XFDRAlgorithm.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.
//
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//  * Redistributions in binary form must reproduce the above copyright
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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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// --------------------------------------------------------------------------
// $Maintainer: Eugen Netz $
// $Authors: Lukas Zimmermann, Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/MATH/STATISTICS/Histogram.h>
 
namespace OpenMS
{
 
  //-------------------------------------------------------------
  // Doxygen docu
  //-------------------------------------------------------------
 
  class OPENMS_DLLAPI XFDRAlgorithm :
  public DefaultParamHandler, public ProgressLogger
  {
 
  public:
 
    enum ExitCodes
    {
      EXECUTION_OK,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT
    };
 
    XFDRAlgorithm();
 
    ~XFDRAlgorithm() override;
 
    ExitCodes run(std::vector<PeptideIdentification>& peptide_ids, ProteinIdentification& protein_id);
 
    ExitCodes validateClassArguments() const;
 
private:
    void updateMembers_() override;
 
    void initDataStructures_(std::vector<PeptideIdentification>& peptide_ids, ProteinIdentification& protein_id);
 
    static void assignTypes_(PeptideHit& pep_id, StringList& types);
 
    void fdr_xprophet_(std::map< String, Math::Histogram<> >& cum_histograms,
                      const String& targetclass, const String& decoyclass, const String& fulldecoyclass,
                      std::vector< double >& fdr, bool mono) const;
 
    static void calc_qfdr_(const std::vector< double >& fdr, std::vector< double >& qfdr);
 
    void findTopUniqueHits_(std::vector<PeptideIdentification>& peptide_ids);
 
    void writeArgumentsLog_() const;
 
    String getId_(const PeptideHit& ph) const;
 
    static Size getMinIonsMatched_(const PeptideHit& ph)
    {
      Size alpha_ions = Size(ph.getMetaValue("matched_linear_alpha")) + Size(ph.getMetaValue("matched_xlink_alpha"));
      Size beta_ions = Size(ph.getMetaValue("matched_linear_beta")) + Size(ph.getMetaValue("matched_xlink_beta"));
      return std::min(alpha_ions, beta_ions);
    }
 
    inline static void setIntraProtein_(PeptideHit& ph, const bool value)
    {
      ph.setMetaValue("XFDR:is_intraprotein", DataValue(value ? "true" : "false"));
    }
 
    inline static void setInterProtein_(PeptideHit& ph, const bool value)
    {
      ph.setMetaValue("XFDR:is_interprotein", DataValue(value ? "true" : "false"));
    }
 
    static bool isSameProtein_(
            String prot1,
            String prot2,
            const String &decoy_string)
    {
      prot1.substitute(decoy_string, "");
      prot2.substitute(decoy_string, "");
      assert( ! prot1.hasSubstring(decoy_string));
      assert( ! prot2.hasSubstring(decoy_string));
      return prot1 == prot2;
    }
 
    // Score range for this of the tool
    Int min_score_;
    Int max_score_;
 
    // unique top hits
    std::vector<String> unique_ids_;
    std::vector<double> unique_id_scores_;
 
    // maps index of peptide id all_pep_ids_ to vector of cross link class
    std::map<String, std::vector<String>> cross_link_classes_;
 
    // Program arguments
    String decoy_string_;
    double arg_mindeltas_;
    double arg_minborder_;
    double arg_maxborder_;
    Int arg_minionsmatched_;
    double arg_minscore_;
    bool arg_uniquex_;
    bool arg_no_qvalues_;
    double arg_binsize_;
 
    // Names of the class parameters
    static const String param_decoy_string_;
    static const String param_minborder_;
    static const String param_maxborder_;
    static const String param_mindeltas_;
    static const String param_minionsmatched_;
    static const String param_uniquexl_;
    static const String param_no_qvalues_;
    static const String param_minscore_;
    static const String param_binsize_;
 
    // Constants related to particular crosslink classes
    static const String crosslink_class_intradecoys_;
    static const String crosslink_class_fulldecoysintralinks_;
    static const String crosslink_class_interdecoys_;
    static const String crosslink_class_fulldecoysinterlinks_;
    static const String crosslink_class_monodecoys_;
    static const String crosslink_class_intralinks_;
    static const String crosslink_class_interlinks_;
    static const String crosslink_class_monolinks_;
    static const String crosslink_class_decoys_;
    static const String crosslink_class_targets_;
    static const String crosslink_class_hybriddecoysintralinks_;
    static const String crosslink_class_hybriddecoysinterlinks_;
  };
}