private EntrySet mergeEntriesIfNecessary(EntrySet entrySet){ if (entrySet == null){ return null; } if (entrySet.getEntries().size() > 1){ Iterator<Entry> entryIterator = entrySet.getEntries().iterator(); Entry originalEntry = entryIterator.next(); while (entryIterator.hasNext()){ Entry newEntry = entryIterator.next(); originalEntry.getExperiments().addAll(newEntry.getExperiments()); originalEntry.getInteractors().addAll(newEntry.getInteractors()); originalEntry.getInteractions().addAll(newEntry.getInteractions()); } return new EntrySet(Arrays.asList(originalEntry), entrySet.getLevel(), entrySet.getVersion(), entrySet.getMinorVersion()); } return entrySet; }
public static Collection<ExperimentDescription> nonRedundantExperimentsFromPsiEntry(Entry psiEntry) { Map<Integer,ExperimentDescription> nonRedundantExps = new HashMap<Integer,ExperimentDescription>(); if( ConverterContext.getInstance().isGenerateCompactXml() ) { for (ExperimentDescription expDesc : psiEntry.getExperiments()) { nonRedundantExps.put(expDesc.getId(), expDesc); } } else { for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) { for (ExperimentDescription exp : interaction.getExperiments()) { nonRedundantExps.put(exp.getId(), exp); } } } return nonRedundantExps.values(); }
entry.getInteractions().addAll(interactions);
private void normalizeEntry(Entry entry) { if (entry.getExperiments().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { interaction.getExperimentRefs().clear(); for (ExperimentDescription exp : interaction.getExperiments()) { entry.getExperiments().add(exp); interaction.getExperimentRefs().add(new ExperimentRef(exp.getId())); } } } if (entry.getInteractors().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { entry.getInteractors().add(participant.getInteractor()); } } } }
public static Entry createEntry(Source source, Collection<Interaction> interactions) { Entry entry = new Entry(); entry.setSource(source); for (Interaction interaction : interactions) { entry.getInteractions().add(interaction); for (ExperimentDescription expDesc : interaction.getExperiments()) { entry.getExperiments().add(expDesc); } for (Participant part : interaction.getParticipants()) { entry.getInteractors().add(part.getInteractor()); } } return entry; }
private void removeInteractorRedundancy( EntrySet mEntrySet ) { if( ConverterContext.getInstance().getConverterConfig().getXmlForm() == PsimiXmlForm.FORM_COMPACT ) { for ( Entry entry : mEntrySet.getEntries() ) { Map<Interactor, Interactor> uniqueInteractors = new HashMap<Interactor, Interactor>(); for ( Interaction interaction : entry.getInteractions() ) { for ( Participant participant : interaction.getParticipants() ) { if( participant.getInteractor() != null ) { final Interactor myInteractor = participant.getInteractor(); if( uniqueInteractors.containsKey( myInteractor ) ) { final Interactor uniq = uniqueInteractors.get( myInteractor ); participant.setInteractor( uniq ); } else { uniqueInteractors.put( myInteractor, myInteractor ); } } } // participants } // interactions // if we had a compact format, we cannot remove interactor redundancy without changing the interactions // and update the interactor xref if (!uniqueInteractors.isEmpty()){ entry.getInteractors().clear(); entry.getInteractors().addAll( uniqueInteractors.keySet() ); } } // entries } // model is compact }
for(Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { for (Interaction interaction : entry.getInteractions()) { if(!participantInteractions.contains(interaction)) {
public void map() { final Collection<Entry> entries = es.getEntries(); for(Entry entry: entries) { mapNetworkMetaData(entry); mapNodes(entry.getInteractors()); mapEdges(entry.getInteractions()); } }
public static Collection<Object> nonRedundantInteractorsFromPsiEntry(Entry psiEntry) { Map<Integer, Object> nonRedundantInteractors = new HashMap<Integer, Object>(); if( ConverterContext.getInstance().isGenerateExpandedXml() ) { // iterate to get the unique experiments/interactors for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) { for (Participant participant : interaction.getParticipants()) { if (participant.getInteractor() != null){ nonRedundantInteractors.put(participant.getInteractor().getId(), participant.getInteractor()); } else if (participant.getInteraction() != null){ nonRedundantInteractors.put(participant.getInteraction().getId(), participant.getInteraction()); } } } } else { for ( psidev.psi.mi.xml.model.Interactor interactor : psiEntry.getInteractors() ) { nonRedundantInteractors.put( interactor.getId(), interactor ); } } return nonRedundantInteractors.values(); }
