private int computeNumberOfExperimentsHavingDetectionMethod(String method, ExportContext context, EncoreInteraction interaction, Set<String> validIntactIds){ Map<MethodTypePair, List<String>> invertedMap = WriterUtils.invertMapFromKeySelection(context.getInteractionToMethod_type(), interaction.getExperimentToPubmed().keySet()); int numberOfExperiment = 0; for (Map.Entry<MethodTypePair, List<String>> entry : invertedMap.entrySet()){ if (entry.getKey().getMethod().equals(method)){ numberOfExperiment += entry.getValue().size(); validIntactIds.addAll(entry.getValue()); } } return numberOfExperiment; }
List<String> typesToRemove = new ArrayList(encore.getTypeToPubmed().keySet()); Collection<String> validInteractions = CollectionUtils.subtract(encore.getExperimentToPubmed().keySet(), wrongInteractions); String pubmedId = encore.getExperimentToPubmed().get(interactionAc); encore.getExperimentToPubmed().remove(interactionAc); encore.getExperimentToDatabase().remove(interactionAc);
Map<String, String> interactionToPubmed = interaction.getExperimentToPubmed();
@Override public boolean canExportEncoreInteraction(EncoreInteraction encore, ExportContext context) throws UniprotExportException { double score = FilterUtils.getMiClusterScoreFor(encore); if (score >= positive_export_threshold){ if (encore.getExperimentToDatabase() == null){ throw new UniprotExportException("The interaction " + encore.getId() + ":" + encore.getInteractorA() + "-" + encore.getInteractorB() +" doesn't have any references to IntAct."); } Set<String> intactInteractions = new HashSet<String>(); intactInteractions.addAll(encore.getExperimentToPubmed().keySet()); if (intactInteractions.isEmpty()){ throw new UniprotExportException("The interaction " + encore.getId() + ":" + encore.getInteractorA() + "-" + encore.getInteractorB() +" doesn't have any references to IntAct."); } for (String ac : intactInteractions){ if (!context.getSpokeExpandedInteractions().contains(ac)){ String type = context.getInteractionToMethod_type().get(ac).getType(); if (!type.equals(COLOCALIZATION)){ logger.info("The interaction " + encore.getId() + " passed the export rules with score = " + score); return true; } } } } return false; }
@Override public boolean canExportNegativeEncoreInteraction(EncoreInteraction encore, ExportContext context, ExportedClusteredInteractions positiveInteractions) throws UniprotExportException { boolean isElgibleForExport = ExporterUtils.isNegativeInteractionEligibleForUniprotExport(encore, positiveInteractions); if (isElgibleForExport){ double score = FilterUtils.getMiClusterScoreFor(encore); if (score >= negative_export_threshold){ if (encore.getExperimentToDatabase() == null){ throw new UniprotExportException("The interaction " + encore.getId() + ":" + encore.getInteractorA() + "-" + encore.getInteractorB() +" doesn't have any references to IntAct."); } Set<String> intactInteractions = new HashSet<String>(); intactInteractions.addAll(encore.getExperimentToPubmed().keySet()); if (intactInteractions.isEmpty()){ throw new UniprotExportException("The interaction " + encore.getId() + ":" + encore.getInteractorA() + "-" + encore.getInteractorB() +" doesn't have any references to IntAct."); } for (String ac : intactInteractions){ if (!context.getSpokeExpandedInteractions().contains(ac)){ String type = context.getInteractionToMethod_type().get(ac).getType(); if (!type.equals(COLOCALIZATION)){ logger.info("The negative interaction " + encore.getId() + " passed the export rules with score = " + score); return true; } } } } } return false; }
Set<String> interactionAcs = interaction.getExperimentToPubmed().keySet(); Set<String> goRefs = collectGoComponentRefsFrom(interactionAcs, context);
Set<String> interactionAcs = interaction.getExperimentToPubmed().keySet(); Set<String> goRefs = collectGoComponentRefsFrom(interactionAcs, context);
int numberEvidences = interaction.getExperimentToPubmed().size();
mappingEcoreInteraction.addExperimentToPubmed(encoreInteraction.getExperimentToPubmed()); mappingEcoreInteraction.addExperimentToDatabase(encoreInteraction.getExperimentToDatabase()); processMethodAndType(encoreInteraction, mappingEcoreInteraction);