/**
* Choose region to be affected by this conversion.
*
* @param conv Conversion object where these sites are stored.
* @return log probability density of chosen attachment.
*/
public double drawAffectedRegion(Conversion conv) {
double logP = 0.0;
// Total effective number of possible start sites
double alpha =
acg.getTotalSequenceLength() + acg.getLoci().size() * deltaInput.get().getValue();
// Draw location of converted region.
int startSite = -1;
int endSite;
Locus locus = null;
double u = Randomizer.nextDouble() * alpha;
for (Locus thisLocus : acg.getLoci()) {
if (u < deltaInput.get().getValue() + thisLocus.getSiteCount()) {
locus = thisLocus;
if (u < deltaInput.get().getValue()) {
startSite = 0;
logP += Math.log(deltaInput.get().getValue() / alpha);
} else {
startSite = (int) (u - deltaInput.get().getValue());
logP += Math.log(1.0 / alpha);
}
break;
}
u -= deltaInput.get().getValue() + thisLocus.getSiteCount();
}
if (locus == null)
throw new IllegalStateException(
"Programmer error: " + "loop in drawAffectedRegion() fell through.");
endSite = startSite + (int) Randomizer.nextGeometric(1.0 / deltaInput.get().getValue());
endSite = Math.min(endSite, locus.getSiteCount() - 1);
// Probability of end site:
double probEnd =
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), endSite - startSite)
/ deltaInput.get().getValue();
// Include probability of going past the end:
if (endSite == locus.getSiteCount() - 1)
probEnd +=
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), locus.getSiteCount() - startSite);
logP += Math.log(probEnd);
conv.setLocus(locus);
conv.setStartSite(startSite);
conv.setEndSite(endSite);
return logP;
}
/**
* Calculate probability of choosing region affected by the given conversion under the
* ClonalOrigin model.
*
* @param conv conversion region is associated with
* @return log probability density
*/
public double getAffectedRegionProb(Conversion conv) {
double logP = 0.0;
// Total effective number of possible start sites
double alpha =
acg.getTotalSequenceLength() + acg.getLoci().size() * deltaInput.get().getValue();
// Calculate probability of converted region.
if (conv.getStartSite() == 0) logP += Math.log((deltaInput.get().getValue() + 1) / alpha);
else logP += Math.log(1.0 / alpha);
// Probability of end site:
double probEnd =
Math.pow(1.0 - 1.0 / deltaInput.get().getValue(), conv.getEndSite() - conv.getStartSite())
/ deltaInput.get().getValue();
// Include probability of going past the end:
if (conv.getEndSite() == conv.getLocus().getSiteCount() - 1)
probEnd +=
Math.pow(
1.0 - 1.0 / deltaInput.get().getValue(),
conv.getLocus().getSiteCount() - conv.getStartSite());
logP += Math.log(probEnd);
return logP;
}