void alignSeqs(ProbabilisticModelPtr model, SequenceList seqs1, SequenceList seqs2, vector<std::string> names1, vector<std::string> names2, ostream & output, ostream & states_output)
{
if(seqs1.size() != seqs2.size()) {
cerr << "Both files must to have the same amount of sequences." << endl;
exit(-1);
}
for(int i = 0; i < (int)seqs1.size(); i++)
{
Sequence s1,s2,path;
std::stringstream aux1,aux2,aux3;
vector<Matrix> a;
model->pairDecodable()->viterbi(seqs1[i], seqs2[i], path, s1, s2, a);
aux1 << names1[i] << "_" << names2[i] << "_al1" ;
aux2 << names1[i] << "_" << names2[i] << "_al2" ;
aux3 << names1[i] << "_" << names2[i] << "_path" ;
SequenceEntry out1(model->alphabet());
SequenceEntry out2(model->alphabet());
SequenceEntry out3(model->pairDecodable()->getStateNames());
out1.setName(aux1.str());
out2.setName(aux2.str());
out3.setName(aux3.str());
out1.setSequence(s1);
out2.setSequence(s2);
out3.setSequence(path);
output << out1;
output << out2 << endl;
states_output << out3 << endl;
}
}
unsigned int NRows(void) const { return sequences->size(); }
