System.out.println(a.toStringVisual() + "\n"+cr);
assertTrue(a.aligned(0, 0));
System.out.println(hmm.backtrace);
hmm = new HMM(tc, ac);
hmm.buildHMMTables(pp);
cr.reset();
a = hmm.viterbiAlign(pp, cr);
double ce2 = cr.getCrossEntropy();
// perplexity should decrease!
assertTrue(ce1 > ce2);
assert(tc.get(1,1) > 0.0f);