Generates theoretical spectra with various options. More...
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
Inheritance diagram for TheoreticalSpectrumGenerator:
Public Member Functions | |
| TheoreticalSpectrumGenerator & | operator= (const TheoreticalSpectrumGenerator &tsg) |
| assignment operator | |
Constructors and Destructors | |
| TheoreticalSpectrumGenerator () | |
| default constructor | |
| TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | |
| copy constructor | |
| virtual | ~TheoreticalSpectrumGenerator () |
| destructor | |
Acessors | |
| virtual void | getSpectrum (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) |
| returns a spectrum with b and y peaks | |
| 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 | |
| virtual void | addPrecursorPeaks (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) |
| adds the precursor peaks to the spectrum | |
| void | addAbundantImmoniumIons (RichPeakSpectrum &spec) |
| Adds the common, most abundant immonium ions to the theoretical specta. | |
Protected Attributes | |
| RichPeak1D | p_ |
Detailed Description
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.
Constructor & Destructor Documentation
default constructor
| TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
| virtual ~TheoreticalSpectrumGenerator | ( | ) | [virtual] |
destructor
Member Function Documentation
| void addAbundantImmoniumIons | ( | RichPeakSpectrum & | spec | ) |
Adds the common, most abundant immonium ions to the theoretical specta.
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
| virtual void addPeaks | ( | RichPeakSpectrum & | spectrum, | |
| const AASequence & | peptide, | |||
| Residue::ResidueType | res_type, | |||
| Int | charge = 1 | |||
| ) | [virtual] |
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
| virtual void addPrecursorPeaks | ( | RichPeakSpectrum & | spec, | |
| const AASequence & | peptide, | |||
| Int | charge = 1 | |||
| ) | [virtual] |
adds the precursor peaks to the spectrum
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
| virtual void getSpectrum | ( | RichPeakSpectrum & | spec, | |
| const AASequence & | peptide, | |||
| Int | charge = 1 | |||
| ) | [virtual] |
returns a spectrum with b and y peaks
| TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator
Member Data Documentation
RichPeak1D p_ [protected] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |