XQuestResultXMLFile.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: Eugen Netz $
// $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/PeptideIdentificationList.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,
              PeptideIdentificationList & pep_ids,
              std::vector< ProteinIdentification > & prot_ids
            );
 
    void store(const String& filename,
               const std::vector<ProteinIdentification>& poid,
               const PeptideIdentificationList& peid) const;
 
    int getNumberOfHits() const;
 
    double getMinScore() const;
 
    double getMaxScore() const;
 
    static void writeXQuestXMLSpec(const String& out_file, const 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, const bool& test_mode = false);
 
    static void writeXQuestXMLSpec(const String& out_file, const String& base_name,
                                   const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
                                   const PeakMap& spectra, const bool& test_mode = false);
 
 
 
private:
 
      static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum& spec, const String& header, const bool& test_mode = false);
 
      static void wrap_(const String& input, Size width, String& output);
 
    int n_hits_; 
    double min_score_; 
    double max_score_; 
  };
} // namespace OpenMS