ProteinIdentification.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/ProteinHit.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/DATASTRUCTURES/DateTime.h>
#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>
#include <OpenMS/METADATA/DataArrays.h>
 
 
 
#include <set>
 
namespace OpenMS
{
  class MSExperiment;
  class PeptideIdentification;
 
  class OPENMS_DLLAPI ProteinIdentification :
    public MetaInfoInterface
  {
public:
    typedef ProteinHit HitType;
 
    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; 
 
      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 computeModifications(
      const std::vector<PeptideIdentification>& pep_ids,
      const StringList& skip_modifications);
 
 
 
    const DateTime& getDateTime() const;
    void setDateTime(const DateTime& date);
    void setSearchEngine(const String& search_engine);
    const String& getSearchEngine() 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;
 
    bool hasInferenceData() const;
 
    bool hasInferenceEngineAsSearchEngine() const;
 
    bool peptideIDsMergeable(const ProteinIdentification& id_run, const String& experiment_type) const;
 
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_;
  };
 
} //namespace OpenMS