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| TheoreticalSpectrumGenerator & | operator= (const TheoreticalSpectrumGenerator &tsg) | 
|  | assignment operator  More... 
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|  | TheoreticalSpectrumGenerator () | 
|  | default constructor  More... 
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|  | TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | 
|  | copy constructor  More... 
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| virtual | ~TheoreticalSpectrumGenerator () | 
|  | destructor  More... 
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| virtual void | getSpectrum (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) | 
|  | returns a spectrum with b and y peaks  More... 
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| virtual void | addPeaks (RichPeakSpectrum &spectrum, const AASequence &peptide, Residue::ResidueType res_type, Int charge=1) | 
|  | adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity  More... 
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| virtual void | addPrecursorPeaks (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) | 
|  | adds the precursor peaks to the spectrum  More... 
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| void | addAbundantImmoniumIons (RichPeakSpectrum &spec) | 
|  | Adds the common, most abundant immonium ions to the theoretical specta.  More... 
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|  Public Member Functions inherited from DefaultParamHandler | 
|  | DefaultParamHandler (const String &name) | 
|  | Constructor with name that is displayed in error messages.  More... 
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|  | DefaultParamHandler (const DefaultParamHandler &rhs) | 
|  | Copy constructor.  More... 
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| virtual | ~DefaultParamHandler () | 
|  | Destructor.  More... 
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| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
|  | Assignment operator.  More... 
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| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
|  | Equality operator.  More... 
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| void | setParameters (const Param ¶m) | 
|  | Sets the parameters.  More... 
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| const Param & | getParameters () const | 
|  | Non-mutable access to the parameters.  More... 
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| const Param & | getDefaults () const | 
|  | Non-mutable access to the default parameters.  More... 
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| const String & | getName () const | 
|  | Non-mutable access to the name.  More... 
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| void | setName (const String &name) | 
|  | Mutable access to the name.  More... 
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| const std::vector< String > & | getSubsections () const | 
|  | Non-mutable access to the registered subsections.  More... 
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Generates theoretical spectra with various options. 
Parameters of this class are:
| Name | Type | Default | Restrictions | Description | 
|---|
  | add_isotopes | string | false | true, false | If set to 1 isotope peaks of the product ion peaks are added | 
  | max_isotope | int | 2 |  | Defines the maximal isotopic peak which is added, add_isotopes must be set to 1 | 
  | add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++ | 
  | add_losses | string | false | true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered | 
  | add_precursor_peaks | string | false | true, false | Adds peaks of the precursor to the spectrum, which happen to occur sometimes | 
  | add_abundant_immonium_ions | string | false | true, false | Add most abundant immonium ions | 
  | add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added | 
  | add_y_ions | string | true | true, false | Add peaks of y-ions to the spectrum | 
  | add_b_ions | string | true | true, false | Add peaks of b-ions to the spectrum | 
  | add_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum | 
  | add_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum | 
  | add_x_ions | string | false | true, false | Add peaks of  x-ions to the spectrum | 
  | add_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum | 
  | y_intensity | float | 1 |  | Intensity of the y-ions | 
  | b_intensity | float | 1 |  | Intensity of the b-ions | 
  | a_intensity | float | 1 |  | Intensity of the a-ions | 
  | c_intensity | float | 1 |  | Intensity of the c-ions | 
  | x_intensity | float | 1 |  | Intensity of the x-ions | 
  | z_intensity | float | 1 |  | Intensity of the z-ions | 
  | relative_loss_intensity | float | 0.1 |  | Intensity of loss ions, in relation to the intact ion intensity | 
  | precursor_intensity | float | 1 |  | Intensity of the precursor peak | 
  | precursor_H2O_intensity | float | 1 |  | Intensity of the H2O loss peak of the precursor | 
  | precursor_NH3_intensity | float | 1 |  | Intensity of the NH3 loss peak of the precursor | 
Note:
  -  If a section name is documented, the documentation is displayed as tooltip.
  
-  Advanced parameter names are italic.