private void computeTransitionMatrices(
Beagle beagle, int[][] probabilityIndices, double[][] edgeLengths, int[] counts) {
Timer timer;
if (MEASURE_RUN_TIME) {
timer = new Timer();
timer.start();
}
if (DEBUG) {
System.out.print("Computing matrices:");
}
for (int i = 0; i < eigenCount; i++) {
if (DEBUG) {
for (int j = 0; j < counts[i]; j++) {
// System.out.print(" " + probabilityIndices[i][j]);
System.out.print(" " + probabilityIndices[i][j] + " (" + edgeLengths[i][j] + ")");
}
}
if (counts[i] > 0) {
beagle.updateTransitionMatrices(
eigenBufferHelper.getOffsetIndex(i),
probabilityIndices[i],
null, // firstDerivativeIndices
null, // secondDerivativeIndices
edgeLengths[i],
counts[i]);
}
}
if (DEBUG) {
System.out.println();
}
if (MEASURE_RUN_TIME) {
timer.stop();
double timeInSeconds = timer.toSeconds();
updateTime += timeInSeconds;
}
} // END: computeTransitionMatrices
