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; }
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 }
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 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 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(); }
mEntry.getInteractors().add( interactorConverter.fromJaxb( jInteractor ) ); if (mEntry.getInteractors().isEmpty()) { List<Integer> participantIds = new ArrayList<Integer>(); mEntry.getInteractors().add(mParticipant.getInteractor()); participantIds.add(mParticipant.getInteractor().getId());
mEntry.getInteractors().add( interactorConverter.fromJaxb( jInteractor ) ); if (mEntry.getInteractors().isEmpty()) { 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 ( uk.ac.ebi.intact.model.Interactor i : intactObject.getInteractors() ) { final psidev.psi.mi.xml.model.Interactor interactor = interactorConverter.intactToPsi( i ); entry.getInteractors().add( interactor );
for ( psidev.psi.mi.xml.model.Interactor mInteractor : mEntry.getInteractors() ) { if (!interactorIds.contains(mInteractor.getId())) { jEntry.getInteractorList().getInteractors().add( interactorConverter.toJaxb( mInteractor ) );
for ( psidev.psi.mi.xml.model.Interactor mInteractor : mEntry.getInteractors() ) { if (!interactorIds.contains(mInteractor.getId())) { jEntry.getInteractorList().getInteractors().add( interactorConverter.toJaxb( mInteractor ) );