DigestionEnzyme.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 2002-2022.
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// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang $
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//

#pragma once

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

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

namespace OpenMS
{
  class OPENMS_DLLAPI DigestionEnzyme
  {
  public:

    DigestionEnzyme(const DigestionEnzyme&) = default;

    DigestionEnzyme(DigestionEnzyme&&) = default;

    explicit DigestionEnzyme(const String& name,
                             const String& cleavage_regex,
                             const std::set<String>& synonyms = std::set<String>(),
                             String regex_description = "");

    explicit DigestionEnzyme(const String& name,
                             String cut_before,
                             const String& nocut_after = "",
                             String sense = "C",
                             const std::set<String>& synonyms = std::set<String>(),
                             String regex_description = "");

    virtual ~DigestionEnzyme();

    DigestionEnzyme& operator=(const DigestionEnzyme&) = default;

    DigestionEnzyme& operator=(DigestionEnzyme&&) & = default;

    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(const String& value);

    const String& getRegExDescription() const;

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

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

    bool operator==(const String& cleavage_regex) const;

    bool operator!=(const String& cleavage_regex) const;

    bool operator<(const DigestionEnzyme& enzyme) const;

    virtual bool setValueFromFile(const String& key, const String& value);

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

  protected:

    DigestionEnzyme();

    // basic
    String name_;

    String cleavage_regex_;

    std::set<String> synonyms_;

    String regex_description_;
  };

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