/**
* Sets the partials from a sequence in an alignment.
*
* @param beagle beagle
* @param patternList patternList
* @param sequenceIndex sequenceIndex
* @param nodeIndex nodeIndex
*/
protected final void setPartials(
Beagle beagle, PatternList patternList, int sequenceIndex, int nodeIndex) {
double[] partials = new double[patternCount * stateCount * categoryCount];
boolean[] stateSet;
int v = 0;
for (int i = 0; i < patternCount; i++) {
int state = patternList.getPatternState(sequenceIndex, i);
stateSet = dataType.getStateSet(state);
for (int j = 0; j < stateCount; j++) {
if (stateSet[j]) {
partials[v] = 1.0;
} else {
partials[v] = 0.0;
}
v++;
}
}
// if there is more than one category then replicate the partials for each
int n = patternCount * stateCount;
int k = n;
for (int i = 1; i < categoryCount; i++) {
System.arraycopy(partials, 0, partials, k, n);
k += n;
}
beagle.setPartials(nodeIndex, partials);
}
/** Stores the additional state other than model components */
protected void storeState() {
partialBufferHelper.storeState();
substitutionModelDelegate.storeState();
if (useScaleFactors || useAutoScaling) { // Only store when actually used
scaleBufferHelper.storeState();
System.arraycopy(
scaleBufferIndices, 0, storedScaleBufferIndices, 0, scaleBufferIndices.length);
// storedRescalingCount = rescalingCount;
}
super.storeState();
}
/** Sets the partials from a sequence in an alignment. */
protected final void setPartials(Beagle beagle, TipStatesModel tipStatesModel, int nodeIndex) {
double[] partials = new double[patternCount * stateCount * categoryCount];
tipStatesModel.getTipPartials(nodeIndex, partials);
// if there is more than one category then replicate the partials for each
int n = patternCount * stateCount;
int k = n;
for (int i = 1; i < categoryCount; i++) {
System.arraycopy(partials, 0, partials, k, n);
k += n;
}
beagle.setPartials(nodeIndex, partials);
}