Percolator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/ID/PercolatorTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <memory>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI Percolator : public DefaultParamHandler
  {
  public:
    Percolator();
    ~Percolator() override;
 
    Percolator(const Percolator&) = delete;
    Percolator& operator=(const Percolator&) = delete;
 
    void rescore(std::vector<PeptideIdentification>& peptide_ids,
                 const StringList& feature_names = {});
 
    RescoreOutput rescore(const RescoreInput& input);
 
    Size rescorePSMs(PeptideIdentificationList& peptide_ids,
                     const StringList& feature_set,
                     const std::string& enzyme,
                     int min_charge,
                     int max_charge,
                     const std::string& score_type = "q-value");
 
    PercolatorModel trainPSMs(PeptideIdentificationList& peptide_ids,
                              const StringList& feature_set,
                              const std::string& enzyme,
                              int min_charge,
                              int max_charge);
 
    Size scorePSMs(PeptideIdentificationList& peptide_ids,
                   const PercolatorModel& model,
                   PeptideIdentificationList& reference_ids,
                   const StringList& feature_set,
                   const std::string& enzyme,
                   int min_charge,
                   int max_charge,
                   const std::string& score_type = "q-value");
 
    const std::vector<std::vector<double>>& getSvmWeights() const;
 
    double getPi0() const;
 
    bool usedDefaultDirection() const;
 
    PercolatorModel train(const RescoreInput& input);
 
    RescoreOutput score(const RescoreInput& input, const PercolatorModel& model);
 
    RescoreOutput score(const RescoreInput& input, const PercolatorModel& model, const RescoreInput& reference);
 
    static void fillPINCompatibleFields(
        const std::vector<PeptideIdentification>& peptide_ids,
        bool flatten_hits,
        RescoreInput& input);
 
    static void saveModel(const PercolatorModel& model, const std::string& filename);
 
    static PercolatorModel loadModel(const std::string& filename);
 
  protected:
    void updateMembers_() override;
 
  private:
    struct ReferenceScale_;
    RescoreOutput score_(const RescoreInput& input, const PercolatorModel& model, ReferenceScale_* scale);
 
    struct Impl;
    std::unique_ptr<Impl> impl_;
  };
}