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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.