public Map<String, List<String>> getMethodToPubmed() { Map<String, List<String>> methodToPubmed = new HashMap<String, List<String>>(); for (Map.Entry<MethodTypePair, List<String>> entry : methodTypePairListMap.entrySet()){ MethodTypePair pair = entry.getKey(); if (methodToPubmed.containsKey(pair.getMethod()) && pair.getMethod() != null){ methodToPubmed.get(pair.getMethod()).addAll(entry.getValue()); } else { if (pair.getMethod() != null){ methodToPubmed.put(pair.getMethod(), entry.getValue()); } } } return methodToPubmed; }
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; }
public boolean equals(Object o) { if (this == o) { return true; } if (o == null || getClass() != o.getClass()) { return false; } MethodTypePair pair2 = (MethodTypePair) o; if ((method == null && pair2.getMethod() != null) || (method != null && pair2.getMethod() == null)){ return false; } else if (method != null && !method.equalsIgnoreCase(pair2.getMethod())){ return false; } if ((type == null && pair2.getType() != null) || (type != null && pair2.getType() == null)){ return false; } else if (type != null && !type.equalsIgnoreCase(pair2.getType())){ return false; } return true; }
private int computeForBinaryInteractionNumberOfExperimentsHavingDetectionMethod(String method, ExportContext context, BinaryInteraction interaction, Set<String> validIntactIds){ Set<String> intactAcs = FilterUtils.extractIntactAcFrom(interaction.getInteractionAcs()); Map<MethodTypePair, List<String>> invertedMap = WriterUtils.invertMapFromKeySelection(context.getInteractionToMethod_type(), intactAcs); int numberOfExperiment = 0; for (Map.Entry<MethodTypePair, List<String>> entry : invertedMap.entrySet()){ if (entry.getKey().getMethod().equals(method)){ for (String intactId : entry.getValue()){ if (!context.getSpokeExpandedInteractions().contains(intactId)){ numberOfExperiment ++; validIntactIds.add(intactId); } } } } return numberOfExperiment; }
String detectionMI = pair.getMethod();
if (!context.getSpokeExpandedInteractions().contains(ac)){ String method = context.getInteractionToMethod_type().get(ac).getMethod();
String detectionMI = pair.getMethod();
List<String> uniquePublications = eI.getMethodTypePairListMap().get(methodType); String method = methodType.getMethod(); String type = methodType.getType();