DigestionEnzymeProtein.h

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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();

    explicit DigestionEnzymeProtein(const DigestionEnzyme& d);

    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,
                                    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;

    void setCometID(Int value);

    Int getCometID() const;

    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_;

    Int msgf_id_;

    Int omssa_id_;

  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzymeProtein& enzyme);

  typedef DigestionEnzymeProtein Protease;
}