IDScoreGetterSetter.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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// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
 
#include <vector>
#include <unordered_set>
#include <unordered_map>
 
namespace OpenMS
{
  typedef std::pair<double, double> ScoreToTgtDecLabelPair;
 
  struct ScoreToTgtDecLabelPairs // Not a typedef to allow forward declaration.
      : public std::vector<ScoreToTgtDecLabelPair>
  {
    typedef std::vector<ScoreToTgtDecLabelPair> Base;
    using Base::Base;
  };
 
  class IDScoreGetterSetter
  {
 
  private:
 
    template<typename T>
    struct IsIDType
    {
      static bool const value =
          std::is_same<T, PeptideIdentification>::value || std::is_same<T, ProteinIdentification>::value;
    };
 
    template<typename T>
    struct IsHitType
    {
      static bool const value = std::is_same<T, PeptideHit>::value || std::is_same<T, ProteinHit>::value;
    };
 
  public:
    static void getPickedProteinScores_(
        std::unordered_map<String, ScoreToTgtDecLabelPair>& picked_scores,
        const ProteinIdentification& id,
        const String& decoy_string,
        bool decoy_prefix);
 
    static void getPickedProteinGroupScores_(
        const std::unordered_map<String, ScoreToTgtDecLabelPair>& picked_scores,
        ScoreToTgtDecLabelPairs& scores_labels,
        const std::vector<ProteinIdentification::ProteinGroup>& grps,
        const String& decoy_string,
        bool decoy_prefix);
 
    static std::pair<bool,String> removeDecoyStringIfPresent_(const String& acc, const String& decoy_string, bool decoy_prefix);
 
    static void fillPeptideScoreMap_(
      std::unordered_map<String, ScoreToTgtDecLabelPair>& seq_to_score_labels,
      std::vector<PeptideIdentification> const& ids);
 
    static void fillPeptideScoreMap_(
      std::unordered_map<String, ScoreToTgtDecLabelPair>& seq_to_score_labels,
      ConsensusMap const& map,
      bool include_unassigned);
 
 
    //TODO could be done with set of target accessions, too
    //TODO even better: store nr targets and nr decoys when creating the groups!
    //TODO alternative scoring is possible, too (e.g. ratio of tgts vs decoys)
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const std::vector<ProteinIdentification::ProteinGroup> &grps,
        const std::unordered_set<std::string> &decoy_accs);
 
 
    template<class ...Args>
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const std::vector<PeptideIdentification> &ids,
        Args &&... args)
    {
      for (const PeptideIdentification &id : ids)
      {
        getScores_(scores_labels, id, std::forward<Args>(args)...);
      }
    }
 
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const ProteinIdentification &id)
    {
      scores_labels.reserve(scores_labels.size() + id.getHits().size());
      std::transform(id.getHits().begin(), id.getHits().end(),
                     std::back_inserter(scores_labels),
                     [](const ProteinHit &hit)
                     {
                       checkTDAnnotation_(hit);
                       return std::make_pair<double, bool>(hit.getScore(), getTDLabel_(hit));
                     }
      );
    }
 
    template<class ...Args>
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const PeptideIdentification &id,
        bool all_hits,
        Args &&... args
        )
    {
      if (all_hits)
      {
        for (const PeptideHit &hit : id.getHits())
        {
          getScores_(scores_labels, hit, std::forward<Args>(args)...);
        }
      }
      else
      {
        //TODO for speed and constness I assume that they are sorted and first = best.
        //id.sort();
        const PeptideHit &hit = id.getHits()[0];
        getScores_(scores_labels, hit, std::forward<Args>(args)...);
      }
    }
 
    template<typename IDPredicate, class ...Args>
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const PeptideIdentification &id,
        IDPredicate &&fun,
        bool all_hits,
        Args &&... args
        )
    {
      if (fun(id))
      {
        if (all_hits)
        {
          for (const PeptideHit &hit : id.getHits())
          {
            getScores_(scores_labels, hit, std::forward<Args>(args)...);
          }
        }
        else
        {
          //TODO for speed I assume that they are sorted and first = best.
          //id.sort();
          const PeptideHit &hit = id.getHits()[0];
          getScores_(scores_labels, hit, std::forward<Args>(args)...);
        }
      }
    }
 
