MascotXMLFile.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
 
 
namespace OpenMS
{
  class ProteinIdentification;
 
  class OPENMS_DLLAPI MascotXMLFile :
    public Internal::XMLFile
  {
public:
 
    MascotXMLFile();
 
    void load(const String& filename,
              ProteinIdentification& protein_identification,
              std::vector<PeptideIdentification>& id_data,
              const SpectrumMetaDataLookup& lookup);
 
    void load(const String& filename,
              ProteinIdentification& protein_identification,
              std::vector<PeptideIdentification>& id_data, 
              std::map<String, std::vector<AASequence> >& peptides, 
              const SpectrumMetaDataLookup& lookup);
 
    static void initializeLookup(SpectrumMetaDataLookup& lookup, const PeakMap& experiment, const String& scan_regex = "");
 
  };
 
} // namespace OpenMS