How to use

getBinaryInteractionForScoring

method

in

uk.ac.ebi.enfin.mi.cluster.Encore2Binary

@Override
public Map<Integer, BinaryInteraction<Interactor>> getBinaryInteractionCluster() {
  Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames());
  Map<Integer, BinaryInteraction<Interactor>> binaryInteractionCluster = new HashMap<Integer, BinaryInteraction<Interactor>>();
  for(Integer mappingId:getInteractionMapping().keySet()){
    EncoreInteraction eI = getInteractionMapping().get(mappingId);
    if (eI != null){
      BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI);
      binaryInteractionCluster.put(mappingId, bI);
    }
  }
  return binaryInteractionCluster;
}

@Override
public void saveResultsInMitab(String fileName) throws IOException {
  PsimiTabWriter writer = new PsimiTabWriter();
  File file = new File(fileName);
  BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file));
  try{
    Map<Integer, EncoreInteraction> interactionMapping = getInteractionMapping();
    Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames());
    for(Integer mappingId:interactionMapping.keySet()){
      EncoreInteraction eI = interactionMapping.get(mappingId);
      BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI);
      writer.write(bI, bufferedWriter);
    }
  }
  finally {
    bufferedWriter.close();
  }
}

fstream.flush();
BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI);
writer.write(bI, mitabWriter);

/**
 * Save clustered results including scores in mitab files
 * @param interactionClusterScore
 */
private void saveMitabOutputFile(InteractionClusterScore interactionClusterScore) throws IOException, PsimiTabException {
  /* Retrieve results */
  Map<Integer, EncoreInteraction> interactionMapping = interactionClusterScore.getInteractionMapping();
  PsimiTabWriter writer = new PsimiTabWriter(PsimiTabVersion.v2_5);
  BufferedWriter outputWriter = new BufferedWriter(new FileWriter(mitabOutputFile));
  try{
    if (header){
      writer.writeMitabHeader(outputWriter);
    }
    Encore2Binary iConverter = new Encore2Binary(interactionClusterScore.getMappingIdDbNames());
    for(Integer mappingId:interactionMapping.keySet()){
      EncoreInteraction eI = interactionMapping.get(mappingId);
      BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI);
      writer.write(bI, outputWriter);
    }
  }
  finally {
    outputWriter.close();
  }
}