![]() |
OpenMS
2.4.0
|
Generates theoretical spectra with various options. More...
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
Public Member Functions | |
Constructors and Destructors | |
TheoreticalSpectrumGenerator () | |
default constructor More... | |
TheoreticalSpectrumGenerator (const TheoreticalSpectrumGenerator &source) | |
copy constructor More... | |
~TheoreticalSpectrumGenerator () override | |
destructor More... | |
TheoreticalSpectrumGenerator & | operator= (const TheoreticalSpectrumGenerator &tsg) |
assignment operator More... | |
![]() | |
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... | |
Acessors | |
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_ |
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_ () override |
overwrite More... | |
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... | |
Additional Inherited Members | |
![]() | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
![]() | |
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.
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.
default constructor
TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
|
override |
destructor
|
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.
|
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
|
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
|
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
|
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
|
virtual |
returns a spectrum with the ion types, that are set in the tool parameters
Referenced by RNPxlSearch::RNPxlFragmentIonGenerator::generatePartialLossSpectrum(), SimpleSearchEngine::main_(), RNPxlSearch::main_(), RNPxlSearch::postScoreHits_(), and TOPPViewBase::showSpectrumGenerationDialog().
TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator
|
protected |
helper for mapping residue type to letter
|
overridevirtual |
overwrite
Reimplemented from DefaultParamHandler.
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |