/** * Sets the partials from a sequence in an alignment. * * @param beagle beagle * @param patternList patternList * @param sequenceIndex sequenceIndex * @param nodeIndex nodeIndex */ protected final void setStates( Beagle beagle, PatternList patternList, int sequenceIndex, int nodeIndex) { int i; int[] states = new int[patternCount]; for (i = 0; i < patternCount; i++) { states[i] = patternList.getPatternState(sequenceIndex, i); } beagle.setTipStates(nodeIndex, states); }