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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.