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 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// --------------------------------------------------------------------------
// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang $
// --------------------------------------------------------------------------
//
 
#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);
 
    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);
 
    String getRegEx() const;
 
    void setRegExDescription(const String& value);
 
    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);
}