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()); } }
/** * Build a new Interaction with no participants but holding a copy of all other attributes of the given interaction. * <br/> WARNING: all attributes of the newly created interaction are the same as the source's (that is same object * instance). This is not an object clone. * * @param source the source interaction. * @return a target interaction which is a copy of the source interaction but the participants or * inferredInteractions. */ protected Interaction copyInteraction(Interaction source) { Interaction target = new Interaction(); // clone inner attributes target.setId(source.getId()); target.setImexId(source.getImexId()); // objects target.setNames(source.getNames()); target.setXref(source.getXref()); // collections target.getConfidences().addAll(source.getConfidences()); target.getExperiments().addAll(source.getExperiments()); target.getInteractionTypes().addAll(source.getInteractionTypes()); // added with mitab 27 target.setModelled(source.isModelled()); target.setIntraMolecular(source.isIntraMolecular()); target.setNegative(source.isNegative()); target.getParameters().addAll(source.getParameters()); target.getAttributes().addAll(source.getAttributes()); target.setAvailability(source.getAvailability()); return target; }
for (Confidence confidence : interaction.getConfidences()) { final Unit unit = confidence.getUnit();
interaction.getConfidences().add(confidence);
interaction.getConfidences().add( confidence);
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()); }
mInteraction.getConfidences().add( confidenceConverter.fromJaxb( jConfidence ) );
mInteraction.getConfidences().add( confidenceConverter.fromJaxb( jConfidence ) );
for (Confidence conf : interaction.getConfidences()){ if (conf.hasExperimentRefs()){ for (ExperimentRef eref : conf.getExperimentRefs()){
for ( Confidence mConfidence : mInteraction.getConfidences() ) { jInteraction.getConfidenceList().getConfidences().add( confidenceConverter.toJaxb( mConfidence ) );
for ( Confidence mConfidence : mInteraction.getConfidences() ) { jInteraction.getConfidenceList().getConfidences().add( confidenceConverter.toJaxb( mConfidence ) );
for (psidev.psi.mi.xml.model.Confidence psiConfidence : psiObject.getConfidences()){ Confidence confidence = confConverter.psiToIntact( psiConfidence );