Package psidev.psi.mi.jami.enricher.util

Class EnricherUtils

java.lang.Object

psidev.psi.mi.jami.enricher.util.EnricherUtils

public class EnricherUtils
extends Object

Utilities for enrichers.

Since:

10/07/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	BLANK_SPACE	Constant BLANK_SPACE="-"
static String	COLUMN_SEPARATOR	Constant COLUMN_SEPARATOR="\t"
static String	NEW_LINE	Constant NEW_LINE="\n"

Constructor Summary

Constructors

Constructor	Description
EnricherUtils()

Method Summary

Modifier and Type	Method	Description
static <T> void	mergeAliases(T termToEnrich, Collection<Alias> toEnrichAliases, Collection<Alias> fetchedAliases, boolean remove, AliasesChangeListener<T> aliasListener)	mergeAliases.
static <T> void	mergeAnnotations(T termToEnrich, Collection<Annotation> toEnrichAnnotations, Collection<Annotation> fetchedAnnotations, boolean remove, AnnotationsChangeListener<T> annotationListener)	mergeAnnotations.
static void	mergeCausalRelationships(Entity termToEnrich, Collection<CausalRelationship> toEnrichRelationships, Collection<CausalRelationship> fetchedRelationships, boolean remove, EntityChangeListener entityListener)	mergeCausalRelationships.
static <T> void	mergeChecksums(T termToEnrich, Collection<Checksum> toEnrichChecksums, Collection<Checksum> fetchedCehcksum, boolean remove, ChecksumsChangeListener<T> aliasListener)	mergeChecksums.
static <T,C extends Confidence> void	mergeConfidences(T termToEnrich, Collection<C> toEnrichConfidences, Collection<C> fetchedConfidences, boolean remove, ConfidencesChangeListener<T> confListener)	mergeConfidences.
static <F extends Feature> void	mergeFeatures(Entity termToEnrich, Collection<F> toEnrichFeatures, Collection<F> fetchedFeatures, boolean remove, EntityChangeListener entityListener, FeatureEnricher<F> featureEnricher)	mergeFeatures.
static <T,P extends Parameter> void	mergeParameters(T termToEnrich, Collection<P> toEnrichParameters, Collection<P> fetchedParameters, boolean remove, ParametersChangeListener<T> paramListener)	mergeParameters.
static <P extends ParticipantCandidate> void	mergeParticipantCandidates(ParticipantPool termToEnrich, Collection<P> toEnrichParticipants, Collection<P> fetchedParticipants, boolean remove, ParticipantPoolChangeListener poolListener, EntityEnricher participantEnricher)	mergeParticipantCandidates.
static <P extends Participant> void	mergeParticipants(Interaction termToEnrich, Collection<P> toEnrichParticipants, Collection<P> fetchedParticipants, boolean remove, InteractionChangeListener interactionListener, ParticipantEnricher participantEnricher)	mergeParticipants.
static <T extends Feature> void	mergeRanges(T termToEnrich, Collection<Range> toEnrichRanges, Collection<Range> fetchedRanges, boolean remove, FeatureChangeListener<T> featureListener)	mergeRanges.
static <T> void	mergeXrefs(T termToEnrich, Collection<Xref> toEnrichXrefs, Collection<Xref> fetchedXrefs, boolean remove, boolean isIdentifier, XrefsChangeListener<T> xrefListener, IdentifiersChangeListener<T> identifierListener)	Takes two lists of Xrefs and produces a list of those to add and those to remove.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NEW_LINE

public static final String NEW_LINE

Constant NEW_LINE="\n"

See Also:

Constant Field Values

COLUMN_SEPARATOR

public static final String COLUMN_SEPARATOR

Constant COLUMN_SEPARATOR="\t"

See Also:

Constant Field Values

BLANK_SPACE

public static final String BLANK_SPACE

Constant BLANK_SPACE="-"

See Also:

Constant Field Values

Constructor Detail

EnricherUtils

public EnricherUtils()

Method Detail

mergeXrefs

public static <T> void mergeXrefs(T termToEnrich,
                                  Collection<Xref> toEnrichXrefs,
                                  Collection<Xref> fetchedXrefs,
                                  boolean remove,
                                  boolean isIdentifier,
                                  XrefsChangeListener<T> xrefListener,
                                  IdentifiersChangeListener<T> identifierListener)

Takes two lists of Xrefs and produces a list of those to add and those to remove.

It will add in toEnrichXrefs all xref from fetchedXrefs that are not there. It will also remove extra identifiers from toEnrichXrefs if remove boolean is true.

Type Parameters:

T - a T object.

Parameters:

termToEnrich - The object to enrich

fetchedXrefs - The new xrefs to be added.

remove - : if true, we remove xrefs that are not in enriched list

isIdentifier - if true compare identifiers, otherwise xrefs

toEnrichXrefs - a Collection object.

xrefListener - a XrefsChangeListener object.

identifierListener - a IdentifiersChangeListener object.

mergeRanges

public static <T extends Feature> void mergeRanges(T termToEnrich,
                                                   Collection<Range> toEnrichRanges,
                                                   Collection<Range> fetchedRanges,
                                                   boolean remove,
                                                   FeatureChangeListener<T> featureListener)

mergeRanges.

Type Parameters:

T - a T object.

