PeptideIdentification.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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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/ProteinHit.h>

#include <string>
#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI PeptideIdentification :
    public MetaInfoInterface
  {
public:

    typedef PeptideHit HitType;


    PeptideIdentification();
    virtual ~PeptideIdentification() noexcept;
    PeptideIdentification(const PeptideIdentification&) = default;
    PeptideIdentification(PeptideIdentification&&) noexcept = default;

    PeptideIdentification& operator=(const PeptideIdentification&) = default;
    PeptideIdentification& operator=(PeptideIdentification&&) = default; // TODO: add noexcept (gcc 4.8 bug)
    bool operator==(const PeptideIdentification& rhs) const;
    bool operator!=(const PeptideIdentification& rhs) const;

    double getRT() const;
    void setRT(double rt);
    bool hasRT() const;

    double getMZ() const;
    void setMZ(double mz);
    bool hasMZ() const;

    const std::vector<PeptideHit>& getHits() const;
    std::vector<PeptideHit>& getHits();
    void insertHit(const PeptideHit& hit);
    void insertHit(PeptideHit&& hit);
    void setHits(const std::vector<PeptideHit>& hits);

    double getSignificanceThreshold() const;
    void setSignificanceThreshold(double value);

    const String& getScoreType() const;
    void setScoreType(const String& type);

    bool isHigherScoreBetter() const;
    void setHigherScoreBetter(bool value);

    const String& getIdentifier() const;
    void setIdentifier(const String& id);

    const String& getBaseName() const;
    void setBaseName(const String& base_name);

    const String getExperimentLabel() const;
    void setExperimentLabel(const String& type);

    void assignRanks();

    void sort();

    void sortByRank();

    bool empty() const;

    static std::vector<PeptideHit> getReferencingHits(const std::vector<PeptideHit>&, const std::set<String>& accession);

protected:

    String id_; 
    std::vector<PeptideHit> hits_; 
    double significance_threshold_; 
    String score_type_; 
    bool higher_score_better_; 
    // hint: here is an alignment gap of 7 bytes <-- here --> use it when introducing new members with sizeof(m)<=4
    String base_name_;
    double mz_;
    double rt_;

  };

} //namespace OpenMS