ProteinIdentification.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinHit.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/DATASTRUCTURES/DateTime.h>
#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/METADATA/DataArrays.h>
#include <OpenMS/CONCEPT/Constants.h>

#include <set>

namespace OpenMS
{
  class MSExperiment;
  class PeptideIdentification;
  class PeptideEvidence;
  class ConsensusMap;

  class OPENMS_DLLAPI ProteinIdentification :
    public MetaInfoInterface
  {
public:
    typedef ProteinHit HitType;

    struct Mapping
    {
      std::map<String, StringList> identifier_to_msrunpath;
      std::map<StringList, String> runpath_to_identifier;

      Mapping() = default;

      explicit Mapping(const std::vector<ProteinIdentification>& prot_ids)
      {
        create(prot_ids);
      }

      void create(const std::vector<ProteinIdentification>& prot_ids)
      {
        identifier_to_msrunpath.clear();
        runpath_to_identifier.clear();
        StringList filenames;
        for (const ProteinIdentification& prot_id : prot_ids)
        {
          prot_id.getPrimaryMSRunPath(filenames);
          if (filenames.empty())
          {
            throw Exception::MissingInformation(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "No MS run path annotated in ProteinIdentification.");
          }
          identifier_to_msrunpath[prot_id.getIdentifier()] = filenames;
          const auto& it = runpath_to_identifier.find(filenames);
          if (it != runpath_to_identifier.end())
          {
            throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                          "Multiple protein identifications with the same ms-run-path in Consensus/FeatureXML. Check input!\n",
                                          ListUtils::concatenate(filenames, ","));
          }
          runpath_to_identifier[filenames] = prot_id.getIdentifier();
        }
      }

      String getPrimaryMSRunPath(const PeptideIdentification& pepid) const
      { 
        // if a merge index n is annotated, we use the filename annotated at index n in the protein identification, otherwise the one at index 0        
        size_t merge_index = pepid.getMetaValue(Constants::UserParam::ID_MERGE_INDEX, 0);
        const auto& filenames = identifier_to_msrunpath.at(pepid.getIdentifier());        
        return (merge_index < filenames.size()) ?  filenames[merge_index] : ""; // return filename or empty string if missing
      }
    };

    class OPENMS_DLLAPI ProteinGroup
    {
    public:
      typedef OpenMS::DataArrays::FloatDataArray FloatDataArray ;
      typedef std::vector<FloatDataArray> FloatDataArrays;
      typedef OpenMS::DataArrays::StringDataArray StringDataArray ;
      typedef std::vector<StringDataArray> StringDataArrays;
      typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray ;
      typedef std::vector<IntegerDataArray> IntegerDataArrays;

      double probability;

      std::vector<String> accessions;

      ProteinGroup();

      bool operator==(const ProteinGroup& rhs) const;

      /*
        @brief Comparison operator (for sorting)

        This operator is intended for sorting protein groups in a "best first"
        manner. That means higher probabilities are "less" than lower
        probabilities (!); smaller groups are "less" than larger groups;
        everything else being equal, accessions are compared lexicographically.
      */
      bool operator<(const ProteinGroup& rhs) const;


      const FloatDataArrays& getFloatDataArrays() const;

      FloatDataArrays& getFloatDataArrays()
      {
        return float_data_arrays_;
      }

      void setFloatDataArrays(const FloatDataArrays& fda);

      const StringDataArrays& getStringDataArrays() const;

      StringDataArrays& getStringDataArrays();

      void setStringDataArrays(const StringDataArrays& sda);

      const IntegerDataArrays& getIntegerDataArrays() const;

      IntegerDataArrays& getIntegerDataArrays();

      void setIntegerDataArrays(const IntegerDataArrays& ida);

      inline IntegerDataArray& getIntegerDataArrayByName(String name)
      {
        return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(),
          [&name](const IntegerDataArray& da) { return da.getName() == name; } );
      }

      inline StringDataArray& getStringDataArrayByName(String name)
      {
        return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(),
          [&name](const StringDataArray& da) { return da.getName() == name; } );
      }

      inline FloatDataArray& getFloatDataArrayByName(String name)
      {
        return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(),
          [&name](const FloatDataArray& da) { return da.getName() == name; } );
      }

      inline const IntegerDataArray& getIntegerDataArrayByName(String name) const
      {
        return *std::find_if(integer_data_arrays_.begin(), integer_data_arrays_.end(),
          [&name](const IntegerDataArray& da) { return da.getName() == name; } );
      }

      inline const StringDataArray& getStringDataArrayByName(String name) const
      {
        return *std::find_if(string_data_arrays_.begin(), string_data_arrays_.end(),
          [&name](const StringDataArray& da) { return da.getName() == name; } );
      }

      inline const FloatDataArray& getFloatDataArrayByName(String name) const
      {
        return *std::find_if(float_data_arrays_.begin(), float_data_arrays_.end(),
          [&name](const FloatDataArray& da) { return da.getName() == name; } );
      }

    private:
      FloatDataArrays float_data_arrays_;

      StringDataArrays string_data_arrays_;

      IntegerDataArrays integer_data_arrays_;
    };

    enum PeakMassType
    {
      MONOISOTOPIC,
      AVERAGE,
      SIZE_OF_PEAKMASSTYPE
    };

    static const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE];

    struct OPENMS_DLLAPI SearchParameters :
      public MetaInfoInterface
    {
      String db; 
      String db_version; 
      String taxonomy; 
      String charges; 
      PeakMassType mass_type; 
      std::vector<String> fixed_modifications; 
      std::vector<String> variable_modifications; 
      UInt missed_cleavages; 
      double fragment_mass_tolerance; 
      bool fragment_mass_tolerance_ppm; 
      double precursor_mass_tolerance; 
      bool precursor_mass_tolerance_ppm; 
      Protease digestion_enzyme; 
      EnzymaticDigestion::Specificity enzyme_term_specificity; 

