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.error("Taxonomy: " + ncbiId + " of organism: " + organism + ", interactor: " + interactor.getId() + " does not belong to '" + name + "'; the name will be removed. "
psiIndex.addInteractor( interactor.getId(), isr );
psiIndex.addInteractor( interactor.getId(), isr );
throw new TabConversionException("Could not find any identifiers for interactor " + xmlInteractor.getId());
private void processEdge(final Participant source, final Participant target, final Interaction interaction, final Collection<Participant> nodes, CyTable nodeTable, CyTable edgeTable) { Interactor sourceInteractor = source.getInteractor(); Interactor targetInteractor = target.getInteractor(); if (sourceInteractor == null || targetInteractor == null) { return; } final CyNode sourceCyNode = id2NodeMap.get(sourceInteractor.getId()); final CyNode targetCyNode = id2NodeMap.get(targetInteractor.getId()); // PPI does not have directinarity final CyEdge edge = network.addEdge(sourceCyNode, targetCyNode, false); // TODO: what's the best value for interaction? edgeTable.getRow(edge.getSUID()).set(CyEdge.INTERACTION, "pp"); final String sourceName = nodeTable.getRow(sourceCyNode.getSUID()).get(CyNetwork.NAME, String.class); final String targetName = nodeTable.getRow(targetCyNode.getSUID()).get(CyNetwork.NAME, String.class); edgeTable.getRow(edge.getSUID()).set(CyNetwork.NAME, sourceName + " (pp) " + targetName); mapNames(edgeTable, edge.getSUID(), interaction.getNames(), null); mapAttributes(interaction.getAttributes(), edgeTable, edge.getSUID()); final Collection<InteractionType> types = interaction.getInteractionTypes(); mapInteractionType(types, edgeTable, edge.getSUID()); }
LOG.warn("EntryMapper.createParticipant(): skip for interactor: " + interactor.getId() + " that has type: " + entityType + ", participant:" + participant.getId() + ")."); String newUri = baseUri + "_" + (counter++); LOG.warn("A different " + er.getModelInterface().getSimpleName() + ", URI=" + baseUri + ", was found; for interactor:" + interactor.getId() + ", a new ("+entityReferenceClass.getSimpleName()+") URI will be used:" + newUri); baseUri = newUri;
participantIds.add(mParticipant.getInteractor().getId());
jExperimentalInteractor.setInteractorRef( mExperimentalInteractor.getInteractor().getId() );
jExperimentalInteractor.setInteractorRef( mExperimentalInteractor.getInteractor().getId() );
jInteractor.setId( mInteractor.getId() );
participant.setInteractor(interactor); } else { participant.setInteractorRef(new InteractorRef(interactor.getId()));
jInteractor.setId( mInteractor.getId() );
Interactor interactor = experimentalInteractor.getInteractor(); LOG.debug("createBiopaxEntity, participant: " + participant.getId() + ", exp. interactor: " + interactor.getId()); Entity expEntity = createParticipant(participant, interactor, avail, pro, true); assert expEntity!=null : "expEntity is null";
return; final int id = interactor.getId();
jParticipant.setInteractorRef( mParticipant.getInteractorRef().getRef() ); else jParticipant.setInteractorRef( mParticipant.getInteractor().getId() );
jParticipant.setInteractorRef( mParticipant.getInteractorRef().getRef() ); else jParticipant.setInteractorRef( mParticipant.getInteractor().getId() );