ProteinHit.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 2002-2018.
//
// 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 <vector>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>

namespace OpenMS
{
  class OPENMS_DLLAPI ProteinHit :
    public MetaInfoInterface
  {
public:
    static const double COVERAGE_UNKNOWN; // == -1


    class OPENMS_DLLAPI ScoreMore
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wfloat-equal"
        if (a.getScore() != b.getScore())
#pragma clang diagnostic pop
        {
          return a.getScore() > b.getScore();
        }
        return a.getAccession() > b.getAccession();
      }

    };

    class OPENMS_DLLAPI ScoreLess
    {
public:
      template <typename Arg>
      bool operator()(const Arg & a, const Arg & b)
      {
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wfloat-equal"
        if (a.getScore() != b.getScore())
#pragma clang diagnostic pop
        {
          return a.getScore() < b.getScore();
        }
        return a.getAccession() < b.getAccession();
      }

    };


    ProteinHit();

    ProteinHit(double score, UInt rank, String accession, String sequence);

    ProteinHit(const ProteinHit & source);

    virtual ~ProteinHit();

    ProteinHit & operator=(const ProteinHit & source);

    ProteinHit & operator=(const MetaInfoInterface & source);

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

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



    float getScore() const;

    UInt getRank() const;

    const String & getSequence() const;

    const String & getAccession() const;
    
    String getDescription() const;

    double getCoverage() const;

    void setScore(const double score);

    void setRank(UInt newrank);

    void setSequence(const String & sequence);

    void setAccession(const String & accession);

    void setDescription(const String & description);

    void setCoverage(const double coverage);


protected:
    float score_;                        
    UInt rank_;                         
    String accession_;          
    String sequence_;               
    double coverage_;         

  };

} // namespace OpenMS