public void updateSubstitutionModels(Beagle beagle) {
for (int i = 0; i < eigenCount; i++) {
eigenBufferHelper.flipOffset(i);
EigenDecomposition ed = substitutionModelList.get(i).getEigenDecomposition();
beagle.setEigenDecomposition(
eigenBufferHelper.getOffsetIndex(i),
ed.getEigenVectors(),
ed.getInverseEigenVectors(),
ed.getEigenValues());
}
}
public void flipMatrixBuffer(int branchIndex) {
matrixBufferHelper.flipOffset(branchIndex);
}