libopenms-dev 1.11.1-5 / usr / include / OpenMS / METADATA / Modification.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 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_METADATA_MODIFICATION_H
#define OPENMS_METADATA_MODIFICATION_H

#include <OpenMS/METADATA/SampleTreatment.h>

#include <OpenMS/DATASTRUCTURES/String.h>

namespace OpenMS
{
  /**
      @brief Meta information about chemical modification of a sample

      Representation of some kind of modification.
      It hold information about what amino acids are modified and how much the mass changes.

      @ingroup Metadata
  */
  class OPENMS_DLLAPI Modification :
    public SampleTreatment
  {
public:
    /// specificity of the reagent.
    enum SpecificityType
    {
      AA       ///< specified amino acids are modified
      , AA_AT_CTERM      ///< specified amino acids are modified, if they are at the C-terminus
      , AA_AT_NTERM      ///< specified amino acids are modified, if they are at the N-terminus
      , CTERM      ///< the C-termiuns is modified
      , NTERM      ///< the N-termiuns is modified
      , SIZE_OF_SPECIFICITYTYPE
    };
    /// Names of specifitiy types
    static const std::string NamesOfSpecificityType[SIZE_OF_SPECIFICITYTYPE];

    /// default constructor
    Modification();
    /// copy constructor
    Modification(const Modification &);
    /// destructor
    virtual ~Modification();

    /// assignment operator
    Modification & operator=(const Modification &);

    /**
        @brief Equality operator

    Although this operator takes a reference to a SampleTreatment as argument
    it tests for the equality of Tagging instances!
  */
    virtual bool operator==(const SampleTreatment & rhs) const;

    /// clone method. See SampleTreatment
    virtual SampleTreatment * clone() const;

    /// returns the name of the reagent that was used (default: "")
    const String & getReagentName() const;
    /// sets the name of the reagent that was used
    void setReagentName(const String & reagent_name);

    /// returns the mass change (default: 0.0)
    DoubleReal getMass() const;
    /// sets the mass change
    void setMass(DoubleReal mass);

    /// returns the specificity of the the reagent (default: AA)
    const SpecificityType & getSpecificityType() const;
    /// sets the specificity of the the reagent
    void setSpecificityType(const SpecificityType & specificity_type);

    /// returns a string containing the one letter code of the amino acids that are affected by the reagent. (default: "")
    const String & getAffectedAminoAcids() const;
    /// returns a string containing the one letter code of the amino acids that are affected by the reagent. Do not separate them by space, tab or comma!
    void setAffectedAminoAcids(const String & affected_amino_acids);

protected:
    String reagent_name_;
    DoubleReal mass_;
    SpecificityType specificity_type_;
    String affected_amino_acids_;
  };
} // namespace OpenMS

#endif // OPENMS_METADATA_MODIFICATION_H