/** Create interval trees (forest) */
public void buildForest() {
intervalForest = new IntervalForest();
// Add all chromosomes to forest
if (useChromosomes) {
for (Chromosome chr : genome) intervalForest.add(chr);
}
// Add all genes to forest
for (Gene gene : genome.getGenes()) intervalForest.add(gene);
// ---
// Create (and add) up-down stream, splice sites, intergenic, etc
// ---
markers.add(createGenomicRegions());
// Add all 'markers' to forest (includes custom intervals)
intervalForest.add(markers);
// Build interval forest
intervalForest.build();
}
/**
* 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;
}
public int size() {
if (intervalForest == null) return 0;
return intervalForest.size();
}
/** Return a collection of intervals that intersect 'marker' */
public Markers query(Marker marker) {
return intervalForest.query(marker);
}