SearchDatabase Reupload für Codereview

src/openms/include/OpenMS/ANALYSIS/ID/FragmentIndex.h

@@ -0,0 +1,156 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
+//
+// 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: Chris Bielow $
+// $Authors: Max Alcer, Heike Einsfeld $
+// --------------------------------------------------------------------------
+
+
+#pragma once
+
+#include <OpenMS/CHEMISTRY/AASequence.h>
+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/FORMAT/FASTAFile.h>
+#include <OpenMS/KERNEL/MSExperiment.h>
+#include <OpenMS/KERNEL/Peak1D.h>
+
+#include <vector>
+
+namespace OpenMS
+{
+  //class MSExperiment;
+
+  /** @brief Creating a two-level tree from a given FASTAFile by generating the theoretical peptides and their b-y-ions and sorting
+    * them in the outer tree by fragment-m/z and the inner tree by precursor-m/z. Search function to find candidates to experimental MS2 sepctra
+    * (implementation inspired by https://lazear.github.io/sage/)
+    * @ingroup ID
+   */
+class OPENMS_DLLAPI FragmentIndex : public DefaultParamHandler
+{
+  public:
+
+  /** @brief Storing found candiates from search 
+   */
+  struct Candidate
+  {
+    size_t peptide_start; ///< Start position of peptide in protein
+    size_t peptide_end; ///< End position of peptide in protein
+    size_t protein_index; ///< Index to Entry of std::vector<FASTAFile::FASTAEntry>
+    bool is_modified_; ///< true if candidate is modified
+    size_t modification_index_; ///< index to modified version of this peptide
+  };
+
+  /** @brief Storing vector of found candiates from search with the Index of the MSSpectrum in the MSExperiment
+   */
+  struct CandidatesWithIndex
+  {
+    std::vector<FragmentIndex::Candidate> candidates; ///< Vector of found candidates
+    size_t spectrum_index; ///< Index to the MSSpectrum in the MSExperiment
+    CandidatesWithIndex(std::vector<FragmentIndex::Candidate>&& cand, size_t spectrum_i): candidates(std::move(cand)), spectrum_index(spectrum_i){}
+  };
+
+
+  /** @brief Sets default parameters     
+  */
+  FragmentIndex();
+
+  /** @brief Builds up the Search Datastructure     
+  * @param entries Input vector of FASTAFile-Entries to base SearchDatastructure on
+  */
+  void build(const std::vector<FASTAFile::FASTAEntry>& entries);
+
+  /** @brief Searches Peaks of every MSSpectrum of the MSExperiment in the Database       
+     * @param experiment Input MSExperiment containing of MS2 Spectra (MS1 Spectra has an empty output)
+     * @param candidates Output vector of found candidates with the index of MSSpectrum in experiment
+    */
+  void search(MSExperiment& experiment, std::vector<FragmentIndex::CandidatesWithIndex>& candidates) const;
+
+  /** @brief Searches Peaks of the MSSpectrum in the Database       
+     * @param spectrum Input MS2 Spectrum (MS1 Spectra has an empty output)
+     * @param candidates Output vector of found candidatest
+    */
+  void search(MSSpectrum& spectrum, std::vector<FragmentIndex::Candidate>& candidates) const;
+
+  protected:
+
+  void updateMembers_() override;
+
+  //Saving b_y_ion after creating theoretical spectrum with index to precursor-peptide
+  struct Fragment_
+  {
+    size_t peptide_index_;
+    double fragment_mz_;
+    Fragment_(size_t prec, const Peak1D& frag):peptide_index_(prec), fragment_mz_(frag.getMZ()){}
+  };
+
+  //Saving first and last index of precursor in FASTA-Entry, index to protein and the MonoWeight after digesting
+  struct Peptide_
+  {
+    size_t peptide_begin_;
+    size_t peptide_end_;
+    size_t protein_index_;
+    double peptide_mz_;
+    bool is_modified_;
+    size_t modification_index_;
+  };
+
+  /// in-silico digest protein database
+  std::vector<FragmentIndex::Peptide_> generate_peptides_(const std::vector<FASTAFile::FASTAEntry>& entries) const;
+  /// Merges presorted Chunks of Peptide-Fragments inplace
+  void fragment_merge_(int first, int last, const std::vector<int>& chunks, std::vector<FragmentIndex::Fragment_>& input) const;
+  ///generates sorted vector with all theoretical Fragments for all theoretical Peptides
+  std::vector<FragmentIndex::Fragment_> generate_fragments_(const std::vector<FASTAFile::FASTAEntry>& entries) const;
+
+  bool is_build_;
+  std::string digestor_enzyme_;
+  size_t missed_cleavages_; ///< number of missed cleavages
+  double peptide_min_mass_;
+  double peptide_max_mass_;
+  size_t peptide_min_length_;
+  size_t peptide_max_length_;
+  double fragment_min_mz_;
+  double fragment_max_mz_;
+  size_t fragment_min_charge_;
+  size_t fragment_max_charge_;
+  size_t bucketsize_; ///< number of fragments per outer node
+  double precursor_mz_tolerance_;
+  std::string precursor_mz_tolerance_unit_;
+  double fragment_mz_tolerance_;
+  std::string fragment_mz_tolerance_unit_;
+  StringList modifications_fixed_;
+  StringList modifications_variable_;
+  size_t max_variable_mods_per_peptide_;
+  size_t max_missed_peaks_;
+  std::vector<Peptide_> all_peptides_;
+  std::vector<double> bucket_frags_mz_; ///< Minimum fragment-m/z for each other node
+  std::vector<Fragment_> all_fragments_;
+};
+
+}

