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IntactCore.ensureInitializedExperiments
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How to use
ensureInitializedExperiments
method
in
uk.ac.ebi.intact.core.persister.IntactCore

Best Java code snippets using uk.ac.ebi.intact.core.persister.IntactCore.ensureInitializedExperiments (Showing top 10 results out of 315)

origin: uk.ac.ebi.intact.core/intact-core

/**
 * Convenience method to get the experiments - delegates the logic to the interactions
 *
 * @return Experiments
 */
public Collection<Experiment> getExperiments() {
  if (experiments != null) {
    return experiments.keySet();
  }
  else if (!experimentsList.isEmpty()){
    return experimentsList;
  }
  experiments = new IdentityMap();
  for (Interaction interaction : getInteractions()) {
    for (Experiment experiment : IntactCore.ensureInitializedExperiments(interaction)) {
      experiments.put(experiment, null);
    }
  }
  return experiments.keySet();
}
origin: uk.ac.ebi.intact.core/intact-core-readonly

/**
 * Convenience method to get the experiments - delegates the logic to the interactions
 *
 * @return Experiments
 */
public Collection<Experiment> getExperiments() {
  if (experiments != null) {
    return experiments.keySet();
  }
  else if (!experimentsList.isEmpty()){
    return experimentsList;
  }
  experiments = new IdentityMap();
  for (Interaction interaction : getInteractions()) {
    for (Experiment experiment : IntactCore.ensureInitializedExperiments(interaction)) {
      experiments.put(experiment, null);
    }
  }
  return experiments.keySet();
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

protected void failIfInconsistentConversion(Interaction intact, psidev.psi.mi.xml.model.Interaction psi, int numberOfAuthorConfAttributes) {
  Collection<Experiment> experiments;
  Collection<Component> participants;
  Collection<Confidence> confidences;
  if (isCheckInitializedCollections()){
    experiments = IntactCore.ensureInitializedExperiments(intact);
    participants = IntactCore.ensureInitializedParticipants(intact);
    confidences = IntactCore.ensureInitializedConfidences(intact);
  }
  else {
    experiments = intact.getExperiments();
    participants = intact.getComponents();
    confidences = intact.getConfidences();
  }
  failIfInconsistentCollectionSize("experiment", experiments, psi.getExperiments());
  failIfInconsistentCollectionSize("participant", participants, psi.getParticipants());
  Collection<Confidence> confs = confidences;
  if (confs.size() > 0 && psi.getConfidences().size() + numberOfAuthorConfAttributes > 0 && confs.size() != (psi.getConfidences().size() + numberOfAuthorConfAttributes)) {
    throw new InconsistentConversionException("Confidence", confs.size(), psi.getConfidences().size() + numberOfAuthorConfAttributes);
  }
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

protected void failIfInconsistentPsiConversion(Interaction intact, psidev.psi.mi.xml.model.Interaction psi) {
  Collection<Experiment> experiments;
  Collection<Component> participants;
  Collection<Confidence> confidences;
  if (isCheckInitializedCollections()){
    experiments = IntactCore.ensureInitializedExperiments(intact);
    participants = IntactCore.ensureInitializedParticipants(intact);
    confidences = IntactCore.ensureInitializedConfidences(intact);
  }
  else {
    experiments = intact.getExperiments();
    participants = intact.getComponents();
    confidences = intact.getConfidences();
  }
  failIfInconsistentCollectionSize("experiment", experiments, psi.getExperiments());
  failIfInconsistentCollectionSize("participant", participants, psi.getParticipants());
  Collection<Confidence> confs = confidences;
  if (confs.size() > 0 && psi.getConfidences().size() > 0 && (confs.size()) != psi.getConfidences().size()) {
    throw new InconsistentConversionException("Confidence", confs.size(), psi.getConfidences().size());
  }
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

protected void failIfInconsistentConversion(Interaction intact, psidev.psi.mi.xml.model.Interaction psi) {
  Collection<Experiment> experiments;
  Collection<Component> participants;
  Collection<Confidence> confidences;
  if (isCheckInitializedCollections()){
    experiments = IntactCore.ensureInitializedExperiments(intact);
    participants = IntactCore.ensureInitializedParticipants(intact);
    confidences = IntactCore.ensureInitializedConfidences(intact);
  }
  else {
    experiments = intact.getExperiments();
    participants = intact.getComponents();
    confidences = intact.getConfidences();
  }
  failIfInconsistentCollectionSize("experiment", experiments, psi.getExperiments());
  failIfInconsistentCollectionSize("participant", participants, psi.getParticipants());
  failIfInconsistentCollectionSize( "confidence", confidences, psi.getConfidences());
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

