolecule |
Xml implementation of molecule
|
| XmlMoleculeEffector |
XML implementation of allosteric molecule effector
|
| XmlMoleculeEffector |
XML implementation of allosteric molecule effector
|
| XmlMoleculeEffector |
XML implementation of allosteric molecule effector
|
| XmlNamedBinaryInteractionEvidenceWriter |
Compact XML 2.5 writer for a named binary interaction evidence (with full experimental details).
|
| XmlNamedBinaryInteractionEvidenceWriter |
Compact XML 3.0 writer for a named binary interaction evidence (with full experimental details).
|
| XmlNamedBinaryInteractionEvidenceWriter |
Expanded XML 2.5 writer for a named binary interaction evidence (with full experimental details).
|
| XmlNamedBinaryInteractionEvidenceWriter |
Expanded XML 3.0 writer for a named binary interaction evidence (with full experimental details).
|
| XmlNamedBinaryInteractionWriter |
Compact XML 2.5 writer for a basic binary interaction (ignore experimental details) which has a fullname
and aliases in addition to a shortname
|
| XmlNamedBinaryInteractionWriter |
Expanded XML 2.5 writer for a basic binary interaction (ignore experimental details).
|
| XmlNamedExperimentWriter |
XML 2.5 experiment writer for a named experiment having shortlabel, fullname and aliases
|
| XmlNamedExperimentWriter |
XML 3.0 experiment writer for a named experiment having shortlabel, fullname and aliases
|
| XmlNamedInteractionEvidenceWriter |
Compact XML 2.5 writer for a named interaction evidence (with full experimental details).
|
| XmlNamedInteractionEvidenceWriter |
Compact XML 3.0 writer for a named interaction evidence (with full experimental details).
|
| XmlNamedInteractionEvidenceWriter |
Expanded XML 2.5 writer for a named interaction evidence (with full experimental details).
|
| XmlNamedInteractionEvidenceWriter |
Expanded XML 3.0writer for a named interaction evidence (with full experimental details).
|
| XmlNamedInteractionWriter |
Compact XML 2.5 writer for a basic interaction (ignore experimental details) which has a fullname
and aliases in addition to a shortname
|
| XmlNamedInteractionWriter |
Expanded XML 2.5 writer for a basic interaction (ignore experimental details).
|
| XmlNamedModelledBinaryInteractionWriter |
Compact XML 2.5 writer for a modelled binary interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledBinaryInteractionWriter |
Compact XML 3.0 writer for a modelled binary interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledBinaryInteractionWriter |
Expanded XML 2.5 writer for a binary modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledBinaryInteractionWriter |
Expanded XML 3.0 writer for a binary modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledInteractionWriter |
Compact XML 2.5 writer for a modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledInteractionWriter |
Compact XML 3.0 writer for a modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledInteractionWriter |
Expanded XML 2.5 writer for a modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledInteractionWriter |
Expanded XML 3.0 writer for a modelled interaction (ignore experimental details) which have a fullname and aliases in
addition to the shortname.
|
| XmlNamedModelledParticipantWriter |
Compact XML 2.5 writer for a named modelled participant having a fullname and a shortname.
|
| XmlNamedModelledParticipantWriter |
Compact XML 3.0 writer for a named modelled participant having a fullname and a shortname.
|
| XmlNamedModelledParticipantWriter |
Expanded XML 2.5 writer for a named modelled participant having a fullname and a shortname.
|
| XmlNamedModelledParticipantWriter |
Expanded XML 3.0 writer for a named modelled participant having a fullname and a shortname.
|
| XmlNamedParticipantEvidenceWriter |
Compact Xml 2.5 writer for a named participant evidence with a shortname and a fullname.
|
| XmlNamedParticipantEvidenceWriter |
Compact Xml 3.0 writer for a named participant evidence with a shortname and a fullname.
|
| XmlNamedParticipantEvidenceWriter |
Expanded Xml 2.5 writer for a named participant evidence with a shortname and a fullname.
|
| XmlNamedParticipantEvidenceWriter |
Expanded Xml 3.0 writer for a named participant evidence with a shortname and a fullname.
