PrecursorIonSelection.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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/ANALYSIS/TARGETED/PSLPFormulation.h>
#include <set>
 
namespace OpenMS
{
  class PrecursorIonSelectionPreprocessing;
  class PSProteinInference;
  class OPENMS_DLLAPI PrecursorIonSelection :
    public DefaultParamHandler
  {
public:
 
    enum Type
    {
      IPS,
      ILP_IPS,
      SPS,
      UPSHIFT,
      DOWNSHIFT,
      DEX
    };
 
    PrecursorIonSelection();
    PrecursorIonSelection(const PrecursorIonSelection & source);
    ~PrecursorIonSelection() override;
 
    const double & getMaxScore() const;
    void setMaxScore(const double & max_score);
 
 
    struct TotalScoreMore
    {
      inline bool operator()(Feature const & left, Feature const & right) const
      {
        return (double)left.getMetaValue("msms_score") > (double)right.getMetaValue("msms_score");
      }
 
    };
 
    struct SeqTotalScoreMore
    {
      inline bool operator()(Feature const & left, Feature const & right) const
      {
        if (left.getRT() < right.getRT()) return true;
        else if (left.getRT() > right.getRT()) return false;
        else return (double)left.getMetaValue("msms_score") > (double)right.getMetaValue("msms_score");
      }
 
    };
 
 
    void sortByTotalScore(FeatureMap & features)
    {
      FeatureMap::Iterator beg = features.begin();
      FeatureMap::Iterator end  = features.end();
      std::sort(beg, end, TotalScoreMore());
    }
 
    void getNextPrecursors(FeatureMap & features, FeatureMap & next_features, UInt number);
    void getNextPrecursorsSeq(FeatureMap & features, FeatureMap & next_features, UInt number, double & rt);
    void getNextPrecursors(std::vector<Int> & solution_indices, std::vector<PSLPFormulation::IndexTriple> & variable_indices, std::set<Int> & measured_variables,
                           FeatureMap & features, FeatureMap & new_features, UInt step_size, PSLPFormulation & ilp);
 
//      /**
//        @brief Change scoring of features using peptide identifications only from spectra of the last
//        iteration
//
//        @param features FeatureMap with all possible precursors
//        @param new_pep_ids Peptide identifications
//        @param preprocessed_db Information from preprocessed database
//
//     */
//     void rescoreIncremental(FeatureMap& features,std::vector<PeptideIdentification>& new_pep_ids,
//                                                      std::vector<ProteinIdentification>& prot_ids,
//                                                      PrecursorIonSelectionPreprocessing& preprocessed_db);
 
 
    void rescore(FeatureMap & features, std::vector<PeptideIdentification> & new_pep_ids,
                 std::vector<ProteinIdentification> & prot_ids,
                 PrecursorIonSelectionPreprocessing & preprocessed_db, bool check_meta_values = true);
 
 
    void simulateRun(FeatureMap & features, std::vector<PeptideIdentification> & pep_ids,
                     std::vector<ProteinIdentification> & prot_ids,
                     PrecursorIonSelectionPreprocessing & preprocessed_db,
                     const String& path, PeakMap & experiment, const String& precursor_path = "");
 
    void setLPSolver(LPWrapper::SOLVER solver)
    {
      solver_ = solver;
      std::cout << " LPSolver set to " << solver_ << std::endl;
    }
 
    LPWrapper::SOLVER getLPSolver()
    {
      return solver_;
    }
 
    void reset();
 
    const std::map<String, std::set<String> > & getPeptideProteinCounter()
    {
      return prot_id_counter_;
    }
 
private:
    void simulateILPBasedIPSRun_(FeatureMap & features, PeakMap & experiment,
                                 std::vector<PeptideIdentification> & pep_ids,
                                 std::vector<ProteinIdentification> & prot_ids,
                                 PrecursorIonSelectionPreprocessing & preprocessed_db,
                                 const String& output_path, const String& precursor_path = "");
 
    void simulateRun_(FeatureMap & features, std::vector<PeptideIdentification> & pep_ids,
                      std::vector<ProteinIdentification> & prot_ids,
                      PrecursorIonSelectionPreprocessing & preprocessed_db, const String& path, const String& precursor_path = "");
 
    void shiftDown_(FeatureMap & features, PrecursorIonSelectionPreprocessing & preprocessed_db, String protein_acc);
 
    void shiftUp_(FeatureMap & features, PrecursorIonSelectionPreprocessing & preprocessed_db, String protein_acc);
 
    void updateMembers_() override;
 
    void rescore_(FeatureMap & features, std::vector<PeptideIdentification> & new_pep_ids,
                  PrecursorIonSelectionPreprocessing & preprocessed_db, PSProteinInference & protein_inference);
 
    void checkForRequiredUserParams_(FeatureMap & features);
 
    UInt filterProtIds_(std::vector<ProteinIdentification> & prot_ids);
 
    std::vector<PeptideIdentification> filterPeptideIds_(std::vector<PeptideIdentification> & pep_ids);
 
    void convertPeptideIdScores_(std::vector<PeptideIdentification> & pep_ids);
 
    UInt min_pep_ids_;
    double max_score_;
    Type type_;
    std::map<String, std::set<String> > prot_id_counter_;
    std::vector<Size> fraction_counter_;
    double mz_tolerance_;
    String mz_tolerance_unit_;
    UInt max_iteration_;
    Size x_variable_number_;
 
    LPWrapper::SOLVER solver_;
 
  };
 
}