CompNovoIdentificationBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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: Andreas Bertsch $
// --------------------------------------------------------------------------
 
 
#pragma once
 
// OpenMS includes
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringBase.h>
 
// stl includes
#include <vector>
#include <map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI CompNovoIdentificationBase :
    public DefaultParamHandler
  {
 
public:
 
    CompNovoIdentificationBase();
 
    CompNovoIdentificationBase(const CompNovoIdentificationBase & source);
 
    ~CompNovoIdentificationBase() override;
 
    CompNovoIdentificationBase & operator=(const CompNovoIdentificationBase & source);
 
    virtual void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) = 0;
 
    typedef CompNovoIonScoringBase::IonScore IonScore;
 
protected:
 
    void updateMembers_() override;
 
    void filterPermuts_(std::set<String> & permut) const;
 
    void selectPivotIons_(std::vector<Size> & pivots, Size left, Size right, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec, double precursor_weight, bool full_range = false);
 
    void filterDecomps_(std::vector<MassDecomposition> & decomps);
 
    void getDecompositions_(std::vector<MassDecomposition> & decomps, double mass, bool no_caching = false);
 
    static void permute_(const String& prefix, String s, std::set<String> & permutations);
 
    Size countMissedCleavagesTryptic_(const String & peptide) const;
 
    void getCIDSpectrumLight_(PeakSpectrum & spec, const String & sequence, double prefix, double suffix);
 
    void getCIDSpectrum_(PeakSpectrum & spec, const String & sequence, Size charge, double prefix = 0.0, double suffix = 0.0);
 
    void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);
 
    void initIsotopeDistributions_();
 
    void windowMower_(PeakSpectrum & spec, double windowsize, Size no_peaks);
 
    double compareSpectra_(const PeakSpectrum & s1, const PeakSpectrum & s2) const;
 
    AASequence getModifiedAASequence_(const String & sequence);
 
    String getModifiedStringFromAASequence_(const AASequence & sequence);
 
    std::map<char, const Residue *> name_to_residue_;
 
    std::map<const Residue *, char> residue_to_name_;
 
    std::map<char, double> aa_to_weight_;
 
    MassDecompositionAlgorithm mass_decomp_algorithm_;
 
    double min_aa_weight_{};
 
    ZhangSimilarityScore zhang_;
 
    std::map<Size, std::map<Size, std::set<String> > > subspec_to_sequences_;
 
    Size max_number_aa_per_decomp_;
 
    bool tryptic_only_;
 
    double fragment_mass_tolerance_;
 
    Size max_number_pivot_;
 
    double decomp_weights_precision_;
 
    double max_mz_;
 
    double min_mz_;
 
    double max_decomp_weight_;
 
    Size max_subscore_number_;
 
    Size max_isotope_;
 
    std::map<double, std::vector<MassDecomposition> > decomp_cache_;
 
    std::map<String, std::set<String> > permute_cache_;
 
  private:
    std::map<Size, std::vector<double> > isotope_distributions_;
 
public:
 
    class Permut
    {
private:
 
      Permut() :
        score_(0)
      {
      }
 
public:
 
      Permut(const std::set<String>::const_iterator & permut, double s) :
        permut_(permut),
        score_(s)
      {
      }
 
      Permut(const Permut & rhs) = default;
      virtual ~Permut() = default;
 
      Permut & operator=(const Permut & rhs)
      {
        if (&rhs != this)
        {
          permut_ = rhs.permut_;
          score_ = rhs.score_;
        }
        return *this;
      }
 
      const std::set<String>::const_iterator & getPermut() const
      {
        return permut_;
      }
 
      void setPermut(const std::set<String>::const_iterator & it)
      {
        permut_ = it;
      }
 
      double getScore() const
      {
        return score_;
      }
 
      void setScore(double score)
      {
        score_ = score;
      }
 
protected:
 
      std::set<String>::const_iterator permut_;
      double score_;
    };
 
  };
 
  namespace Internal
  {
    bool PermutScoreComparator(const CompNovoIdentificationBase::Permut & p1, const CompNovoIdentificationBase::Permut & p2);
  }
}