FeatureMapping.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
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#pragma once

#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
#include <OpenMS/KERNEL/MSExperiment.h>

namespace OpenMS
{

  class OPENMS_DLLAPI FeatureMapping
      {
          public:

          class FeatureMappingInfo
          {
          public:
            std::vector<FeatureMap> feature_maps; // feature data
            KDTreeFeatureMaps kd_tree; // KDTree references into feature_maps to provides fast spatial queries
          };

          class FeatureToMs2Indices
          {
          public:
             std::map<const BaseFeature*, std::vector<size_t>> assignedMS2;
             std::vector<size_t> unassignedMS2;
          };

          static FeatureToMs2Indices assignMS2IndexToFeature(const MSExperiment& spectra,
                                                             const FeatureMappingInfo& fm_info,
                                                             const double& precursor_mz_tolerance,
                                                             const double& precursor_rt_tolerance,
                                                             bool ppm);

      };
} // namespace OpenMS