uk.ac.ebi.intact.core.persister.IntactCore.ensureInitializedExperiments java code examples

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private void myMethod () {
 ScheduledThreadPoolExecutor s =new ScheduledThreadPoolExecutor(corePoolSize)
ThreadFactory threadFactory;new ScheduledThreadPoolExecutor(corePoolSize, threadFactory)
String str;new ScheduledThreadPoolExecutor(1, new ThreadFactoryBuilder().setNameFormat(str).build())
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}

/**
 * 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();
}

/**
 * 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();
}

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);
  }
}

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());
  }
}

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());
}

experiments = IntactCore.ensureInitializedExperiments(intactObject);
components = IntactCore.ensureInitializedParticipants(intactObject);
confidences = IntactCore.ensureInitializedConfidences(intactObject);

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;
}

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;
}

Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(interaction);

Collection<Experiment> experiments = IntactCore.ensureInitializedExperiments(interaction);

Javadoc

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

Popular methods of IntactCore

ensureInitializedAliases
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How to use ensureInitializedExperimentsmethodin 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)

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