|
| XmlNamedParticipantWriter |
Compact Xml 2.5 writer for a basic named participant with a shortname and a fullname.
|
| XmlNamedParticipantWriter |
Expanded Xml 2.5 writer for a basic named participant with a shortname and a fullname.
|
| XmlNucleicAcid |
Xml implementation of Nucleic acid
|
| XmlNucleicAcid |
Xml implementation of Nucleic acid
|
| XmlNucleicAcid |
Xml implementation of Nucleic acid
|
| XmlOpenCvTerm |
Xml implementation of CvTerm.
|
| XmlOpenCvTerm |
Xml implementation of CvTerm.
|
| XmlOpenCvTerm |
Xml implementation of CvTerm.
|
| XmlOpenCvTermWriter |
Xml writer for open cv terms
|
| XmlOpenCvTermWriter |
Xml writer for open cv terms
|
| XmlOrganism |
Xml implementation of an organism
|
| XmlOrganism |
Xml implementation of an organism
|
| XmlOrganism |
Xml implementation of an organism
|
| XmlOrganismWriter |
PSI-XML writer for organism
|
| XmlOrganismWriter |
PSI-XML writer for organism
|
| XmlParameter |
Xml implementation of Parameter
|
| XmlParameter |
Xml implementation of Parameter
|
| XmlParameter |
Xml implementation of Parameter
|
| XmlParameterWrapper |
Xml parameter wrapper
|
| XmlParameterWrapper |
Xml parameter wrapper
|
| XmlParameterWrapper |
Xml parameter wrapper
|
| XmlParameterWriter |
XML 2.5 writer of a parameter
|
| XmlParameterWriter |
XML 2.5 writer of a parameter
|
| XmlParameterWriter |
XML 3.0 writer of a parameter
|
| XmlParameterWriter |
XML 2.5 writer of a parameter
|
| XmlParameterWriter |
XML 3.0 writer of a parameter
|
| XmlParser |
Parser generating interaction objects that can be interaction evidences or abstract interactions.
|
| XmlParticipant |
Xml implementation of a simple participant
|
| XmlParticipant |
Xml implementation of a simple participant
|
| XmlParticipant |
Xml implementation of a simple participant
|
| XmlParticipant.JAXBFeatureWrapper |
|
| XmlParticipant.JAXBFeatureWrapper |
|
| XmlParticipant.JAXBFeatureWrapper |
|
| XmlParticipantCandidateWrapper |
Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
|
| XmlParticipantCandidateWrapper |
Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
|
| XmlParticipantCandidateWrapper |
Wrapper for XmlParticipantCandidate so it implements ModelledParticipantCanidate
|
| XmlParticipantEvidence |
Xml implementation of ParticipantEvidence
|
| XmlParticipantEvidence |
Xml implementation of ParticipantEvidence
|
| XmlParticipantEvidence |
Xml implementation of ParticipantEvidence
|
| XmlParticipantEvidence.JAXBConfidenceWrapper |
|
| XmlParticipantEvidence.JAXBConfidenceWrapper |
|
| XmlParticipantEvidence.JAXBConfidenceWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalInteractorWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalInteractorWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalInteractorWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalPreparationWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalPreparationWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalPreparationWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalRoleWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalRoleWrapper |
|
| XmlParticipantEvidence.JAXBExperimentalRoleWrapper |
|
| XmlParticipantEvidence.JAXBFeatureWrapper |
|
| XmlParticipantEvidence.JAXBFeatureWrapper |
|
| XmlParticipantEvidence.JAXBFeatureWrapper |
|
| XmlParticipantEvidence.JAXBHostOrganismWrapper |
|
| XmlParticipantEvidence.JAXBHostOrganismWrapper |
|
| XmlParticipantEvidence.JAXBHostOrganismWrapper |
|
| XmlParticipantEvidence.JAXBInteractorCandidatesWrapper |
|
| XmlParticipantEvidence.JAXBInteractorCandidatesWrapper |
|
| XmlParticipantEvidence.JAXBInteractorCandidatesWrapper |
|
| XmlParticipantEvidence.JAXBParameterWrapper |
|
| XmlParticipantEvidence.JAXBParameterWrapper |
|
| XmlParticipantEvidence.JAXBParameterWrapper |
|
| XmlParticipantEvidence.JAXBParticipantIdentificationWrapper |
|
| XmlParticipantEvidence.JAXBParticipantIdentificationWrapper |
|
| XmlParticipantEvidence.JAXBParticipantIdentificationWrapper |
|
| XmlParticipantEvidenceWrapper |
Wrapper for Xml participants
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlParticipantEvidenceWrapper |
Wrapper for Xml participants
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlParticipantEvidenceWrapper |
Wrapper for Xml participants
Addeding new modelled feature to this participant will not add new feature evidences to the wrapped participant evidence as they are incompatibles.
