/**
  * Create a string to serialize to a file
  *
  * @return
  */
 @SuppressWarnings("unchecked")
 @Override
 public String serializeSave(MarkerSerializer markerSerializer) {
   return super.serializeSave(markerSerializer) //
       + "\t"
       + markerSerializer.save((Collection<Marker>) subIntervals.values()) //
   ;
 }
  /** Save nextprot markers */
  void save() {
    String nextProtBinFile = config.getDirDataVersion() + "/nextProt.bin";
    if (verbose) Timer.showStdErr("Saving database to file '" + nextProtBinFile + "'");

    // Add chromosomes
    HashSet<Chromosome> chromos = new HashSet<Chromosome>();
    for (Marker m : markers) chromos.add(m.getChromosome());

    // Create a set of all markers to be saved
    Markers markersToSave = new Markers();
    markersToSave.add(genome);
    for (Chromosome chr : chromos) markersToSave.add(chr);
    for (Marker m : markers) markersToSave.add(m);

    // Save
    MarkerSerializer markerSerializer = new MarkerSerializer();
    markerSerializer.save(nextProtBinFile, markersToSave);
  }
 /** Save predictor to a binary file (specified by the configuration) */
 public void save(Config config) {
   String databaseFile = config.getFileSnpEffectPredictor();
   MarkerSerializer markerSerializer = new MarkerSerializer();
   markerSerializer.save(databaseFile, this);
 }