/**
* 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);
}
