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 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    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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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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 <set>

namespace OpenMS
{
  class PeptideIdentification;

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

    struct OPENMS_DLLAPI ProteinGroup
    {
      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;
    };

    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();

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

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

    };


    ProteinIdentification();
    virtual ~ProteinIdentification();
    ProteinIdentification(const ProteinIdentification& source);
    ProteinIdentification& operator=(const ProteinIdentification& source);
    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 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);

    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);


    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 setSearchParameters(const SearchParameters& search_parameters);
    const SearchParameters& getSearchParameters() const;
    SearchParameters& getSearchParameters();    
    const String& getIdentifier() const;
    void setIdentifier(const String& id);
    void setPrimaryMSRunPath(const StringList& s);
    void getPrimaryMSRunPath(StringList& toFill) 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