PeptideEvidence.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 2002-2020.
//
// 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
// 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: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI PeptideEvidence
  {
public:
    static const int UNKNOWN_POSITION; // == -1
 
    // Note: we use 0 as position of the N-terminus while e.g. mzTab or other formats start counting at 1.
    static const int N_TERMINAL_POSITION;
    static const char UNKNOWN_AA; // PeptideEvidence::UNKNOWN_AA = 'X';
 
    // Note: we use '[' and ']' instead of  e.g. '-' as in mzTab specification
    static const char N_TERMINAL_AA;
    static const char C_TERMINAL_AA;
 
    PeptideEvidence();
 
    PeptideEvidence(const String& accession, Int start, Int end, char aa_before, char aa_after);
 
    PeptideEvidence(const PeptideEvidence&) = default;
 
    PeptideEvidence(PeptideEvidence&&) noexcept = default;
 
    ~PeptideEvidence() {}
 
    PeptideEvidence& operator=(const PeptideEvidence&) = default;
    PeptideEvidence& operator=(PeptideEvidence&&) = default; // TODO: add noexcept (gcc 4.8 bug)
 
    bool operator==(const PeptideEvidence& rhs) const;
    
    bool operator<(const PeptideEvidence& rhs) const;
 
    bool operator!=(const PeptideEvidence& rhs) const;
 
    bool hasValidLimits() const;
 
    const String& getProteinAccession() const;
 
    void setProteinAccession(const String& s);
 
    void setStart(const Int a);
 
    Int getStart() const;
 
    void setEnd(const Int a);
 
    Int getEnd() const;
 
    void setAABefore(const char acid);
 
    char getAABefore() const;
 
    void setAAAfter(const char acid);
 
    char getAAAfter() const;
 
protected:
    String accession_;
 
    Int start_;
 
    Int end_;
 
    char aa_before_;
 
    char aa_after_;
  };
 
}