OpenMS
IsotopeModel.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Clemens Groepl, Chris Bielow $
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34 
35 
36 #pragma once
37 
40 
41 namespace OpenMS
42 {
43  class EmpiricalFormula;
44 
58  class OPENMS_DLLAPI IsotopeModel :
59  public InterpolationModel
60  {
61 
62 public:
65 
66  enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};
67 
70 
72  IsotopeModel(const IsotopeModel & source);
73 
75  ~IsotopeModel() override;
76 
78  virtual IsotopeModel & operator=(const IsotopeModel & source);
79 
80  UInt getCharge() const;
81 
83  static BaseModel<1> * create()
84  {
85  return new IsotopeModel();
86  }
87 
89  static const String getProductName()
90  {
91  return "IsotopeModel";
92  }
93 
101  void setOffset(CoordinateType offset) override;
102 
104 
107 
109  virtual void setSamples(const EmpiricalFormula & formula);
110 
113 
118  CoordinateType getCenter() const override;
119 
126 
127 
128 protected:
131 
135  double averagine_[AVERAGINE_NUM];
140 
141  void updateMembers_() override;
142 
143  };
144 }
145 
Representation of an empirical formula.
Definition: EmpiricalFormula.h:85
Abstract class for 1D-models that are approximated using linear interpolation.
Definition: InterpolationModel.h:56
double CoordinateType
Definition: InterpolationModel.h:61
virtual void setSamples()
set sample/supporting points of interpolation wrt params.
Definition: InterpolationModel.h:162
Definition: IsotopeDistribution.h:65
Isotope distribution approximated using linear interpolation.
Definition: IsotopeModel.h:60
UInt charge_
Definition: IsotopeModel.h:132
CoordinateType isotope_stdev_
Definition: IsotopeModel.h:129
EmpiricalFormula getFormula()
return the Averagine peptide formula (mass calculated from mean mass and charge – use ....
IsotopeDistribution isotope_distribution_
Definition: IsotopeModel.h:139
virtual IsotopeModel & operator=(const IsotopeModel &source)
assignment operator
CoordinateType monoisotopic_mz_
Definition: IsotopeModel.h:134
void setOffset(CoordinateType offset) override
set the offset of the model
double isotope_distance_
Definition: IsotopeModel.h:138
IsotopeModel(const IsotopeModel &source)
copy constructor
InterpolationModel::CoordinateType CoordinateType
Definition: IsotopeModel.h:63
CoordinateType isotope_lorentz_fwhm_
Definition: IsotopeModel.h:130
virtual void setSamples(const EmpiricalFormula &formula)
set sample/supporting points of interpolation
InterpolationModel::CoordinateType IntensityType
Definition: IsotopeModel.h:64
~IsotopeModel() override
destructor
const IsotopeDistribution & getIsotopeDistribution() const
the Isotope distribution (without widening) from the last setSamples() call
CoordinateType getCenter() const override
get the center of the Isotope model
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
static BaseModel< 1 > * create()
create new IsotopeModel object (needed by Factory)
Definition: IsotopeModel.h:83
UInt getCharge() const
Averagines
Definition: IsotopeModel.h:66
double trim_right_cutoff_
Definition: IsotopeModel.h:137
Int max_isotope_
Definition: IsotopeModel.h:136
IsotopeModel()
Default constructor.
static const String getProductName()
name of the model (needed by Factory)
Definition: IsotopeModel.h:89
CoordinateType mean_
Definition: IsotopeModel.h:133
CoordinateType getOffset()
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48