// public CoalescentEventsStatistic(CoalescentIntervalProvider coalescent, TreeModel treeModel) {
public CoalescentEventsStatistic(CoalescentIntervalProvider coalescent) {
this.coalescent = coalescent;
// this.treeModel = treeModel;
this.coalescentEvents = 0;
if (DEBUG) {
System.err.println(
"CoalescentIntervalDimension: " + coalescent.getCoalescentIntervalDimension());
}
if (coalescent instanceof GMRFSkyrideLikelihood) {
this.coalescentEvents = coalescent.getCoalescentIntervalDimension();
} else {
for (int i = 0; i < coalescent.getCoalescentIntervalDimension(); i++) {
// Not yet implemented for the skygrid model
if (coalescent.getCoalescentIntervalType(i) == IntervalType.COALESCENT) {
coalescentEvents++;
}
}
}
// System.err.println("Number of coalescent events: " + this.coalescentEvents);
this.coalescentValues = new double[coalescentEvents];
if (DEBUG) {
System.err.println("CoalescentEventsStatistic constructor: " + this.coalescentEvents);
}
}
public double getStatisticValue(int i) {
// System.err.println(treeModel);
// i will go from 0 to getDimension()
if (i == 0) {
// reset array of coalescent events
for (int j = 0; j < coalescentValues.length; j++) {
coalescentValues[j] = 0.0;
}
// recalculate everything
int counter = 0;
for (int j = 0; j < coalescent.getCoalescentIntervalDimension(); j++) {
if (coalescent instanceof GMRFSkyrideLikelihood) {
this.coalescentValues[counter] =
((GMRFSkyrideLikelihood) coalescent).getSufficientStatistics()[j];
} else {
// System.err.println(coalescent.getCoalescentIntervalType(j) + " " +
// coalescent.getCoalescentInterval(j));
if (coalescent.getCoalescentIntervalType(j) == IntervalType.COALESCENT) {
if (LOG_COMBINATIONS) {
this.coalescentValues[counter] +=
coalescent.getCoalescentInterval(j)
* (coalescent.getCoalescentIntervalLineageCount(j)
* (coalescent.getCoalescentIntervalLineageCount(j) - 1.0))
/ 2.0;
// System.err.println("interval length: " + coalescent.getCoalescentInterval(j));
// System.err.println("lineage count: " +
// coalescent.getCoalescentIntervalLineageCount(j));
// System.err.println("factorial: " +
// (coalescent.getCoalescentIntervalLineageCount(j)*coalescent.getCoalescentIntervalLineageCount(j)-1.0)/2.0);
// System.err.println("counter " + counter + ": " + this.coalescentValues[counter] +
// "\n");
// this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
// this.coalescentValues[counter] =
// (coalescent.getCoalescentIntervalLineageCount(j)*coalescent.getCoalescentIntervalLineageCount(j)-1.0)/(2.0*this.coalescentValues[counter]);
} else {
this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
}
counter++;
} else if (!FULL_FINAL_INTERVAL) {
if (coalescent.getCoalescentIntervalType(j) == IntervalType.SAMPLE && counter != 0) {
if (LOG_COMBINATIONS) {
this.coalescentValues[counter] +=
coalescent.getCoalescentInterval(j)
* (coalescent.getCoalescentIntervalLineageCount(j)
* (coalescent.getCoalescentIntervalLineageCount(j) - 1.0))
/ 2.0;
// System.err.println("interval length: " + coalescent.getCoalescentInterval(j));
// System.err.println("lineage count: " +
// coalescent.getCoalescentIntervalLineageCount(j));
// System.err.println("factorial: " +
// (coalescent.getCoalescentIntervalLineageCount(j)*coalescent.getCoalescentIntervalLineageCount(j)-1.0)/2.0);
// System.err.println("counter " + counter + ": " + this.coalescentValues[counter] +
// "\n");
// this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
} else {
this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
}
}
} else {
if (coalescent.getCoalescentIntervalType(j) == IntervalType.SAMPLE) {
if (LOG_COMBINATIONS) {
// System.err.println("interval length: " + coalescent.getCoalescentInterval(j));
// System.err.println("lineage count: " +
// coalescent.getCoalescentIntervalLineageCount(j));
// System.err.println("factorial: " +
// (coalescent.getCoalescentIntervalLineageCount(j)*coalescent.getCoalescentIntervalLineageCount(j)-1.0)/2.0);
// System.err.println("counter " + counter + ": " + this.coalescentValues[counter] +
// "\n");
this.coalescentValues[counter] +=
coalescent.getCoalescentInterval(j)
* (coalescent.getCoalescentIntervalLineageCount(j)
* (coalescent.getCoalescentIntervalLineageCount(j) - 1.0))
/ 2.0;
// this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
} else {
this.coalescentValues[counter] += coalescent.getCoalescentInterval(j);
}
}
}
}
}
}
/*for (int j = 0; j < this.coalescentEvents; j++) {
System.err.println(this.coalescentValues[j]);
}
System.exit(0);*/
if (RETURN_RECIPROCAL) {
return 1.0 / this.coalescentValues[i];
} else {
return this.coalescentValues[i];
}
}