experiments = IntactCore.ensureInitializedExperiments(intactObject);
components = IntactCore.ensureInitializedParticipants(intactObject);
confidences = IntactCore.ensureInitializedConfidences(intactObject);
origin: uk.ac.ebi.intact.core/intact-core-readonly

public Publication clonePublication(Publication publication) throws IntactClonerException {
  if (publication == null) return null;
  Publication clone = new Publication();
  clonerManager.addClone(publication, clone);
  if (isCollectionClonable(publication.getExperiments())) {
    Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(publication);
    for (Experiment e : experiments) {
      clone.addExperiment(clone(e));
    }
  }
  if (isCollectionClonable(publication.getLifecycleEvents())) {
    Collection<LifecycleEvent> events = IntactCore.ensureInitializedLifecycleEvents(publication);
    for (LifecycleEvent event : events) {
      clone.addLifecycleEvent(clone(event));
    }
  }
  clone.setStatus(clone(publication.getStatus()));
  clone.setCurrentOwner(clone(publication.getCurrentOwner()));
  clone.setCurrentReviewer(clone(publication.getCurrentReviewer()));
  return clone;
}
origin: uk.ac.ebi.intact.core/intact-core

public Publication clonePublication(Publication publication) throws IntactClonerException {
  if (publication == null) return null;
  Publication clone = new Publication();
  clonerManager.addClone(publication, clone);
  if (isCollectionClonable(publication.getExperiments())) {
    Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(publication);
    for (Experiment e : experiments) {
      clone.addExperiment(clone(e));
    }
  }
  if (isCollectionClonable(publication.getLifecycleEvents())) {
    Collection<LifecycleEvent> events = IntactCore.ensureInitializedLifecycleEvents(publication);
    for (LifecycleEvent event : events) {
      clone.addLifecycleEvent(clone(event));
    }
  }
  clone.setStatus(clone(publication.getStatus()));
  clone.setCurrentOwner(clone(publication.getCurrentOwner()));
  clone.setCurrentReviewer(clone(publication.getCurrentReviewer()));
  return clone;
}
origin: uk.ac.ebi.intact.core/intact-core

Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(interaction);
origin: uk.ac.ebi.intact.core/intact-core-readonly

Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(interaction);
uk.ac.ebi.intact.core.persisterIntactCoreensureInitializedExperiments

Javadoc

Retrieves the experiment from an interaction, initializing them if necessary.

Popular methods of IntactCore

  • ensureInitializedAliases
    Retrieves the aliases from an AnnotatedObject, initializing them if necessary.
  • ensureInitializedAnnotations
    Retrieves the annotations from an AnnotatedObject, initializing them if necessary.
  • ensureInitializedComponentConfidences
    Retrieves the confidences from a participant, initializing them if necessary. Do not set the initial
  • ensureInitializedComponentParameters
    Retrieves the parameters from a participant, initializing them if necessary. Do not set the initiali
  • ensureInitializedConfidences
    Retrieves the confidences from an interaction, initializing them if necessary. Do not set the initia
  • ensureInitializedExperimentalPreparations
    Retrieves the experimental preparations from a participant, initializing them if necessary. Do not s
  • ensureInitializedExperimentalRoles
    Retrieves the experimental roles from a participant, initializing them if necessary. Do not set the
  • ensureInitializedFeatures
    Retrieves the features from a participant, initializing them if necessary. Do not set the initialize
  • ensureInitializedInteractionParameters
    Retrieves the parameters from an interaction, initializing them if necessary. Do not set the initial
  • ensureInitializedParticipantIdentificationMethods
    Retrieves the participant detection methods from a participant, initializing them if necessary. Do n
  • ensureInitializedParticipants
    Retrieves the components from an interaction, initializing them if necessary. Do not set the initial
  • ensureInitializedRanges
    Retrieves the ranges from a feature, initializing them if necessary.
  • ensureInitializedParticipants,
  • ensureInitializedRanges,
  • ensureInitializedXrefs,
  • ensureInitializedInteractions,
  • ensureInitializedLifecycleEvents,
  • ensureInitializedPreferences,
  • ensureInitializedRoles,
  • initialize,
  • initializeAnnotatedObject

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