    template<typename HitPredicate>
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const PeptideHit &hit,
        HitPredicate &&fun)
    {
      if (fun(hit))
      {
        getScores_(scores_labels, hit);
      }
    }
 
    template<typename HitType, typename std::enable_if<IsHitType<HitType>::value>::type * = nullptr>
    static void getScores_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const HitType &hit)
    {
      checkTDAnnotation_(hit);
      scores_labels.emplace_back(hit.getScore(), getTDLabel_(hit));
    }
    template<class ...Args>
    static void getPeptideScoresFromMap_(
        ScoreToTgtDecLabelPairs &scores_labels,
        const ConsensusMap &cmap, bool include_unassigned_peptides, Args &&... args)
    {
      auto f =
          [&](const PeptideIdentification &id) -> void
          { getScores_(scores_labels, id, std::forward<Args>(args)...); };
      cmap.applyFunctionOnPeptideIDs(f, include_unassigned_peptides);
    }
 
    static bool getTDLabel_(const MetaInfoInterface &idOrHit)
    {
      return std::string(idOrHit.getMetaValue("target_decoy"))[0] == 't';
    }
 
    template<typename IDType, class ...Args>
    static void setScores_(const std::map<double, double> &scores_to_FDR,
                    std::vector<IDType> &ids,
                    const std::string &score_type,
                    bool higher_better,
                    Args &&... args)
    {
      for (auto &id : ids)
      {
        setScores_(scores_to_FDR, id, score_type, higher_better, std::forward<Args>(args)...);
      }
    }
 
    template<typename IDType>
    static String setScoreType_(IDType &id, const std::string &score_type,
                         bool higher_better)
    {
      String old_score_type = id.getScoreType() + "_score";
      id.setScoreType(score_type);
      id.setHigherScoreBetter(higher_better);
      return old_score_type;
    }
 
    template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id, const std::string &score_type,
                    bool higher_better, bool keep_decoy)
    {
      bool old_higher_better = id.isHigherScoreBetter();
      String old_score_type = setScoreType_(id, score_type, higher_better);
 
      if (keep_decoy) //in-place set scores
      {
        if (old_higher_better)
        {
          setScores_(scores_to_FDR, id, old_score_type);
        }
        else
        {
          setScoresHigherWorse_(scores_to_FDR, id, old_score_type);
        }
      }
      else
      {
        if (old_higher_better)
        {
          setScoresAndRemoveDecoys_(scores_to_FDR, id, old_score_type);
        }
        else
        {
          setScoresHigherWorseAndRemoveDecoys_(scores_to_FDR, id, old_score_type);
        }
      }
    }
 
    template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id,
                    const String &old_score_type)
    {
      std::vector<typename IDType::HitType> &hits = id.getHits();
      for (auto &hit : hits)
      {
        setScore_(scores_to_FDR, hit, old_score_type);
      }
    }
 
    template<typename IDType>
    static void setScoresHigherWorse_(const std::map<double, double> &scores_to_FDR, IDType &id,
                           const String &old_score_type)
    {
      std::vector<typename IDType::HitType> &hits = id.getHits();
      for (auto &hit : hits)
      {
        setScoreHigherWorse_(scores_to_FDR, hit, old_score_type);
      }
    }
 
    template<typename IDType, class ...Args>
    static void setScoresAndRemoveDecoys_(const std::map<double, double> &scores_to_FDR, IDType &id,
                                   const String &old_score_type, Args&& ... args)
    {
      std::vector<typename IDType::HitType> &hits = id.getHits();
      std::vector<typename IDType::HitType> new_hits;
      new_hits.reserve(hits.size());
      for (auto &hit : hits)
      {
        setScoreAndMoveIfTarget_(scores_to_FDR, hit, old_score_type, new_hits, std::forward<Args>(args)...);
      }
      hits.swap(new_hits);
    }
 