|
| XmlParticipantEvidenceWriter |
Compact XML 2.5 writer for a participant evidence with full experimental details
|
| XmlParticipantEvidenceWriter |
Compact XML 3.0 writer for a participant evidence with full experimental details
|
| XmlParticipantEvidenceWriter |
Expanded XML 2.5 writer for a participant evidence with full experimental details
|
| XmlParticipantEvidenceWriter |
Expanded XML 3.0 writer for a participant evidence with full experimental details
|
| XmlParticipantEvidenceWriter |
Compact XML 2.5 writer for an expanded participant evidence with full experimental details and having experimental interactors, list of host organisms and list of experimental roles.
|
| XmlParticipantEvidenceWriter |
Compact XML 3.0 writer for an expanded participant evidence with full experimental details and having experimental interactors, list of host organisms and list of experimental roles.
|
| XmlParticipantEvidenceWriter |
Expanded XML 2.5 writer for an expanded participant evidence with full experimental details and having experimental interactors, list of host organisms and list of experimental roles.
|
| XmlParticipantEvidenceWriter |
Expanded XML 3.0 writer for an expanded participant evidence with full experimental details and having experimental interactors, list of host organisms and list of experimental roles.
|
| XmlParticipantPoolWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantPoolWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantPoolWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantWrapper |
Wrapper for XmlParticipant
|
| XmlParticipantWriter |
Compact XML 2.5 writer for a basic participant (ignore experimental details)
|
| XmlParticipantWriter |
Expanded XML 2.5 writer for a basic participant (ignore experimental details)
|
| XmlParticipantWriter |
Compact XML 2.5 writer for a basic participant (ignore experimental details)
|
| XmlParticipantWriter |
Compact XML 2.5 writer for a basic participant (ignore experimental details)
|
| XmlPolymer |
Xml implementation of Polymer
|
| XmlPolymer |
Xml implementation of Polymer
|
| XmlPolymer |
Xml implementation of Polymer
|
| XmlPosition |
Xml implementation of a simple Position
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlPosition |
Xml implementation of a simple Position
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlPosition |
Xml implementation of a simple Position
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlPreAssembly |
Xml implementation of preassembly
|
| XmlPreAssembly |
Xml implementation of preassembly
|
| XmlPreAssembly |
Xml 3.0 implementation of preassembly
|
| XmlPreAssemblyWriter |
Xml 3.0 writer for preassembly
|
| XmlPreAssemblyWriter |
Xml 3.0 writer for preassembly
|
| XmlProtein |
Xml implementation of protein
|
| XmlProtein |
Xml implementation of protein
|
| XmlProtein |
Xml implementation of protein
|
| XmlPublicationWriter |
Xml25 writer for publications (bibref objects)
|
| XmlPublicationWriter |
Xml30 writer for publications (bibref objects)
|
| XmlPublicationWriter |
Xml25 writer for publications (bibref objects)
|
| XmlPublicationWriter |
Xml30 writer for publications (bibref objects)
|
| XmlRange |
Xml implementation of Range
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlRange |
Xml implementation of Range
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlRange |
Xml implementation of Range
The JAXB binding is designed to be read-only and is not designed for writing
|
| XmlRangeWriter |
Xml 2.5 writer for a feature range
|
| XmlRangeWriter |
Xml 3.0 writer for a feature range
|
| XmlRangeWriter |
Xml 2.5 writer for a feature range
|
| XmlRangeWriter |
Xml 3.0 writer for a feature range
|
| XmlRangeWriter |
Xml writer for a feature range
|
| XmlReaderWithDefaultNamespace |
Namespace filter that sets default namespace when no namespaces are found
|
| XmlResultingSequence |
Xml implementation of resulting sequence for XML 2.5
|
| XmlResultingSequence |
Xml implementation of resulting sequence for XML 2.5
|
| XmlResultingSequence |
Xml implementation of resulting sequence for XML 3.0
|
| XmlResultingSequenceWriter |
Xml 3.0 writer for resulting sequence
|
| XmlResultingSequenceWriter |
Xml 3.0 writer for resulting sequence
|
| XmlSource |
PSI-XML data source that provides interactions (mix of abstract interactions and interaction evidences).
