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(); }
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()); } } } }
protected RepoEntry entryToRepoEntry(Entry entry) { RepoEntry repoEntry = new RepoEntry(); normalizeEntry(entry); String name = entry.getExperiments().iterator().next() .getBibref().getXref().getPrimaryRef().getId(); repoEntry.setPmid(name); repoEntry.setReleaseDate(PsiExchange.getReleaseDate(entry)); return repoEntry; } }
/** * Convert network metadata to CyNetwork table data. * * @param entry */ private void mapNetworkMetaData(final Entry entry) { final CyTable networkTable = network.getDefaultNetworkTable(); final Collection<Attribute> attrs = entry.getAttributes(); final Collection<ExperimentDescription> exp = entry.getExperiments(); // TODO: this takes very long time for some data sets. //mapExperiments(exp, networkTable); // Source is always unique final Source source = entry.getSource(); mapSource(source, networkTable); entry.getAvailabilities(); }
mEntry.getExperiments().add( experimentDescriptionConverter.fromJaxb( jExperiment ) ); if (mEntry.getExperiments().isEmpty()) { List<Integer> experimentIds = new ArrayList<Integer>(); for (psidev.psi.mi.xml.model.ExperimentDescription jExperiment : mInteraction.getExperiments()) { if (!experimentIds.contains(jExperiment.getId())) { mEntry.getExperiments().add(jExperiment); experimentIds.add(jExperiment.getId());
mEntry.getExperiments().add( experimentDescriptionConverter.fromJaxb( jExperiment ) ); if (mEntry.getExperiments().isEmpty()) { for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) { mEntry.getExperiments().addAll(mInteraction.getExperiments());
for ( uk.ac.ebi.intact.model.Experiment e : intactObject.getExperiments() ) { final ExperimentDescription experimentDesc = experimentConverter.intactToPsi( e ); entry.getExperiments().add( experimentDesc );
for ( psidev.psi.mi.xml.model.ExperimentDescription mExperiment : mEntry.getExperiments() ) { if (!experimentIds.contains(mExperiment.getId())) { jEntry.getExperimentList().getExperimentDescriptions().add( experimentDescriptionConverter.toJaxb( mExperiment ) );
for ( psidev.psi.mi.xml.model.ExperimentDescription mExperiment : mEntry.getExperiments() ) { if (!experimentIds.contains(mExperiment.getId())) { jEntry.getExperimentList().getExperimentDescriptions().add( experimentDescriptionConverter.toJaxb( mExperiment ) );