InclusionExclusionList.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Alexandra Zerck, Chris Bielow $
// --------------------------------------------------------------------------
//
#pragma once

#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

namespace OpenMS
{
  class FeatureMap;

  class OPENMS_DLLAPI InclusionExclusionList :
    public DefaultParamHandler
  {
protected:
    struct IEWindow
    {
      IEWindow(const double RTmin, const double RTmax, const double MZ) :
        RTmin_(RTmin),
        RTmax_(RTmax),
        MZ_(MZ)
      {
      }

      double RTmin_;
      double RTmax_;
      double MZ_;
    };

    class WindowDistance_
    {
public:
      WindowDistance_(const double rt_bridge, const double mz_max, const bool mz_as_ppm) :
        rt_bridge_(rt_bridge),
        mz_max_(mz_max),
        mz_as_ppm_(mz_as_ppm)
      {
      }

      // measure of SIMILARITY (not distance, i.e. 1-distance)!!
      double operator()(const IEWindow& first, const IEWindow& second) const
      {
        // get MZ distance:
        double d_mz = fabs(first.MZ_ - second.MZ_);
        if (mz_as_ppm_)
        {
          d_mz = d_mz / first.MZ_ * 1e6;
        }
        if (d_mz > mz_max_) {return 0; }
        // mz is close enough ...

        // is RT overlapping?
        if (first.RTmin_ <= second.RTmin_ && second.RTmin_ <= first.RTmax_) return 1; // intersect #1

        if (first.RTmin_ <= second.RTmax_ && second.RTmax_ <= first.RTmax_) return 1; // intersect #2

        if (second.RTmin_ <= first.RTmin_ && first.RTmax_ <= second.RTmax_) return 1; // complete inclusion (only one case; the other is covered above)

        // when windows to not overlap at all:
        // ... are they at least close?
        if ((fabs(first.RTmin_ - second.RTmax_) <= rt_bridge_) ||
            (fabs(first.RTmax_ - second.RTmin_) <= rt_bridge_))
        {
          return 1;
        }

        // not overlapping...
        return 0;
      }

protected:

      double rt_bridge_; 
      double mz_max_; 
      bool mz_as_ppm_; 

    }; // end of WindowDistance_


    typedef std::vector<IEWindow> WindowList;

    void mergeOverlappingWindows_(WindowList& list) const;


    void writeToFile_(const String& out_path, const WindowList& windows) const;

public:
    InclusionExclusionList();



//     void loadTargets(FeatureMap& map, std::vector<IncludeExcludeTarget>& targets,TargetedExperiment& exp);

//     void loadTargets(std::vector<FASTAFile::FASTAEntry>& fasta_entries, std::vector<IncludeExcludeTarget>& targets,
//                      TargetedExperiment& exp, Size missed_cleavages = 0);


    void writeTargets(const std::vector<FASTAFile::FASTAEntry>& fasta_entries,
                      const String& out_path,
                      const IntList& charges,
                      const String rt_model_path);

    void writeTargets(const FeatureMap& map,
                      const String& out_path);

    void writeTargets(const std::vector<PeptideIdentification>& pep_ids,
                      const String& out_path,
                      const IntList& charges);

  };


}