src/openms/include/OpenMS/ANALYSIS/ID/SearchDatabase.h

@@ -0,0 +1,147 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
+//
+// 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: Chris Bielow $
+// $Authors: Max Alcer, Heike Einsfeld $
+// --------------------------------------------------------------------------
+
+
+#pragma once
+
+#include <OpenMS/CHEMISTRY/AASequence.h>
+#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
+#include <OpenMS/FORMAT/FASTAFile.h>
+#include <OpenMS/KERNEL/MSExperiment.h>
+#include <OpenMS/KERNEL/Peak1D.h>
+
+#include <vector>
+
+namespace OpenMS
+{
+  //class MSExperiment;
+
+  /** @brief Creating a two-level tree from a given FASTAFile by generating the theoretical peptides and their b-y-ions and sorting
+    * them in the outer tree by fragment-m/z and the inner tree by precursor-m/z. Search function to find candidates to experimental MS2 sepctra
+    * (implementation inspired by https://lazear.github.io/sage/)
+    * @ingroup ID
+   */
+class OPENMS_DLLAPI SearchDatabase : public DefaultParamHandler
+{
+  public:
+
+  /** @brief Storing found candiates from search 
+   */
+  struct Candidate
+  {
+    const AASequence* sequence; ///< Pointer to AASequence of candidate
+    size_t protein_index; ///< Index to Entry of std::vector<FASTAFile::FASTAEntry>
+    Candidate(const AASequence* seq, size_t pi) : sequence(seq), protein_index(pi){}
+  };
+
+  /** @brief Storing vector of found candiates from search with the Index of the MSSpectrum in the MSExperiment
+   */
+  struct CandidatesWithIndex
+  {
+    std::vector<SearchDatabase::Candidate> candidates; ///< Vector of found candidates
+    size_t spectrum_index; ///< Index to the MSSpectrum in the MSExperiment
+    CandidatesWithIndex(const std::vector<SearchDatabase::Candidate>& cand, size_t spectrum_i): candidates(cand), spectrum_index(spectrum_i){}
+  };
+
+  /** @brief Builds up the Search Datastructure     
+     * @param entries Input vector of FASTAFile-Entries to base SearchDatastructure on
+    */
+  SearchDatabase(const std::vector<FASTAFile::FASTAEntry>& entries);
+
+  /** @brief Searches Peaks of every MSSpectrum of the MSExperiment in the Database       
+     * @param experiment Input MSExperiment containing of MS2 Spectra (MS1 Spectra has an empty output)
+     * @param candidates Output vector of found candidates with the index of MSSpectrum in experiment
+    */
+  void search(MSExperiment& experiment, std::vector<SearchDatabase::CandidatesWithIndex>& candidates) const;
+
+  /** @brief Searches Peaks of the MSSpectrum in the Database       
+     * @param spectrum Input MS2 Spectrum (MS1 Spectra has an empty output)
+     * @param candidates Output vector of found candidatest
+    */
+  void search(MSSpectrum& spectrum, std::vector<SearchDatabase::Candidate>& candidates) const;
+
+  protected:
+
+  void updateMembers_() override;
+