    template<typename IDType, class ...Args>
    static void setScoresHigherWorseAndRemoveDecoys_(const std::map<double, double> &scores_to_FDR, IDType &id,
                                          const String &old_score_type, Args&& ... args)
    {
      std::vector<typename IDType::HitType> &hits = id.getHits();
      std::vector<typename IDType::HitType> new_hits;
      new_hits.reserve(hits.size());
      for (auto &hit : hits)
      {
        setScoreHigherWorseAndMoveIfTarget_(scores_to_FDR, hit, old_score_type, new_hits, std::forward<Args>(args)...);
      }
      hits.swap(new_hits);
    }
 
    template<typename HitType>
    static void setScore_(const std::map<double, double> &scores_to_FDR, HitType &hit, const std::string &old_score_type)
    {
      hit.setMetaValue(old_score_type, hit.getScore());
      hit.setScore(scores_to_FDR.lower_bound(hit.getScore())->second);
    }
 
    template<typename HitType>
    static void setScoreHigherWorse_(const std::map<double, double> &scores_to_FDR, HitType &hit, const std::string &old_score_type)
    {
      hit.setMetaValue(old_score_type, hit.getScore());
      auto ub = scores_to_FDR.upper_bound(hit.getScore());
      if (ub != scores_to_FDR.begin()) ub--;
      hit.setScore(ub->second);
    }
 
    /*template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id, const std::string &score_type,
                    bool higher_better)
    {
      bool old_higher_better = id.isHigherScoreBetter();
      String old_score_type = setScoreType_(id, score_type, higher_better);
      setScores_(scores_to_FDR, id, old_score_type, old_higher_better);
    }*/
 
    static void setScores_(const std::map<double, double> &scores_to_FDR,
                    PeptideIdentification &id,
                    const std::string &score_type,
                    bool higher_better,
                    bool keep_decoy,
                    int charge)
    {
      String old_score_type = setScoreType_(id, score_type, higher_better);
      if (keep_decoy) //in-place set scores
      {
        setScores_(scores_to_FDR, id, old_score_type, higher_better, charge);
      }
      else
      {
        setScoresAndRemoveDecoys_<PeptideIdentification>(scores_to_FDR, id, old_score_type, charge);
      }
    }
 
    static void setScores_(const std::map<double, double> &scores_to_FDR,
                    PeptideIdentification &id,
                    const std::string &score_type,
                    bool higher_better,
                    bool keep_decoy,
                    int charge,
                    const String &identifier)
    {
      if (id.getIdentifier() == identifier)
      {
        setScores_(scores_to_FDR, id, score_type, higher_better, keep_decoy, charge);
      }
    }
 
    template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id, const std::string &score_type,
                    bool higher_better, bool keep_decoy, const String &identifier)
    {
      if (id.getIdentifier() == identifier)
      {
        setScores_(scores_to_FDR, id, score_type, higher_better, keep_decoy);
      }
    }
 
    static void setScores_(const std::map<double, double> &scores_to_FDR,
                    PeptideIdentification &id,
                    const std::string &score_type,
                    bool higher_better,
                    int charge,
                    const String &identifier)
    {
      if (id.getIdentifier() == identifier)
      {
        setScores_(scores_to_FDR, id, score_type, higher_better, charge);
      }
    }
 
    template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id, const std::string &score_type,
                    bool higher_better, const String &identifier)
    {
      if (id.getIdentifier() == identifier)
      {
        setScores_(scores_to_FDR, id, score_type, higher_better);
      }
    }
 
    template<typename IDType>
    static void setScores_(const std::map<double, double> &scores_to_FDR, IDType &id, const std::string &score_type,
                           bool higher_better, int charge)
    {
      for (auto& hit : id.getHits())
      {
        if (hit.getCharge() == charge)
        {
          if (higher_better)
          {
            setScore_(scores_to_FDR, hit, score_type);
          }
          else
          {
            setScoreHigherWorse_(scores_to_FDR, hit, score_type);
          }
        }
      }
    }
 
