FeatureFinder_impl.h

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// $Maintainer: Clemens Groepl $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_IMPL_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_IMPL_H

#include <OpenMS/CONCEPT/Factory.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm_impl.h>

namespace OpenMS
{
  // This is documented in the declaration, see FeatureFinder.h
  template <class PeakType, class FeatureType>
  void FeatureFinder::run(const String & algorithm_name, MSExperiment<PeakType> & input_map, FeatureMap<FeatureType> & features, const Param & param, const FeatureMap<FeatureType> & seeds)
  {
    // Nothing to do if there is no data
    if ((algorithm_name != "mrm" && input_map.empty()) || (algorithm_name == "mrm" && input_map.getChromatograms().empty()))
    {
      features.clear(true);
      return;
    }

    // check input
    {
      // We need updated ranges => check number of peaks
      if (algorithm_name != "mrm" && input_map.getSize() == 0)
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "FeatureFinder needs updated ranges on input map. Aborting.");
      }

      // We need MS1 data only => check levels
      if (algorithm_name != "mrm" && (input_map.getMSLevels().size() != 1 || input_map.getMSLevels()[0] != 1))
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "FeatureFinder can only operate on MS level 1 data. Please do not use MS/MS data. Aborting.");
      }

      //Check if the peaks are sorted according to m/z
      if (!input_map.isSorted(true))
      {
        LOG_WARN << "Input map is not sorted by RT and m/z! This is done now, before applying the algorithm!" << std::endl;
        input_map.sortSpectra(true);
        input_map.sortChromatograms(true);
      }
      for (Size s = 0; s < input_map.size(); ++s)
      {
        if (input_map[s].empty())
          continue;
        if (input_map[s][0].getMZ() < 0)
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "FeatureFinder can only operate on spectra that contain peaks with positive m/z values. Filter the data accordingly beforehand! Aborting.");
        }
      }
    }

    // initialize
    if (algorithm_name != "mrm" && algorithm_name != "centroided")
    {
      // Resize peak flag vector
      flags_.resize(input_map.size());
      for (Size i = 0; i < input_map.size(); ++i)
      {
        flags_[i].assign(input_map[i].size(), UNUSED);
      }
    }

    // do the work
    if (algorithm_name != "none")
    {
      FeatureFinderAlgorithm<PeakType, FeatureType> * algorithm = Factory<FeatureFinderAlgorithm<PeakType, FeatureType> >::create(algorithm_name);
      algorithm->setParameters(param);
      algorithm->setData(input_map, features, *this);
      algorithm->setSeeds(seeds);
      algorithm->run();
      delete(algorithm);
    }

    if (algorithm_name != "mrm")   // mrm  works on chromatograms; the next section is only for conventional data
    {
      //report RT apex spectrum index and native ID for each feature
      for (Size i = 0; i < features.size(); ++i)
      {
        //index
        Size spectrum_index = input_map.RTBegin(features[i].getRT()) - input_map.begin();
        features[i].setMetaValue("spectrum_index", spectrum_index);
        //native id
        if (spectrum_index < input_map.size())
        {
          String native_id = input_map[spectrum_index].getNativeID();
          features[i].setMetaValue("spectrum_native_id", native_id);
        }
        else
        {
          std::cerr << "FeatureFinderAlgorithm_impl, line=" << __LINE__ << "; FixMe this cannot be, but happens" << std::endl;
        }
      }
    }
  }

} // namespace OpenMS

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_IMPL_H