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

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}

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());
  }
}

Collection<Confidence> initializedConfidence1 = IntactCore.ensureInitializedConfidences(this);
Collection<Confidence> initializedConfidence2 = IntactCore.ensureInitializedConfidences(interaction);

Collection<Confidence> initializedConfidence1 = IntactCore.ensureInitializedConfidences(this);
Collection<Confidence> initializedConfidence2 = IntactCore.ensureInitializedConfidences(interaction);

experiments = IntactCore.ensureInitializedExperiments(intactObject);
components = IntactCore.ensureInitializedParticipants(intactObject);
confidences = IntactCore.ensureInitializedConfidences(intactObject);
parameters = IntactCore.ensureInitializedInteractionParameters(intactObject);
annotations = IntactCore.ensureInitializedAnnotations(intactObject);

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());
}

Collection<Confidence> confidences = IntactCore.ensureInitializedConfidences(interaction);

Collection<Confidence> confidences = IntactCore.ensureInitializedConfidences(interaction);

Javadoc

Retrieves the confidences from an interaction, initializing them if necessary. Do not set the initialized collection of confidences because confidences cannot be orphan

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
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
ensureInitializedExperiments
Retrieves the experiment from a publication, initializing them if necessary.
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.

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How to use ensureInitializedConfidencesmethodin uk.ac.ebi.intact.core.persister.IntactCore

Best Java code snippets using uk.ac.ebi.intact.core.persister.IntactCore.ensureInitializedConfidences (Showing top 8 results out of 315)

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