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 More... | |
Constructors and Destructors | |
| TheoreticalSpectrumGenerator () | |
| default constructor More... | |
| TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | |
| copy constructor More... | |
| virtual | ~TheoreticalSpectrumGenerator () |
| destructor More... | |
Acessors | |
| virtual void | getSpectrum (PeakSpectrum &spec, const AASequence &peptide, Int min_charge, Int max_charge) const |
| returns a spectrum with the ion types, that are set in the tool parameters More... | |
| void | updateMembers_ () |
| overwrite More... | |
 Public Member Functions inherited from DefaultParamHandler | |
| 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... | |
Protected Member Functions | |
| virtual void | addPeaks_ (PeakSpectrum &spectrum, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Residue::ResidueType res_type, Int charge=1) const |
| adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More... | |
| virtual void | addPrecursorPeaks_ (PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Int charge=1) const |
| adds the precursor peaks to the spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More... | |
| void | addAbundantImmoniumIons_ (PeakSpectrum &spec, const AASequence &peptide, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges) const |
| Adds the common, most abundant immonium ions to the theoretical spectra if the residue is contained in the peptide sequence, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true. More... | |
| void | addIsotopeCluster_ (PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, Residue::ResidueType res_type, Int charge, double intensity) const |
| helper to add an isotope cluster to a spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More... | |
| char | residueTypeToIonLetter_ (Residue::ResidueType res_type) const |
| helper for mapping residue type to letter More... | |
| void | addLosses_ (PeakSpectrum &spectrum, const AASequence &ion, DataArrays::StringDataArray &ion_names, DataArrays::IntegerDataArray &charges, double intensity, Residue::ResidueType res_type, int charge) const |
| helper to add full neutral loss ladders, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true More... | |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
| bool | add_b_ions_ |
| bool | add_y_ions_ |
| bool | add_a_ions_ |
| bool | add_c_ions_ |
| bool | add_x_ions_ |
| bool | add_z_ions_ |
| bool | add_first_prefix_ion_ |
| bool | add_losses_ |
| bool | add_metainfo_ |
| bool | add_isotopes_ |
| bool | add_precursor_peaks_ |
| bool | add_all_precursor_charges_ |
| bool | add_abundant_immonium_ions_ |
| double | a_intensity_ |
| double | b_intensity_ |
| double | c_intensity_ |
| double | x_intensity_ |
| double | y_intensity_ |
| double | z_intensity_ |
| Int | max_isotope_ |
| double | rel_loss_intensity_ |
| double | pre_int_ |
| double | pre_int_H2O_ |
| double | pre_int_NH3_ |
| Protected Attributes inherited from DefaultParamHandler | |
| 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... | |
Detailed Description
Generates theoretical spectra with various options.
If the tool parameter add_metainfo is set to true, ion names like y8+ or [M-H2O+2H]++ are written as strings in a StringDataArray with the name "IonNames" and charges are written as integers in an IntegerDataArray with the name "Charges" in the returned PeakSpectrum.
The getSpectrum function can be called with the same PeakSpectrum multiple times to add additional peaks. If the PeakSpectrum already has DataArrays, then the first StringDataArray and the first IntegerDataArray are extended. Therefore it is not recommended to add to or change the PeakSpectrum or these DataArrays between calls of the getSpectrum function with the same PeakSpectrum.
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_all_precursor_charges | string | false | true, false | Adds precursor peaks with all charges in the given range |
| 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
◆ TheoreticalSpectrumGenerator() [1/2]
default constructor
◆ TheoreticalSpectrumGenerator() [2/2]
| TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
◆ ~TheoreticalSpectrumGenerator()
|
virtual |
destructor
Member Function Documentation
◆ addAbundantImmoniumIons_()
|
protected |
Adds the common, most abundant immonium ions to the theoretical spectra if the residue is contained in the peptide sequence, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true.
◆ addIsotopeCluster_()
|
protected |
helper to add an isotope cluster to a spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true
◆ addLosses_()
|
protected |
helper to add full neutral loss ladders, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true
◆ addPeaks_()
|
protectedvirtual |
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true
◆ addPrecursorPeaks_()
|
protectedvirtual |
adds the precursor peaks to the spectrum, also adds charges and ion names to the DataArrays, if the add_metainfo parameter is set to true
◆ getSpectrum()
|
virtual |
returns a spectrum with the ion types, that are set in the tool parameters
Referenced by SimpleSearchEngine::main_(), RNPxlSearch::main_(), RNPxlSearch::postScoreHits_(), and TOPPViewBase::showSpectrumGenerationDialog().
◆ operator=()
| TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator
◆ residueTypeToIonLetter_()
|
protected |
helper for mapping residue type to letter
◆ updateMembers_()
|
virtual |
overwrite
Reimplemented from DefaultParamHandler.
Member Data Documentation
◆ a_intensity_
|
protected |
◆ add_a_ions_
|
protected |
◆ add_abundant_immonium_ions_
|
protected |
◆ add_all_precursor_charges_
|
protected |
◆ add_b_ions_
|
protected |
◆ add_c_ions_
|
protected |
◆ add_first_prefix_ion_
|
protected |
◆ add_isotopes_
|
protected |
◆ add_losses_
|
protected |
◆ add_metainfo_
|
protected |
◆ add_precursor_peaks_
|
protected |
◆ add_x_ions_
|
protected |
◆ add_y_ions_
|
protected |
◆ add_z_ions_
|
protected |
◆ b_intensity_
|
protected |
◆ c_intensity_
|
protected |
◆ max_isotope_
|
protected |
◆ pre_int_
|
protected |
◆ pre_int_H2O_
|
protected |
◆ pre_int_NH3_
|
protected |
◆ rel_loss_intensity_
|
protected |
◆ x_intensity_
|
protected |
◆ y_intensity_
|
protected |
◆ z_intensity_
|
protected |