SimpleSearchEngineAlgorithm.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:
//  * 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.
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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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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/ANALYSIS/RNPXL/ModifiedPeptideGenerator.h>
#include <OpenMS/ANALYSIS/RNPXL/HyperScore.h>

#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

#include <OpenMS/CONCEPT/Constants.h>

#include <OpenMS/DATASTRUCTURES/Param.h>

// preprocessing and filtering
#include <OpenMS/FILTERING/DATAREDUCTION/Deisotoper.h>
#include <OpenMS/FILTERING/ID/IDFilter.h>
#include <OpenMS/FILTERING/TRANSFORMERS/ThresholdMower.h>
#include <OpenMS/FILTERING/TRANSFORMERS/NLargest.h>
#include <OpenMS/FILTERING/TRANSFORMERS/WindowMower.h>
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>

#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>

#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/METADATA/SpectrumSettings.h>

#include <map>
#include <algorithm>

#ifdef _OPENMP
  #include <omp.h>
  #define NUMBER_OF_THREADS (omp_get_num_threads())
#else
  #define NUMBER_OF_THREADS (1)
#endif


namespace OpenMS
{

class OPENMS_DLLAPI SimpleSearchEngineAlgorithm :
  public DefaultParamHandler,
  public ProgressLogger
{
  public:
    SimpleSearchEngineAlgorithm(); 

    enum class ExitCodes
    {
      EXECUTION_OK,
      INPUT_FILE_EMPTY,
      UNEXPECTED_RESULT,
      UNKNOWN_ERROR,
      ILLEGAL_PARAMETERS
    };

    // @brief search spectra against database
    ExitCodes search(const String& in_mzML, 
      const String& in_db, 
      std::vector<ProteinIdentification>& prot_ids,
      std::vector<PeptideIdentification>& pep_ids) const;
  protected:
    void updateMembers_() override;

    struct AnnotatedHit_
    {
      StringView sequence;
      SignedSize peptide_mod_index; // enumeration index of the non-RNA peptide modification
      double score = 0; // main score
      std::vector<PeptideHit::PeakAnnotation> fragment_annotations;
      static bool hasBetterScore(const AnnotatedHit_& a, const AnnotatedHit_& b)
      {
        return a.score > b.score;
      }
    };

    // @brief filter, deisotope, decharge spectra
    static void preprocessSpectra_(PeakMap& exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);

    // @brief filter and annotate search results
    // most of the parameters are used to properly add meta data to the id objects
    static void postProcessHits_(const PeakMap& exp, 
      std::vector<std::vector<SimpleSearchEngineAlgorithm::AnnotatedHit_> >& annotated_hits, 
      std::vector<ProteinIdentification>& protein_ids, 
      std::vector<PeptideIdentification>& peptide_ids, 
      Size top_hits,
      const std::vector<ResidueModification>& fixed_modifications, 
      const std::vector<ResidueModification>& variable_modifications, 
      Size max_variable_mods_per_peptide,
      const StringList& modifications_fixed,
      const StringList& modifications_variable,
      Int peptide_missed_cleavages,
      double precursor_mass_tolerance,
      double fragment_mass_tolerance,
      const String& precursor_mass_tolerance_unit_ppm,
      const String& fragment_mass_tolerance_unit_ppm,
      const Int precursor_min_charge,
      const Int precursor_max_charge,
      const String& enzyme,
      const String& database_name);

    // @brief helper to retrieve modifications by name
    static std::vector<ResidueModification> getModifications_(const StringList& modNames);

    double precursor_mass_tolerance_;
    String precursor_mass_tolerance_unit_;

    Size precursor_min_charge_;
    Size precursor_max_charge_;

    IntList precursor_isotopes_;

    double fragment_mass_tolerance_;

    String fragment_mass_tolerance_unit_;

    StringList modifications_fixed_;

    StringList modifications_variable_;

    Size modifications_max_variable_mods_per_peptide_;

    String enzyme_;

    Size peptide_min_size_;
    Size peptide_max_size_;
    Size peptide_missed_cleavages_;

    String peptide_motif_;

    Size report_top_hits_;
};

} // namespace