+  //Saving b_y_ion after creating theoretical spectrum with index to precursor-peptide
+  struct Fragment_
+  {
+    size_t peptide_index_;
+    double fragment_mz_;
+    Fragment_(size_t prec, const Peak1D& frag):peptide_index_(prec), fragment_mz_(frag.getMZ()){}
+  };
+
+  //Saving precursors AASequence (, index to protein and the MonoWeight) after digesting
+  struct Peptide_
+  {
+    AASequence sequence_;
+    size_t protein_index_;
+    double peptide_mz_;
+    Peptide_(const Peptide_&) = default;
+    Peptide_(Peptide_&&) = default;
+    Peptide_(const AASequence& pep, size_t index, double mass):sequence_(pep), protein_index_(index), peptide_mz_(mass){}
+    Peptide_& operator=(Peptide_&&) = default;
+    Peptide_& operator=(const Peptide_&) = default;
+  };
+
+  /// generates theoretical Peptides from all Proteins in fasta-File 
+  std::vector<SearchDatabase::Peptide_> generate_peptides_(const std::vector<FASTAFile::FASTAEntry>& entries) const;
+  /// Merges presorted Chunks of Peptide-Fragments inplace
+  void fragment_merge_(int first, int last, const std::vector<int>& chunks, std::vector<SearchDatabase::Fragment_>& input) const;
+  ///generates sorted vector with all theoretical Fragments for all theoretical Peptides
+  std::vector<SearchDatabase::Fragment_> generate_fragments_() const;
+
+  std::string digestor_enzyme_;
+  size_t missed_cleavages_; ///< number of missed cleavages
+  double peptide_min_mass_;
+  double peptide_max_mass_;
+  size_t peptide_min_length_;
+  size_t peptide_max_length_;
+  double fragment_min_mz_;
+  double fragment_max_mz_;
+  size_t bucketsize_; ///< number of fragments per outer node
+  double precursor_mz_tolerance_;
+  std::string precursor_mz_tolerance_unit_;
+  double fragment_mz_tolerance_;
+  std::string fragment_mz_tolerance_unit_;
+  StringList modifications_fixed_;
+  StringList modifications_variable_;
+  size_t max_variable_mods_per_peptide_;
+  std::vector<Peptide_> all_peptides_{};
+  std::vector<double> bucket_frags_mz_{}; ///< Minimum fragment-m/z for each other node
+  std::vector<Fragment_> all_fragments_{};
+};
+
+}

src/openms/include/OpenMS/ANALYSIS/ID/sources.cmake

@@ -21,6 +21,7 @@ ConsensusMapMergerAlgorithm.h
 FalseDiscoveryRate.h
 FIAMSDataProcessor.h
 FIAMSScheduler.h
+FragmentIndex.h
 HiddenMarkovModel.h
 IDBoostGraph.h
 IDDecoyProbability.h

src/openms/include/OpenMS/CONCEPT/Constants.h

@@ -575,6 +575,16 @@ namespace OpenMS
               String
       */
       inline const std::string   MSM_SUM_FORMULA = "Sum_Formula";
+
+      /** User parameter for the unit type of the m/z tolerance. (Required for SearchDatabase)
+              String
+      */
+      inline const std::string   UNIT_DA = "Da";
+
+      /** User parameter for the unit type of the m/z tolerance. (Required for SearchDatabase)
+              String
+      */
+      inline const std::string   UNIT_PPM = "ppm";
     }
 
     //@}