/** 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);
}
/**
* Is the chromosome missing in this marker?
*
* @param marker
* @return
*/
boolean isChromosomeMissing(Marker marker) {
// Missing chromosome in marker?
if (marker.getChromosome() == null) return true;
// Missing chromosome in genome?
String chrName = marker.getChromosomeName();
Chromosome chr = genome.getChromosome(chrName);
if (chr == null) return true;
// Chromosome length is 1 or less?
if (chr.size() < 1) return true;
// Tree not found in interval forest?
if (!intervalForest.hasTree(chrName)) return true;
// OK, we have the chromosome
return false;
}