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 2002-2018.
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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();

    PeptideEvidence(const String& accession, Int start, Int end, char aa_before, char aa_after);

    PeptideEvidence(const PeptideEvidence& source);

    ~PeptideEvidence() {}

    PeptideEvidence& operator=(const PeptideEvidence& source);

    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_;
  };

}