SiriusExportAlgorithm.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: Oliver Alka, Axel Walter $
// $Authors: Oliver Alka, Lukas Zimmermann $
// --------------------------------------------------------------------------
 
#pragma once 
 
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>
 
#include <OpenMS/SYSTEM/File.h>
 
#include <QtCore/QStringList>
 
using namespace std;
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusExportAlgorithm : public DefaultParamHandler
    {
    public:
      SiriusExportAlgorithm();
      
      // accessor for preprocessing parameters
      bool isFeatureOnly() const { return param_.getValue("feature_only").toBool(); }
      UInt getFilterByNumMassTraces() const { return param_.getValue("filter_by_num_masstraces"); }
      double getPrecursorMzTolerance() const { return param_.getValue("precursor_mz_tolerance"); }
      double getPrecursorRtTolerance() const { return param_.getValue("precursor_rt_tolerance"); }
      bool precursorMzToleranceUnitIsPPM() const { return param_.getValue("precursor_mz_tolerance_unit") == "ppm"; }
      bool isNoMasstraceInfoIsotopePattern() const { return param_.getValue("no_masstrace_info_isotope_pattern").toBool(); }
      int getIsotopePatternIterations() const { return  param_.getValue("isotope_pattern_iterations"); }
 
      void preprocessing(const String& featureinfo,
                               const MSExperiment& spectra,
                               FeatureMapping::FeatureMappingInfo& feature_mapping_info,
                               FeatureMapping::FeatureToMs2Indices& feature_ms2_indices) const;
 
      void logFeatureSpectraNumber(const String& featureinfo,
                                   const FeatureMapping::FeatureToMs2Indices& feature_ms2_indices,
                                   const MSExperiment& spectra) const;
 
      void run(const StringList& mzML_files,
               const StringList& featureXML_files,
               const String& out_ms,
               const String& out_compoundinfo) const;
 
    };
} // namespace OpenMS