Method evaluate

src/openms/source/ANALYSIS/ID/HiddenMarkovModel.cpp:623–666

  }

  void HiddenMarkovModel::evaluate()
  {
    for (std::map<HMMState *, std::map<HMMState *, double> >::const_iterator it1 = count_trans_.begin(); it1 != count_trans_.end(); ++it1)
    {
#ifdef EVALUATE_DEBUG
      cerr <<  it1->first->getName() << endl;
#endif
      double sum(0);
      for (std::map<HMMState *, double>::const_iterator it2 = it1->second.begin(); it2 != it1->second.end(); ++it2)
      {
        if (count_trans_.find(it1->first) != count_trans_.end() &&
            count_trans_[it1->first].find(it2->first) != count_trans_[it1->first].end())
        {
          sum += count_trans_[it1->first][it2->first];
#ifdef EVALUATE_DEBUG
          cerr << it1->first->getName() << " " << it2->first->getName() << " ";

          //<< count_trans_[it1->first][it2->first] << endl;
          for (vector<double>::const_iterator it = train_count_trans_all_[it1->first][it2->first].begin(); it != train_count_trans_all_[it1->first][it2->first].end(); ++it)
          {
            cerr << *it << " ";
          }
          vector<double> data = train_count_trans_all_[it1->first][it2->first];
          std::sort(data.begin(), data.end());
          double mean = Math::mean(data.begin(), data.end());
          double variance = Math::variance(data.begin(), data.end(), mean);
          cerr << "mean=" << mean << ", variance=" << variance << endl;
#endif
        }
      }

      if (sum != 0)
      {
        for (std::map<HMMState *, double>::const_iterator it2 = it1->second.begin(); it2 != it1->second.end(); ++it2)
        {
          if (count_trans_.find(it1->first) != count_trans_.end() &&
              count_trans_[it1->first].find(it2->first) != count_trans_[it1->first].end())
          {
            trans_[it1->first][it2->first] = count_trans_[it1->first][it2->first] / sum;
          }
        }
      }
    }
  }

  void HiddenMarkovModel::setInitialTransitionProbability(const String & state, double prob)
  {