SiriusAdapterAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------

#pragma once 

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>

#include <OpenMS/SYSTEM/File.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>

#include <QString>

namespace OpenMS
{
  class OPENMS_DLLAPI SiriusAdapterAlgorithm : public DefaultParamHandler
    {
    public:
      SiriusAdapterAlgorithm();

      struct SiriusTmpStruct
      {
        String tmp_dir;
        String tmp_ms_file;
        String tmp_out_dir;
      };

      static SiriusAdapterAlgorithm::SiriusTmpStruct constructSiriusTmpStruct();

      static std::pair<String, String> checkSiriusExecutablePath(String& executable);


      static void preprocessingSirius(const String& featureinfo,
                                      MSExperiment& spectra,
                                      std::vector<FeatureMap>& v_fp,
                                      KDTreeFeatureMaps& fp_map_kd,
                                      const SiriusAdapterAlgorithm& sirius_algo,
                                      FeatureMapping::FeatureToMs2Indices& feature_mapping);

      static void checkFeatureSpectraNumber(const String& featureinfo,
                                            const FeatureMapping::FeatureToMs2Indices& feature_mapping, 
                                            const MSExperiment& spectra, 
                                            const SiriusAdapterAlgorithm& sirius_algo);

      
      static std::vector<String> callSiriusQProcess(const String& tmp_ms_file,
                                                    const String& tmp_out_dir,
                                                    String& executable,
                                                    const String& out_csifingerid,
                                                    const SiriusAdapterAlgorithm& sirius_algo);

      // getter (used to call functions from SiriusMSConverter, SiriusMzTabWriter, CsiFingerIDMzTabWriter)
      String getFeatureOnly();  
      String getNoMasstraceInfoIsotopePattern();
      String getConverterMode();
      int getIsotopePatternIterations();
      int getCandidates();
      int getTopNHits();

    protected:

      // adapter parameters (preprocessing)
      unsigned int filter_by_num_masstraces_;
      double precursor_mz_tolerance_;
      String precursor_mz_tolerance_unit_;
      double precursor_rt_tolerance_;
      int isotope_pattern_iterations_;
      // flags
      String feature_only_;
      String no_masstrace_info_isotope_pattern_;
      String converter_mode_;
      // parameters for SIRIUS (sirius)
      String profile_;
      int candidates_;
      String database_;
      int noise_;
      int ppm_max_;
      String isotope_;
      String elements_;
      int compound_timeout_;
      int tree_timeout_;
      int top_n_hits_;
      int cores_;
      // flags
      String auto_charge_;
      String ion_tree_;
      String no_recalibration_;
      String most_intense_ms2_;

      void updateMembers_() override;
    };
} // namespace OpenMS