DigestionEnzymeProtein.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 2002-2020.
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// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang $
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//
 
#pragma once
 
#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI DigestionEnzymeProtein :
    public DigestionEnzyme
  {
  public:
 
 
    DigestionEnzymeProtein();
 
    DigestionEnzymeProtein(const DigestionEnzymeProtein&) = default;
 
    DigestionEnzymeProtein(DigestionEnzymeProtein&&) = default;
 
    explicit DigestionEnzymeProtein(const String& name,
                                    const String& cleavage_regex,
                                    const std::set<String>& synonyms = std::set<String>(),
                                    String regex_description = "",
                                    EmpiricalFormula n_term_gain = EmpiricalFormula("H"),
                                    EmpiricalFormula c_term_gain = EmpiricalFormula("OH"),
                                    String psi_id = "",
                                    String xtandem_id = "",
                                    Int comet_id = -1,
                                    String crux_id = "",
                                    Int msgf_id = -1,
                                    Int omssa_id = -1);
 
    ~DigestionEnzymeProtein() override;
 
    DigestionEnzymeProtein& operator=(const DigestionEnzymeProtein&) = default;
 
    DigestionEnzymeProtein& operator=(DigestionEnzymeProtein&&) & = default;
 
    void setNTermGain(const EmpiricalFormula& value);
 
    EmpiricalFormula getNTermGain() const;
 
    void setCTermGain(const EmpiricalFormula& value);
 
    EmpiricalFormula getCTermGain() const;
 
    void setPSIID(const String& value);
 
    String getPSIID() const;
 
    void setXTandemID(const String& value);
 
    String getXTandemID() const;
 
    Int getCometID() const;
 
    void setCometID(Int value);
 
    String getCruxID() const;
 
    void setCruxID(const String& value);
 
    void setMSGFID(Int value);
 
    Int getMSGFID() const;
 
    void setOMSSAID(Int value);
 
    Int getOMSSAID() const;
 
 
    bool operator==(const DigestionEnzymeProtein& enzyme) const;
 
    bool operator!=(const DigestionEnzymeProtein& enzyme) const;
 
    // Note: comparison operator is not inherited. TODO rename and make virtual
    bool operator==(const String& cleavage_regex) const;
 
    bool operator!=(const String& cleavage_regex) const;
 
    bool operator<(const DigestionEnzymeProtein& enzyme) const;
 
    bool setValueFromFile(const String& key, const String& value) override;
 
    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
 
  protected:
    EmpiricalFormula n_term_gain_;
 
    EmpiricalFormula c_term_gain_;
 
    String psi_id_;
 
    String xtandem_id_;
 
    Int comet_id_;
 
    String crux_id_;
 
    Int msgf_id_;
 
    Int omssa_id_;
 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);
 
  typedef DigestionEnzymeProtein Protease;
}