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 (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... | |
 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... | |
Additional Inherited Members | |
| Protected Member Functions inherited from DefaultParamHandler | |
| 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... | |
| 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.
Constructor & Destructor Documentation
default constructor
| TheoreticalSpectrumGenerator | ( | const TheoreticalSpectrumGenerator & | source | ) |
copy constructor
|
virtual |
destructor
Member Function Documentation
| void addAbundantImmoniumIons | ( | RichPeakSpectrum & | spec | ) | const |
Adds the common, most abundant immonium ions to the theoretical spectra.
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
|
virtual |
adds peaks to a spectrum of the given ion-type, peptide, charge, and intensity
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
|
virtual |
adds the precursor peaks to the spectrum
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
|
virtual |
returns a spectrum with b and y peaks
Referenced by SimpleSearchEngine::main_().
| TheoreticalSpectrumGenerator& operator= | ( | const TheoreticalSpectrumGenerator & | tsg | ) |
assignment operator