libopenms-dev 1.11.1-5 / usr / include / OpenMS / CHEMISTRY / ModificationDefinition.h

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// $Maintainer: Andreas Bertsch $
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#ifndef OPENMS_CHEMISTRY_MODIFICATIONDEFINITION_H
#define OPENMS_CHEMISTRY_MODIFICATIONDEFINITION_H

#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 modifications name
    ModificationDefinition(const String & mod);

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

    /** @name Accessors
    */
    //@{
    /// sets the allowed position of the modification
    void setTermSpecificity(ResidueModification::Term_Specificity pos);

    /// returns the allowed position of the modification
    ResidueModification::Term_Specificity getTermSpecificity() const;

    /// 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 occurences per peptide, unbound if 0
    void setMaxOccurences(UInt num);

    /// returns the maximal number of occurences per peptide
    UInt getMaxOccurences() const;

    /// returns the modification set
    String getModification() const;

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

    /** @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:

    /// allowed position
    ResidueModification::Term_Specificity term_spec_;

    /// the modification
    const ResidueModification * mod_;

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

    /// maximal number of occurences per peptide
    UInt max_occurences_;
  };

} // namespace OpenMS

#endif