    //TODO could also get a keep_decoy flag when we define what a "decoy group" is -> keep all always for now
    static void setScores_(
        const std::map<double, double> &scores_to_FDR,
        std::vector<ProteinIdentification::ProteinGroup> &grps,
        const std::string &score_type,
        bool higher_better);
 
    template<typename HitType>
    static void setScoreAndMoveIfTarget_(const std::map<double, double> &scores_to_FDR,
                                  HitType &hit,
                                  const std::string &old_score_type,
                                  std::vector<HitType> &new_hits)
    {
      const String &target_decoy(hit.getMetaValue("target_decoy"));
      if (target_decoy[0] == 't')
      {
        hit.setMetaValue(old_score_type, hit.getScore());
        hit.setScore(scores_to_FDR.lower_bound(hit.getScore())->second);
        new_hits.push_back(std::move(hit));
      } // else do not move over
    }
 
    template<typename HitType>
    static void setScoreHigherWorseAndMoveIfTarget_(const std::map<double, double> &scores_to_FDR,
                                         HitType &hit,
                                         const std::string &old_score_type,
                                         std::vector<HitType> &new_hits)
    {
      const String &target_decoy(hit.getMetaValue("target_decoy"));
      if (target_decoy[0] == 't')
      {
        hit.setMetaValue(old_score_type, hit.getScore());
        auto ub = scores_to_FDR.upper_bound(hit.getScore());
        if (ub != scores_to_FDR.begin()) ub--;
        hit.setScore(ub->second);
        new_hits.push_back(std::move(hit));
      } // else do not move over
    }
 
 
    static void setScoreAndMoveIfTarget_(const std::map<double, double> &scores_to_FDR,
                                  PeptideHit &hit,
                                  const std::string &old_score_type,
                                  std::vector<PeptideHit> &new_hits,
                                  int charge)
    {
      if (charge == hit.getCharge())
      {
        const String &target_decoy(hit.getMetaValue("target_decoy"));
        if (target_decoy[0] == 't')
        {
          hit.setMetaValue(old_score_type, hit.getScore());
          hit.setScore(scores_to_FDR.lower_bound(hit.getScore())->second);
          new_hits.push_back(std::move(hit));
        } // else do not move over
      }
      else // different charge, move over unchanged to process later at correct charge.
      {
        new_hits.push_back(std::move(hit));
      }
    }
 
    template<class ...Args>
    static void setPeptideScoresForMap_(const std::map<double, double> &scores_to_FDR,
                                 ConsensusMap &cmap,
                                 bool include_unassigned_peptides,
                                 const std::string &score_type,
                                 bool higher_better,
                                 bool keep_decoy,
                                 Args&&... args)
    {
      //Note: Gcc4.8 cannot handle variadic templates in lambdas
      auto f =
          [&](PeptideIdentification &id) -> void
          { setScores_(scores_to_FDR, id, score_type,
                       higher_better, keep_decoy, std::forward<Args>(args)...); };
      cmap.applyFunctionOnPeptideIDs(f, include_unassigned_peptides);
    }
 
    static void checkTDAnnotation_(const MetaInfoInterface &id_or_hit)
    {
      if (!id_or_hit.metaValueExists("target_decoy"))
      {
        throw Exception::MissingInformation(__FILE__,
                                            __LINE__,
                                            OPENMS_PRETTY_FUNCTION,
                                            "Meta value 'target_decoy' does not exist in all ProteinHits! Reindex the idXML file with 'PeptideIndexer'");
      }
    }
 
    static void setPeptideScoresFromMap_(std::unordered_map<String, ScoreToTgtDecLabelPair> const& seq_to_fdr,
                                         std::vector<PeptideIdentification>& ids,
                                         std::string const& score_type,
                                         bool keep_decoys);
 
    static void setPeptideScoresFromMap_(std::unordered_map<String, ScoreToTgtDecLabelPair> const& seq_to_fdr,
                                         ConsensusMap& map,
                                         std::string const& score_type,
                                         bool keep_decoys,
                                         bool include_unassigned);
  };
} // namespace OpenMS