MascotXMLFile.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 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer $
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#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