Parameters:

termToEnrich - a T object.

toEnrichRanges - a Collection object.

fetchedRanges - a Collection object.

remove - a boolean.

featureListener - a FeatureChangeListener object.

mergeAliases

public static <T> void mergeAliases(T termToEnrich,
                                    Collection<Alias> toEnrichAliases,
                                    Collection<Alias> fetchedAliases,
                                    boolean remove,
                                    AliasesChangeListener<T> aliasListener)

mergeAliases.

Type Parameters:

T - a T object.

Parameters:

termToEnrich - a T object.

toEnrichAliases - a Collection object.

fetchedAliases - a Collection object.

remove - a boolean.

aliasListener - a AliasesChangeListener object.

mergeChecksums

public static <T> void mergeChecksums(T termToEnrich,
                                      Collection<Checksum> toEnrichChecksums,
                                      Collection<Checksum> fetchedCehcksum,
                                      boolean remove,
                                      ChecksumsChangeListener<T> aliasListener)

mergeChecksums.

Type Parameters:

T - a T object.

Parameters:

termToEnrich - a T object.

toEnrichChecksums - a Collection object.

fetchedCehcksum - a Collection object.

remove - a boolean.

aliasListener - a ChecksumsChangeListener object.

mergeAnnotations

public static <T> void mergeAnnotations(T termToEnrich,
                                        Collection<Annotation> toEnrichAnnotations,
                                        Collection<Annotation> fetchedAnnotations,
                                        boolean remove,
                                        AnnotationsChangeListener<T> annotationListener)

mergeAnnotations.

Type Parameters:

T - a T object.

Parameters:

termToEnrich - a T object.

toEnrichAnnotations - a Collection object.

fetchedAnnotations - a Collection object.

remove - a boolean.

annotationListener - a AnnotationsChangeListener object.

mergeConfidences

public static <T,C extends Confidence> void mergeConfidences(T termToEnrich,
                                                                   Collection<C> toEnrichConfidences,
                                                                   Collection<C> fetchedConfidences,
                                                                   boolean remove,
                                                                   ConfidencesChangeListener<T> confListener)

mergeConfidences.

Type Parameters:

T - a T object.

C - a C object.

Parameters:

termToEnrich - a T object.

toEnrichConfidences - a Collection object.

fetchedConfidences - a Collection object.

remove - a boolean.

confListener - a ConfidencesChangeListener object.

mergeParameters

public static <T,P extends Parameter> void mergeParameters(T termToEnrich,
                                                                 Collection<P> toEnrichParameters,
                                                                 Collection<P> fetchedParameters,
                                                                 boolean remove,
                                                                 ParametersChangeListener<T> paramListener)

mergeParameters.

Type Parameters:

T - a T object.

P - a P object.

Parameters:

termToEnrich - a T object.

toEnrichParameters - a Collection object.

fetchedParameters - a Collection object.

remove - a boolean.

paramListener - a ParametersChangeListener object.

mergeParticipants

public static <P extends Participant> void mergeParticipants(Interaction termToEnrich,
                                                             Collection<P> toEnrichParticipants,
                                                             Collection<P> fetchedParticipants,
                                                             boolean remove,
                                                             InteractionChangeListener interactionListener,
                                                             ParticipantEnricher participantEnricher)
                                                      throws EnricherException

mergeParticipants.

Type Parameters:

P - a P object.

Parameters:

termToEnrich - a Interaction object.

toEnrichParticipants - a Collection object.

fetchedParticipants - a Collection object.

remove - a boolean.

interactionListener - a InteractionChangeListener object.

participantEnricher - a ParticipantEnricher object.

Throws:

EnricherException - if any.

mergeParticipantCandidates

public static <P extends ParticipantCandidate> void mergeParticipantCandidates(ParticipantPool termToEnrich,
                                                                               Collection<P> toEnrichParticipants,
                                                                               Collection<P> fetchedParticipants,
                                                                               boolean remove,
                                                                               ParticipantPoolChangeListener poolListener,
                                                                               EntityEnricher participantEnricher)
                                                                        throws EnricherException

mergeParticipantCandidates.

Type Parameters:

P - a P object.

Parameters:

termToEnrich - a ParticipantPool object.

toEnrichParticipants - a Collection object.

fetchedParticipants - a Collection object.

remove - a boolean.

poolListener - a ParticipantPoolChangeListener object.

participantEnricher - a EntityEnricher object.

Throws:

EnricherException - if any.

mergeCausalRelationships

public static void mergeCausalRelationships(Entity termToEnrich,
                                            Collection<CausalRelationship> toEnrichRelationships,
                                            Collection<CausalRelationship> fetchedRelationships,
                                            boolean remove,
                                            EntityChangeListener entityListener)
                                     throws EnricherException

mergeCausalRelationships.

Parameters:

termToEnrich - a Entity object.

toEnrichRelationships - a Collection object.

fetchedRelationships - a Collection object.

remove - a boolean.

entityListener - a EntityChangeListener object.

Throws:

EnricherException - if any.

mergeFeatures

public static <F extends Feature> void mergeFeatures(Entity termToEnrich,
                                                     Collection<F> toEnrichFeatures,
                                                     Collection<F> fetchedFeatures,
                                                     boolean remove,
                                                     EntityChangeListener entityListener,
                                                     FeatureEnricher<F> featureEnricher)
                                              throws EnricherException

mergeFeatures.

Type Parameters:

F - a F object.

Parameters:

termToEnrich - a Entity object.

toEnrichFeatures - a Collection object.

fetchedFeatures - a Collection object.

remove - a boolean.

entityListener - a EntityChangeListener object.

featureEnricher - a FeatureEnricher object.

Throws:

EnricherException - if any.