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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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//

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>

namespace OpenMS
{
  /** @ingroup Chemistry

          @brief Representation of modification definition

          This class defines a modification type e.g. a input parameter of a search engine.
          The modification is defined using an unique name of the modification present
          in the modifications DB instance.
  */
  class OPENMS_DLLAPI ModificationDefinition
  {
public:

    /** @name Constructor and Destructors
    */
    //@{
    /// default constructor
    ModificationDefinition();

    /// copy constructor
    ModificationDefinition(const ModificationDefinition& rhs);

    /// detailed constructor specifying the modification by name
    explicit ModificationDefinition(const String& mod, bool fixed = true, UInt max_occur = 0);

    /// direct constructor from a residue modification
    explicit ModificationDefinition(const ResidueModification& mod, bool fixed = true, UInt max_occur = 0);

    /// destructor
    virtual ~ModificationDefinition();
    //@}

    /** @name Accessors
    */
    //@{
    /// sets whether this modification definition is fixed or variable (modification must occur vs. can occur)
    void setFixedModification(bool fixed);

    /// returns if the modification if fixed true, else false
    bool isFixedModification() const;

    /// set the maximal number of occurrences per peptide (unbounded if 0)
    void setMaxOccurrences(UInt num);

    /// returns the maximal number of occurrences per peptide
    UInt getMaxOccurrences() const;

    /// returns the name of the modification
    String getModificationName() const;

    /// sets the modification, allowed are unique names provided by ModificationsDB
    void setModification(const String& modification);

    /**
       @brief Returns the modification

       @throw Exception::InvalidValue if no modification was set
    */
    const ResidueModification& getModification() const;
    //@}

    /** @name Assignment
    */
    //@{
    /// assignment operator
    ModificationDefinition& operator=(const ModificationDefinition& element);
    //@}

    /** @name Predicates
    */
    //@{
    /// equality operator
    bool operator==(const ModificationDefinition& rhs) const;

    /// inequality operator
    bool operator!=(const ModificationDefinition& rhs) const;

    /// less than operator for e.g. usage in maps; only mod FullIds are compared!
    bool operator<(const OpenMS::ModificationDefinition&) const;
    //@}

protected:

    /// the modification
    const ResidueModification* mod_;

    /// fixed (true) or variable (false)
    bool fixed_modification_;

    /// maximal number of occurrences per peptide
    UInt max_occurrences_;
  };

} // namespace OpenMS

