public void testCorrectness(
int i,
int cluster,
int clusterIndex1,
int clusterIndex2,
int[] shuffle,
int[] mergedClusterSites,
double[] lik1,
double[] lik2)
throws Exception {
// System.out.println("testCorrectness: ");
int[] tempWeights = new int[tempLikelihood.dataInput.get().getPatternCount()];
tempWeights[tempLikelihood.dataInput.get().getPatternIndex(mergedClusterSites[shuffle[i]])] = 1;
tempLikelihood.setPatternWeights(tempWeights);
double temp1 =
Math.exp(
tempLikelihood
.calculateLogP(
paramList.getParameter(clusterIndex1),
modelList.getParameter(clusterIndex1),
freqsList.getParameter(clusterIndex1),
new int[] {mergedClusterSites[shuffle[i]]})[0]);
double temp2 =
Math.exp(
tempLikelihood
.calculateLogP(
paramList.getParameter(clusterIndex2),
modelList.getParameter(clusterIndex2),
freqsList.getParameter(clusterIndex2),
new int[] {mergedClusterSites[shuffle[i]]})[0]);
if (temp1 != lik1[shuffle[i]] || temp2 != lik2[shuffle[i]]) {
System.out.println("temp1");
System.out.println("shuffle_i: " + shuffle[i]);
System.out.println("mergedClusterSites[shuffle]: " + mergedClusterSites[shuffle[i]]);
System.out.println("cluster: " + cluster);
System.out.println(+mergedClusterSites.length + " " + lik1.length);
for (int j = 0; j < lik1.length; j++) {
System.out.println("merged lik1: " + mergedClusterSites[j] + " " + lik1[j]);
}
for (int j = 0; j < lik2.length; j++) {
System.out.println("merged lik2: " + mergedClusterSites[j] + " " + lik2[j]);
}
throw new RuntimeException(
temp1 + " " + lik1[shuffle[i]] + " " + temp2 + " " + lik2[shuffle[i]]);
}
}
