public void EstimateParameters(string outcome, string path)
{
_transition = new Transition(_states);
_transition.Estimate(path);
_emission = new Emission(_states, _alphabet);
_emission.Estimate(outcome, path);
}
public void BuildProfile(List <string> alignment, double theta)
{
// build profile matrix
List <ProfileState> profile = new List <ProfileState>();
for (int i = 0; i < alignment[0].Length; ++i)
{
ProfileState ps = new ProfileState();
for (int j = 0; j < alignment.Count; ++j)
{
ps.Add(alignment[j][i]);
}
ps.gray = ps.Pr('-') > theta;
profile.Add(ps);
}
// build states
_states.Add("S");
_states.Add("I0");
int m = 1;
for (int i = 0; i < profile.Count; ++i)
{
if (!profile[i].gray)
{
_states.Add("M" + m.ToString());
_states.Add("D" + m.ToString());
_states.Add("I" + m.ToString());
++m;
}
}
_states.Add("E");
// build transition matrix
_transition = new Transition(_states);
// build emission matrix
_emission = new Emission(_states, _alphabet);
}
public void ParseEmission(List <string> matrix)
{
_emission = new Emission(_states, _alphabet);
_emission.Parse(matrix);
}