OpenSwathHelper.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/CONCEPT/LogStream.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathHelper
  {
 
public:
 
    static String computePrecursorId(const String& transition_group_id, int isotope)
    {
      return transition_group_id + "_Precursor_i" + String(isotope);
    }
 
    static String computeTransitionGroupId(const String& precursor_id)
    {
      std::vector<String> substrings;
      precursor_id.split("_", substrings);
 
      if (substrings.size() == 3) return substrings[0];
      else if (substrings.size() > 3)
      {
        String r;
        for (Size k = 0; k < substrings.size() - 2; k++) r += substrings[k] + "_";
        return r.prefix(r.size() - 1);
      }
      return "";
    }
 
    static void selectSwathTransitions(const OpenMS::TargetedExperiment& targeted_exp,
                                       OpenMS::TargetedExperiment& selected_transitions,
                                       double min_upper_edge_dist,
                                       double lower, double upper);
 
    static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment& targeted_exp,
                                       OpenSwath::LightTargetedExperiment& selected_transitions,
                                       double min_upper_edge_dist,
                                       double lower, double upper);
    static void selectSwathTransitionsPasef(const OpenSwath::LightTargetedExperiment& transition_exp, std::vector<int>& tr_win_map,
                         double min_upper_edge_dist, const std::vector< OpenSwath::SwathMap > & swath_maps);
 
    static void checkSwathMap(const OpenMS::PeakMap& swath_map,
                              double& lower, double& upper, double& center);
 
    template <class TargetedExperimentT>
    static bool checkSwathMapAndSelectTransitions(const OpenMS::PeakMap& exp,
                                                  const TargetedExperimentT& targeted_exp,
                                                  TargetedExperimentT& selected_transitions,
                                                  double min_upper_edge_dist)
    {
      if (exp.empty() || exp[0].getPrecursors().empty())
      {
        std::cerr << "WARNING: File " << exp.getLoadedFilePath()
                  << " does not have any experiments or any precursors. Is it a SWATH map? "
                  << "I will move to the next map."
                  << std::endl;
        return false;
      }
      double upper, lower, center;
      OpenSwathHelper::checkSwathMap(exp, lower, upper, center);
      OpenSwathHelper::selectSwathTransitions(targeted_exp, selected_transitions, min_upper_edge_dist, lower, upper);
      if (selected_transitions.getTransitions().size() == 0)
      {
        std::cerr << "WARNING: For File " << exp.getLoadedFilePath()
                  << " no transition were within the precursor window of " << lower << " to " << upper
                  << std::endl;
        return false;
      }
      return true;
 
    }
 
    static std::pair<double,double> estimateRTRange(const OpenSwath::LightTargetedExperiment & exp);
 
    static OpenSwath::LightTargetedExperiment sampleExperiment(
      const OpenSwath::LightTargetedExperiment & exp,
      Size bins,
      Size peptides_per_bin,
      unsigned int seed = 0,
      bool sort_by_intensity = false,
      double top_fraction = 1.0,
      const std::unordered_set<std::string> & priority_peptides = std::unordered_set<std::string>());
 
    static std::map<std::string, double> simpleFindBestFeature(const OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType & transition_group_map, 
                                                               bool useQualCutoff = false,
                                                               double qualCutoff = 0.0);
  };
 
} // namespace OpenMS