PeptideEvidence.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $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();
 
    explicit PeptideEvidence(const String& accession, Int start=UNKNOWN_POSITION, Int end=UNKNOWN_POSITION, char aa_before=UNKNOWN_AA, char aa_after=UNKNOWN_AA);
 
    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_;
  };
 
}