ResidueModification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_CHEMISTRY_RESIDUEMODIFICATION_H
#define OPENMS_CHEMISTRY_RESIDUEMODIFICATION_H

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

#include <set>

namespace OpenMS
{
  // forward declaration
  class Residue;

  class OPENMS_DLLAPI ResidueModification
  {
public:

    enum Term_Specificity
    {
      ANYWHERE = 0,
      C_TERM = 1,
      N_TERM = 2,
      NUMBER_OF_TERM_SPECIFICITY
    };

    enum Source_Classification
    {
      ARTIFACT = 0,
      HYPOTHETICAL,
      NATURAL,
      POSTTRANSLATIONAL,
      MULTIPLE,
      CHEMICAL_DERIVATIVE,
      ISOTOPIC_LABEL,
      PRETRANSLATIONAL,
      OTHER_GLYCOSYLATION,
      NLINKED_GLYCOSYLATION,
      AA_SUBSTITUTION,
      OTHER,
      NONSTANDARD_RESIDUE,
      COTRANSLATIONAL,
      OLINKED_GLYCOSYLATION,
      UNKNOWN,
      NUMBER_OF_SOURCE_CLASSIFICATIONS
    };




    ResidueModification();

    ResidueModification(const ResidueModification & modification);

    virtual ~ResidueModification();


    ResidueModification & operator=(const ResidueModification & modification);


    void setId(const String & id);

    const String & getId() const;

    void setFullId(const String & full_id);

    const String & getFullId() const;

    void setUniModAccession(const String & id);

    const String & getUniModAccession() const;

    void setPSIMODAccession(const String & id);

    const String & getPSIMODAccession() const;

    void setFullName(const String & full_name);

    const String & getFullName() const;

    void setName(const String & name);

    const String & getName() const;

    void setTermSpecificity(Term_Specificity term_spec);

    void setTermSpecificity(const String & name);

    Term_Specificity getTermSpecificity() const;

    String getTermSpecificityName(Term_Specificity = NUMBER_OF_TERM_SPECIFICITY) const;

    void setOrigin(const String & origin);

    const String & getOrigin() const;

    void setSourceClassification(const String & classification);

    void setSourceClassification(Source_Classification classification);

    Source_Classification getSourceClassification() const;

    String getSourceClassificationName(Source_Classification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;

    void setAverageMass(DoubleReal mass);

    DoubleReal getAverageMass() const;

    void setMonoMass(DoubleReal mass);

    DoubleReal getMonoMass() const;

    void setDiffAverageMass(DoubleReal mass);

    DoubleReal getDiffAverageMass() const;

    void setDiffMonoMass(DoubleReal mass);

    DoubleReal getDiffMonoMass() const;

    void setFormula(const String & composition);

    const String & getFormula() const;

    void setDiffFormula(const EmpiricalFormula & diff_formula);

    const EmpiricalFormula & getDiffFormula() const;

    void setSynonyms(const std::set<String> & synonyms);

    void addSynonym(const String & synonym);

    const std::set<String> & getSynonyms() const;

    void setNeutralLossDiffFormula(const EmpiricalFormula & loss);

    const EmpiricalFormula & getNeutralLossDiffFormula() const;

    void setNeutralLossMonoMass(DoubleReal mono_mass);

    DoubleReal getNeutralLossMonoMass() const;

    void setNeutralLossAverageMass(DoubleReal average_mass);

    DoubleReal getNeutralLossAverageMass() const;


    bool hasNeutralLoss() const;

    bool operator==(const ResidueModification & modification) const;

    bool operator!=(const ResidueModification & modification) const;

protected:

    String id_;

    String full_id_;

    String psi_mod_accession_;

    String unimod_accession_;

    String full_name_;

    String name_;

    Term_Specificity term_spec_;

    String origin_;

    Source_Classification classification_;

    DoubleReal average_mass_;

    DoubleReal mono_mass_;

    DoubleReal diff_average_mass_;

    DoubleReal diff_mono_mass_;

    String formula_;

    EmpiricalFormula diff_formula_;

    std::set<String> synonyms_;

    EmpiricalFormula neutral_loss_diff_formula_;

    DoubleReal neutral_loss_mono_mass_;

    DoubleReal neutral_loss_average_mass_;
  };
}

#endif