PercolatorInfile.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/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/FORMAT/TextFile.h>
 
#include <map>
#include <set>
#include <utility>
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PercolatorInfile
  {
    public:
      using PinFeatureMetaValueMap = std::map<std::pair<size_t, size_t>, std::set<std::string>>;
 
      static void store(const std::string& pin_file, 
        const PeptideIdentificationList& peptide_ids, 
        const StringList& feature_set, 
        const std::string& enz, 
        int min_charge, 
        int max_charge);
 
 
      static PeptideIdentificationList load(const std::string& pin_file, 
        bool higher_score_better, 
        const std::string& score_name, 
        const StringList& extra_scores,
        StringList& filenames, 
        std::string decoy_prefix = "",
        double threshold = 0.01, 
        bool SageAnnotation = false);
 
      // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
      static std::string getScanIdentifier(const PeptideIdentification& pid, size_t index);
 
      static std::string getFileIdentifier(const PeptideIdentification& pid);
 
      static StringList getStandardFeatureSet(int min_charge, int max_charge);
 
      static std::set<std::pair<size_t, size_t>> stampPinFeaturesOnHits(
        PeptideIdentificationList& peptide_ids,
        const std::string& enz,
        int min_charge,
        int max_charge);
 
      static std::set<std::pair<size_t, size_t>> stampPinFeaturesOnHits(
        PeptideIdentificationList& peptide_ids,
        const std::string& enz,
        int min_charge,
        int max_charge,
        PinFeatureMetaValueMap& added_meta_values);
 
      static double getFeatureValue(const DataValue& value, const std::string& feature);
 
    protected:
 
      //id <tab> label <tab> scannr <tab> calcmass <tab> expmass <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM
      static TextFile preparePin_(
        const PeptideIdentificationList& peptide_ids, 
        const StringList& feature_set, 
        const std::string& enz, 
        int min_charge, 
        int max_charge);
 
      static bool isEnz_(const char& n, const char& c, const std::string& enz);
 
      static Size countEnzymatic_(const std::string& peptide, const std::string& enz);
 
  };
} // namespace OpenMS