Generates theoretical spectra with various options. More...
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
Public Member Functions | |
TheoreticalSpectrumGenerator & | operator= (const TheoreticalSpectrumGenerator &tsg) |
assignment operator More... | |
Constructors and Destructors | |
TheoreticalSpectrumGenerator () | |
default constructor More... | |
TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | |
copy constructor More... | |
virtual | ~TheoreticalSpectrumGenerator () |
destructor More... | |
Acessors | |
virtual void | getSpectrum (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) const |
returns a spectrum with b and y peaks More... | |
virtual void | addPeaks (RichPeakSpectrum &spectrum, const AASequence &peptide, Residue::ResidueType res_type, Int charge=1) const |
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity More... | |
virtual void | addPrecursorPeaks (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1) const |
adds the precursor peaks to the spectrum More... | |
void | addAbundantImmoniumIons (RichPeakSpectrum &spec) const |
Adds the common, most abundant immonium ions to the theoretical spectra. More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Additional Inherited Members | |
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virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Generates theoretical spectra with various options.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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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 |
default constructor
TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
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virtual |
destructor
void addAbundantImmoniumIons | ( | RichPeakSpectrum & | spec | ) | const |
Adds the common, most abundant immonium ions to the theoretical spectra.
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
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virtual |
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
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virtual |
adds the precursor peaks to the spectrum
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
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virtual |
returns a spectrum with b and y peaks
Referenced by SimpleSearchEngine::main_().
TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:45 using doxygen 1.8.5 |