log.debug("Interaction count: " + entry.getInteractions().size()); for (Interaction interaction : entry.getInteractions()) {
protected void failIfInconsistentConversion(IntactEntry intactEntry, Entry psiEntry) { failIfInconsistentCollectionSize("interaction", intactEntry.getInteractions(), psiEntry.getInteractions()); failIfInconsistentCollectionSize("experiment", intactEntry.getExperiments(), PsiConverterUtils.nonRedundantExperimentsFromPsiEntry(psiEntry)); failIfInconsistentCollectionSize("interactor", intactEntry.getInteractors(), PsiConverterUtils.nonRedundantInteractorsFromPsiEntry(psiEntry)); }
for ( Interaction interaction : entry.getInteractions() ) { System.out.println( interaction.getNames().getShortLabel() );
for ( EntryType.InteractionList.Interaction jInteraction : jEntry.getInteractionList().getInteractions() ) { mEntry.getInteractions().add( interactionConverter.fromJaxb( jInteraction ) ); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { mEntry.getExperiments().addAll(mInteraction.getExperiments()); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) { mEntry.getInteractors().add(mParticipant.getInteractor());
for ( Interaction jInteraction : jEntry.getInteractionList().getInteractions() ) { mEntry.getInteractions().add( interactionConverter.fromJaxb( jInteraction ) ); List<Integer> experimentIds = new ArrayList<Integer>(); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.ExperimentDescription jExperiment : mInteraction.getExperiments()) { if (!experimentIds.contains(jExperiment.getId())) { List<Integer> participantIds = new ArrayList<Integer>(); for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) {
for (psidev.psi.mi.xml.model.Interaction psiInteraction : entry.getInteractions()) {
entry.getInteractions().add(interaction);
public IntactEntry psiToIntact(Entry psiObject) { psiStartConversion(psiObject); Institution institution = institutionConverter.psiToIntact(psiObject.getSource()); setInstitution(institution); Collection<Interaction> interactions = new ArrayList<Interaction>(); for (psidev.psi.mi.xml.model.Interaction psiInteraction : psiObject.getInteractions()) { Interaction interaction = interactionConverter.psiToIntact(psiInteraction); interactions.add(interaction); } IntactEntry ientry = new IntactEntry(interactions); ientry.setInstitution(getInstitution()); IntactConverterUtils.populateAnnotations(psiObject, ientry, institution, this.annotationConverter); if (psiObject.getSource().getReleaseDate() != null) { ientry.setReleasedDate(psiObject.getSource().getReleaseDate()); } ConversionCache.clear(); psiEndConversion(psiObject); ConverterContext.getInstance().getLocation().resetPosition(); failIfInconsistentConversion(ientry, psiObject); return ientry; }
for ( Interaction mInteraction : mEntry.getInteractions() ) { if ( jEntry.getInteractionList() == null ) { jEntry.setInteractionList( new EntryType.InteractionList() ); for (psidev.psi.mi.xml.model.Interaction jInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.ExperimentDescription jExperiment : jInteraction.getExperiments()) { if (!experimentIds.contains(jExperiment.getId())) { for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) { if (!participantIds.contains(mParticipant.getId())) {
for ( psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions() ) { if ( jEntry.getInteractionList() == null ) { jEntry.setInteractionList( new InteractionList() ); for (psidev.psi.mi.xml.model.Interaction jInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.ExperimentDescription jExperiment : jInteraction.getExperiments()) { if (!experimentIds.contains(jExperiment.getId())) { for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) { if (!participantIds.contains(mParticipant.getId())) {