Enzyme.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 2002-2017.
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// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang $
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//

#ifndef OPENMS_CHEMISTRY_ENZYME_H
#define OPENMS_CHEMISTRY_ENZYME_H

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/DATASTRUCTURES/String.h>

#include <iosfwd>
#include <set>
#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI Enzyme
  {
public:

    Enzyme(const Enzyme& enzyme);

    explicit Enzyme(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 = "",
                    UInt comet_id = 0,
                    Int msgf_id = -1,
                    UInt omssa_id = 0);

    virtual ~Enzyme();

    Enzyme& operator=(const Enzyme& enzyme);

    void setName(const String& name);

    const String& getName() const;

    void setSynonyms(const std::set<String>& synonyms);

    void addSynonym(const String& synonym);

    const std::set<String>& getSynonyms() const;

    void setRegEx(const String& cleavage_regex);

    const String& getRegEx() const;

    void setRegExDescription(String value);

    String getRegExDescription() const;

    void setNTermGain(EmpiricalFormula value);

    EmpiricalFormula getNTermGain() const;

    void setCTermGain(EmpiricalFormula value);

    EmpiricalFormula getCTermGain() const;

    void setPSIID(String value);

    String getPSIID() const;

    void setXTandemID(String value);

    String getXTandemID() const;

    UInt getCometID() const;
    
    void setCometID(UInt value);

    void setMSGFID(Int value);

    Int getMSGFID() const;

    void setOMSSAID(UInt value);

    UInt getOMSSAID() const;
    

    bool operator==(const Enzyme& enzyme) const;

    bool operator!=(const Enzyme& enzyme) const;

    bool operator==(String cleavage_regex) const;

    bool operator!=(String cleavage_regex) const;

    bool operator<(const Enzyme& enzyme) const;

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

protected:
    Enzyme();

    // basic
    String name_;

    String cleavage_regex_;

    std::set<String> synonyms_;

    String regex_description_;

    EmpiricalFormula n_term_gain_;

    EmpiricalFormula c_term_gain_;

    String psi_id_;

    String xtandem_id_;

    UInt comet_id_;

    Int msgf_id_;
    
    UInt omssa_id_;

  };

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

}

#endif