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TheoreticalSpectrumGenerator Class Reference

Generates theoretical spectra with various options. More...

#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>

Inheritance diagram for TheoreticalSpectrumGenerator:
DefaultParamHandler

Public Member Functions

TheoreticalSpectrumGeneratoroperator= (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)
 returns a spectrum with b and y peaks More...
 
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 More...
 
virtual void addPrecursorPeaks (RichPeakSpectrum &spec, const AASequence &peptide, Int charge=1)
 adds the precursor peaks to the spectrum More...
 
void addAbundantImmoniumIons (RichPeakSpectrum &spec)
 Adds the common, most abundant immonium ions to the theoretical specta. 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 Attributes

RichPeak1D p_
 
- 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< Stringsubsections_
 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...
 

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...
 

Detailed Description

Generates theoretical spectra with various options.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
add_isotopes stringfalse true, falseIf set to 1 isotope peaks of the product ion peaks are added
max_isotope int2  Defines the maximal isotopic peak which is added, add_isotopes must be set to 1
add_metainfo stringfalse true, falseAdds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
add_losses stringfalse true, falseAdds common losses to those ion expect to have them, only water and ammonia loss is considered
add_precursor_peaks stringfalse true, falseAdds peaks of the precursor to the spectrum, which happen to occur sometimes
add_abundant_immonium_ions stringfalse true, falseAdd most abundant immonium ions
add_first_prefix_ion stringfalse true, falseIf set to true e.g. b1 ions are added
add_y_ions stringtrue true, falseAdd peaks of y-ions to the spectrum
add_b_ions stringtrue true, falseAdd peaks of b-ions to the spectrum
add_a_ions stringfalse true, falseAdd peaks of a-ions to the spectrum
add_c_ions stringfalse true, falseAdd peaks of c-ions to the spectrum
add_x_ions stringfalse true, falseAdd peaks of x-ions to the spectrum
add_z_ions stringfalse true, falseAdd peaks of z-ions to the spectrum
y_intensity float1  Intensity of the y-ions
b_intensity float1  Intensity of the b-ions
a_intensity float1  Intensity of the a-ions
c_intensity float1  Intensity of the c-ions
x_intensity float1  Intensity of the x-ions
z_intensity float1  Intensity of the z-ions
relative_loss_intensity float0.1  Intensity of loss ions, in relation to the intact ion intensity
precursor_intensity float1  Intensity of the precursor peak
precursor_H2O_intensity float1  Intensity of the H2O loss peak of the precursor
precursor_NH3_intensity float1  Intensity of the NH3 loss peak of the precursor

Note:

Constructor & Destructor Documentation

default constructor

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

assignment operator

Member Data Documentation

RichPeak1D p_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5