/**
* Find closest gene to this marker
*
* <p>In case more than one 'closest' gene is found (e.g. two or more genes at the same distance).
* The following rules apply:
*
* <p>i) If many genes have the same 'closest distance', coding genes are preferred.
*
* <p>ii) If more than one coding gene has the same 'closet distance', a random gene is returned.
*
* @param inputInterval
*/
public Gene queryClosestGene(Marker inputInterval) {
int initialExtension = 1000;
String chrName = inputInterval.getChromosomeName();
Chromosome chr = genome.getChromosome(chrName);
if (chr == null) return null;
if (chr.size() > 0) {
// Extend interval to capture 'close' genes
for (int extend = initialExtension; extend < chr.size(); extend *= 2) {
int start = Math.max(inputInterval.getStart() - extend, 0);
int end = inputInterval.getEnd() + extend;
Marker extended = new Marker(chr, start, end, 1, "");
// Find all genes that intersect with the interval
Markers markers = query(extended);
Markers genes = new Markers();
int minDist = Integer.MAX_VALUE;
for (Marker m : markers) {
if (m instanceof Gene) {
int dist = m.distance(inputInterval);
if (dist < minDist) {
genes.add(m);
minDist = dist;
}
}
}
// Found something?
if (genes.size() > 0) {
// Find a gene having distance 'minDist'. Prefer coding genes
Gene minDistGene = null;
for (Marker m : genes) {
int dist = m.distance(inputInterval);
if (dist == minDist) {
Gene gene = (Gene) m;
if (minDistGene == null) minDistGene = gene;
else if (!minDistGene.isProteinCoding() && gene.isProteinCoding()) minDistGene = gene;
}
}
return minDistGene;
}
}
}
// Nothing found
return null;
}
