2.6.0/html/SiriusAdapterAlgorithm_8h_source.html

// --------------------------------------------------------------------------

//                   OpenMS -- Open-Source Mass Spectrometry

// --------------------------------------------------------------------------

// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,

// ETH Zurich, and Freie Universitaet Berlin 2002-2020.

//

// This software is released under a three-clause BSD license:

//  * Redistributions of source code must retain the above copyright

//    notice, this list of conditions and the following disclaimer.

//  * Redistributions in binary form must reproduce the above copyright

//    notice, this list of conditions and the following disclaimer in the

//    documentation and/or other materials provided with the distribution.

//  * Neither the name of any author or any participating institution

//    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.

// --------------------------------------------------------------------------

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING

// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,

// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,

// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;

// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,

// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR

// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF

// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

//

// --------------------------------------------------------------------------

// $Maintainer: Oliver Alka $

// $Authors: Oliver Alka $

// --------------------------------------------------------------------------


#pragma once


#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureMapping.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>


namespace OpenMS

{

  class FeatureMap;

  class File;

  class KDTreeFeatureMaps;


  class OPENMS_DLLAPI SiriusAdapterAlgorithm : public DefaultParamHandler

    {

    public:

      SiriusAdapterAlgorithm();


      struct OPENMS_DLLAPI SiriusTemporaryFileSystemObjects

      {

      public:


        SiriusTemporaryFileSystemObjects(int debug_level);


        ~SiriusTemporaryFileSystemObjects();


        const String& getTmpDir() const;

        const String& getTmpOutDir() const;

        const String& getTmpMsFile() const;


      private:

        int debug_level_;


        String tmp_dir_;

        String tmp_ms_file_;

        String tmp_out_dir_;


      };


      static void preprocessingSirius(const String& featureinfo,

                                      const 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);


      const 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();

      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_;

      // 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