XQuestResultXMLFile.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 2002-2017.
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// $Maintainer: Lukas Zimmermann $
// $Authors: Lukas Zimmermann, Eugen Netz $
// --------------------------------------------------------------------------
#pragma once

#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>

namespace OpenMS
{

  class OPENMS_DLLAPI XQuestResultXMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    XQuestResultXMLFile();
    ~XQuestResultXMLFile() override;

    void load(const String & filename,
              std::vector< PeptideIdentification > & pep_ids,
              std::vector< ProteinIdentification > & prot_ids
            );

    void store(const String& filename,
               const std::vector<ProteinIdentification>& poid,
               const std::vector<PeptideIdentification>& peid) const;

    int getNumberOfHits() const;

    double getMinScore() const;

    double getMaxScore() const;

      static void writeXQuestXMLSpec(String out_file, String base_name, const OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra, const std::vector< std::pair<Size, Size> >& spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, const PeakMap& spectra);

      static void writeXQuestXMLSpec(String out_file, String base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, const PeakMap& spectra);



private:
      static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum& spec, String header);

      static void wrap_(const String& input, Size width, String & output);

    int n_hits_; // Total number of hits within the result file

    double min_score_; // Minimum score encountered in file
    double max_score_; // Maximum score encountered in file
  };
} // namespace OpenMS