      SearchParameters();
      SearchParameters(const SearchParameters&) = default;
      SearchParameters(SearchParameters&&) = default;
      ~SearchParameters() = default;

      SearchParameters& operator=(const SearchParameters&) = default;
      SearchParameters& operator=(SearchParameters&&)& = default;

      bool operator==(const SearchParameters& rhs) const;

      bool operator!=(const SearchParameters& rhs) const;

      std::pair<int,int> getChargeRange() const;

      bool mergeable(const ProteinIdentification::SearchParameters& sp, const String& experiment_type) const;

      private:
      int getChargeValue_(String& charge_str) const;
    };

    ProteinIdentification();
    ProteinIdentification(const ProteinIdentification&) = default;
    ProteinIdentification(ProteinIdentification&&) = default;
    virtual ~ProteinIdentification();

    ProteinIdentification& operator=(const ProteinIdentification&) = default;
    ProteinIdentification& operator=(ProteinIdentification&&) = default;

    bool operator==(const ProteinIdentification& rhs) const;
    bool operator!=(const ProteinIdentification& rhs) const;


    const std::vector<ProteinHit>& getHits() const;
    std::vector<ProteinHit>& getHits();
    void insertHit(const ProteinHit& input);
    void insertHit(ProteinHit&& input);

    void setHits(const std::vector<ProteinHit>& hits);

    std::vector<ProteinHit>::iterator findHit(const String& accession);

    const std::vector<ProteinGroup>& getProteinGroups() const;
    std::vector<ProteinGroup>& getProteinGroups();
    void insertProteinGroup(const ProteinGroup& group);

    const std::vector<ProteinGroup>& getIndistinguishableProteins() const;
    std::vector<ProteinGroup>& getIndistinguishableProteins();
    void insertIndistinguishableProteins(const ProteinGroup& group);
    void fillIndistinguishableGroupsWithSingletons();

    double getSignificanceThreshold() const;
    void setSignificanceThreshold(double value);
    const String& getScoreType() const;
    void setScoreType(const String& type);
    bool isHigherScoreBetter() const;
    void setHigherScoreBetter(bool higher_is_better);
    void sort();
    void assignRanks();
    void computeCoverage(const std::vector<PeptideIdentification>& pep_ids);
    void computeCoverage(const ConsensusMap& cmap, bool use_unassigned_ids);

    void computeModifications(
      const std::vector<PeptideIdentification>& pep_ids,
      const StringList& skip_modifications);
    void computeModifications(
      const ConsensusMap& cmap,
      const StringList& skip_modifications,
      bool use_unassigned_ids);



    const DateTime& getDateTime() const;
    void setDateTime(const DateTime& date);
    void setSearchEngine(const String& search_engine);
    const String& getSearchEngine() const;
    const String getOriginalSearchEngineName() const;
    void setSearchEngineVersion(const String& search_engine_version);
    const String& getSearchEngineVersion() const;
    void setInferenceEngine(const String& search_engine);
    const String getInferenceEngine() const;
    void setInferenceEngineVersion(const String& inference_engine_version);
    const String getInferenceEngineVersion() const;
    void setSearchParameters(const SearchParameters& search_parameters);
    void setSearchParameters(SearchParameters&& search_parameters);
    const SearchParameters& getSearchParameters() const;
    SearchParameters& getSearchParameters();
    const String& getIdentifier() const;
    void setIdentifier(const String& id);
    void setPrimaryMSRunPath(const StringList& s, bool raw = false);

    void setPrimaryMSRunPath(const StringList& s, MSExperiment& e);
    void addPrimaryMSRunPath(const String& s, bool raw = false);
    void addPrimaryMSRunPath(const StringList& s, bool raw = false);

    void getPrimaryMSRunPath(StringList& output, bool raw = false) const;

    Size nrPrimaryMSRunPaths(bool raw = false) const;

    bool hasInferenceData() const;

    bool hasInferenceEngineAsSearchEngine() const;

    bool peptideIDsMergeable(const ProteinIdentification& id_run, const String& experiment_type) const;

    std::vector<std::pair<String,String>> getSearchEngineSettingsAsPairs(const String& se = "") const;


    void copyMetaDataOnly(const ProteinIdentification&);
protected:

    String id_;
    String search_engine_;
    String search_engine_version_;
    SearchParameters search_parameters_;
    DateTime date_;


    String protein_score_type_;
    bool higher_score_better_;
    std::vector<ProteinHit> protein_hits_;
    std::vector<ProteinGroup> protein_groups_;
    std::vector<ProteinGroup> indistinguishable_proteins_;
    double protein_significance_threshold_;

  private:
    void computeCoverageFromEvidenceMapping_(const std::unordered_map<String, std::set<PeptideEvidence>>& map);
    void fillEvidenceMapping_(std::unordered_map<String, std::set<PeptideEvidence> >& map_acc_2_evidence,
                              const std::vector<PeptideIdentification>& pep_ids) const;

    void fillModMapping_(const std::vector<PeptideIdentification>& pep_ids, const StringList& skip_modifications,
                         std::unordered_map<String, std::set<std::pair<Size, ResidueModification>>>& prot2mod) const;
  };


} //namespace OpenMS