for (int s_next = 0; s_next < numStates; s_next++) {
//System.out.println(" s_next="+s_next + " b(j+1,s_next)="+ betas.get(j+1, s_next) + " * " +
// hmm.getTransitionProb(s, s_next) + " * " + hmm.getEmissionProb(s_next, j));
float trans = getTransitionProb(s, s_next);
if (use_m1) {
if (s <= l && s > 0 && m1a.aligned(j-1, s-1))
trans = m1boost;
else
trans *= m1penalty;
}
beta += betas.get(j+1, s_next) *