}
}
public IHMMParameters parameters(int nstates, boolean _isReversible, boolean _isStationary)
{
IHMMParameters par = new HMMParameters(nstates, _isReversible, _isStationary);
// initialize transition matrix
IDoubleArray T0 = doublesNew.matrix(nstates,nstates);
doubles.fill(T0, 1.0/(double)nstates);
par.setTransitionMatrix(T0);
return par;
}