PeptideIdentification.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: 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 ConsensusMap;
  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);
    void setHits(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);
 
    static std::multimap<String, std::pair<Size, Size>> buildUIDsFromAllPepIDs(const ConsensusMap &cmap);
 
    static String buildUIDFromPepID(const PeptideIdentification& pep_id,
                                    const std::map<String, StringList>& fidentifier_to_msrunpath);
 
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