PercolatorInfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/TextFile.h>
 
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PercolatorInfile
  {
    public:
      static void store(const String& pin_file, 
        const std::vector<PeptideIdentification>& peptide_ids, 
        const StringList& feature_set, 
        const std::string& enz, 
        int min_charge, 
        int max_charge);
 
      static std::vector<PeptideIdentification> load(const String& pin_file, bool higher_score_better, const String& score_name, String decoy_prefix = "");
 
      // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
      static String getScanIdentifier(const PeptideIdentification& pid, size_t index);
      
    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 std::vector<PeptideIdentification>& peptide_ids, 
        const StringList& feature_set, 
        const std::string& enz, 
        int min_charge, 
        int max_charge);
 
 
      static Int getScanNumber_(const String& scan_identifier);
 
      static bool isEnz_(const char& n, const char& c, const std::string& enz);
 
      static Size countEnzymatic_(const String& peptide, const std::string& enz);
 
  };
} // namespace OpenMS