|
| XmlSource |
Desciption of the source of the entry, usually an organisation
|
| XmlSource |
Desciption of the source of the entry, usually an organisation
|
| XmlSource |
Desciption of the source of the entry, usually an organisation
|
| XmlSourceWriter |
XML 2.5 writer for expanded XML source having a release description and a release date
|
| XmlSourceWriter |
XML 3.0 writer for expanded XML source having a release description and a release date
|
| XmlSourceWriter |
Writer of a source in an 2.5 entry.
|
| XmlSourceWriter |
Writer of a source in a 3.0 entry.
|
| XmlStoichiometry |
Xml implementation of stoichiometry
|
| XmlStoichiometryRange |
Xml 2.5 implementation of stoichiometry range values
|
| XmlStoichiometryRange |
Xml 2.5 implementation of stoichiometry range values
|
| XmlStoichiometryRange |
Xml 3.0 implementation of stoichiometry range values
|
| XmlStoichiometryWriter |
XML 3.0 writer for stoichiometry
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| XmlStreamSource |
Datasource for PSI-xml returning mix of abstract interactions and interaction evidences
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| XmlVariableParameter |
XML 2.5 implementation of variable parameter
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| XmlVariableParameter |
XML 2.5 implementation of variable parameter
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| XmlVariableParameter |
XML 3.0 implementation of variable parameter
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| XmlVariableParameter.JAXBVariableValueWrapper |
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| XmlVariableParameter.JAXBVariableValueWrapper |
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| XmlVariableParameter.JAXBVariableValueWrapper |
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| XmlVariableParameterValue |
XML 2.5 implementation of variable parameter value
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| XmlVariableParameterValue |
XML 2.5 implementation of variable parameter value
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| XmlVariableParameterValue |
XML 3.0 implementation of variable parameter value
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| XmlVariableParameterValueSet |
XML 3.0 implementation of variable parameter value set
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| XmlVariableParameterValueSetWriter |
XML 3.0 writer for variable parameter value set
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| XmlVariableParameterValueWriter |
XML 3.0 writer for variable parameter value
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| XmlVariableParameterWriter |
XML 3.0 writer for variable parameter
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| XmlVariableParameterWriter |
XML 3.0 writer for variable parameter
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| XmlXref |
Refers to a unique object in an external database.
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| XmlXref |
Refers to a unique object in an external database.
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| XmlXref |
Refers to a unique object in an external database.
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| XmlXref.JAXBAttributeWrapper |
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| XmlXref.JAXBAttributeWrapper |
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| XmlXref.JAXBAttributeWrapper |
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| Xref |
Cross reference to an external database/resource which can give more information about an object.
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| XrefContainer |
Xref container in XML implementation
The JAXB binding is designed to be read-only and is not designed for writing
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| XrefContainer |
Xref container in XML implementation
The JAXB binding is designed to be read-only and is not designed for writing
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| XrefContainer |
Xref container in XML implementation
The JAXB binding is designed to be read-only and is not designed for writing
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| XrefsChangeListener<T> |
A listener for changes to a bioactiveEntity.
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| XrefsCollectionComparator |
Comparator for collection of Xrefs
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| XrefUtils |
Utility class for Xrefs
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