OpenMS
NucleicAcidSpectrumGenerator Class Reference

Generates theoretical spectra for nucleic acid sequences. More...

#include <OpenMS/CHEMISTRY/NucleicAcidSpectrumGenerator.h>

Inheritance diagram for NucleicAcidSpectrumGenerator:
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Collaboration diagram for NucleicAcidSpectrumGenerator:
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Public Member Functions

Constructors and Destructors
 NucleicAcidSpectrumGenerator ()
 default constructor More...
 
 NucleicAcidSpectrumGenerator (const NucleicAcidSpectrumGenerator &source)
 copy constructor More...
 
 ~NucleicAcidSpectrumGenerator () override
 destructor More...
 
NucleicAcidSpectrumGeneratoroperator= (const NucleicAcidSpectrumGenerator &source)
 assignment operator 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...
 
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...
 

Acessors

bool add_a_ions_
 
bool add_b_ions_
 
bool add_c_ions_
 
bool add_d_ions_
 
bool add_w_ions_
 
bool add_x_ions_
 
bool add_y_ions_
 
bool add_z_ions_
 
bool add_aB_ions_
 
bool add_first_prefix_ion_
 
bool add_metainfo_
 
bool add_precursor_peaks_
 
bool add_all_precursor_charges_
 
double a_intensity_
 
double b_intensity_
 
double c_intensity_
 
double d_intensity_
 
double w_intensity_
 
double x_intensity_
 
double y_intensity_
 
double z_intensity_
 
double aB_intensity_
 
double precursor_intensity_
 
void getSpectrum (MSSpectrum &spectrum, const NASequence &oligo, Int min_charge, Int max_charge) const
 Generates a spectrum for an oligonucleotide sequence, with the ion types that are set in the tool parameters. More...
 
void getMultipleSpectra (std::map< Int, MSSpectrum > &spectra, const NASequence &oligo, const std::set< Int > &charges, Int base_charge=1) const
 Generates spectra in multiple charge states for an oligonucleotide sequence. More...
 
void updateMembers_ () override
 overwrite More...
 
void addFragmentPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const String &ion_type, double offset, double intensity, Size start=0) const
 Helper function to add (uncharged) fragment peaks to a spectrum. More...
 
void addAMinusBPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const NASequence &oligo, Size start=0) const
 Special version of addFragmentPeaks_() for a-B ions. More...
 
MSSpectrum getUnchargedSpectrum_ (const NASequence &oligo) const
 Generates a spectrum containing peaks for uncharged fragment masses. More...
 
void addChargedSpectrum_ (MSSpectrum &spectrum, const MSSpectrum &uncharged_spectrum, Int charge, bool add_precursor) const
 Adds a charged version of an uncharged spectrum to another spectrum. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
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< 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...
 

Detailed Description

Generates theoretical spectra for nucleic acid sequences.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
add_metainfo stringfalse true, falseAdds the type of peaks as meta information to the peaks, e.g. c1, y2, a3-B
add_precursor_peaks stringfalse true, falseAdds peaks of the unfragmented precursor ion to the spectrum
add_all_precursor_charges stringfalse true, falseAdds precursor peaks with all charges in the given range
add_first_prefix_ion stringfalse true, falseIf set to true a1, b1, ..., z1 ions are added
add_a_ions stringfalse true, falseAdd peaks of a-ions to the spectrum
add_b_ions stringtrue true, falseAdd peaks of b-ions to the spectrum
add_c_ions stringfalse true, falseAdd peaks of c-ions to the spectrum
add_d_ions stringfalse true, falseAdd peaks of d-ions to the spectrum
add_w_ions stringfalse true, falseAdd peaks of w-ions to the spectrum
add_x_ions stringfalse true, falseAdd peaks of x-ions to the spectrum
add_y_ions stringtrue true, falseAdd peaks of y-ions to the spectrum
add_z_ions stringfalse true, falseAdd peaks of z-ions to the spectrum
add_a-B_ions stringfalse true, falseAdd peaks of a-B-ions to the spectrum
a_intensity float1.0  Intensity of the a-ions
b_intensity float1.0  Intensity of the b-ions
c_intensity float1.0  Intensity of the c-ions
d_intensity float1.0  Intensity of the d-ions
w_intensity float1.0  Intensity of the w-ions
x_intensity float1.0  Intensity of the x-ions
y_intensity float1.0  Intensity of the y-ions
z_intensity float1.0  Intensity of the z-ions
a-B_intensity float1.0  Intensity of the a-B-ions
precursor_intensity float1.0  Intensity of the precursor peak

Note:
  • If a section name is documented, the documentation is displayed as tooltip.
  • Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ NucleicAcidSpectrumGenerator() [1/2]

default constructor

◆ NucleicAcidSpectrumGenerator() [2/2]

copy constructor

◆ ~NucleicAcidSpectrumGenerator()

destructor

Member Function Documentation

◆ addAMinusBPeaks_()

void addAMinusBPeaks_ ( MSSpectrum spectrum,
const std::vector< double > &  fragment_masses,
const NASequence oligo,
Size  start = 0 
) const
protected

Special version of addFragmentPeaks_() for a-B ions.

◆ addChargedSpectrum_()

void addChargedSpectrum_ ( MSSpectrum spectrum,
const MSSpectrum uncharged_spectrum,
Int  charge,
bool  add_precursor 
) const
protected

Adds a charged version of an uncharged spectrum to another spectrum.

◆ addFragmentPeaks_()

void addFragmentPeaks_ ( MSSpectrum spectrum,
const std::vector< double > &  fragment_masses,
const String ion_type,
double  offset,
double  intensity,
Size  start = 0 
) const
protected

Helper function to add (uncharged) fragment peaks to a spectrum.

◆ getMultipleSpectra()

void getMultipleSpectra ( std::map< Int, MSSpectrum > &  spectra,
const NASequence oligo,
const std::set< Int > &  charges,
Int  base_charge = 1 
) const

Generates spectra in multiple charge states for an oligonucleotide sequence.

Parameters
spectraOutput spectra
oligoTarget oligonucleotide sequence
chargesSet of charge states to generate
base_chargeMinimum charge for peaks in each spectrum

One spectrum per element in charges is generated in spectra.

All values in charges must be either positive or negative.

This function is more efficient than calling getSpectrum() multiple times, because spectra of lower charge states are reused.

Referenced by NucleicAcidSearchEngine::main_().

◆ getSpectrum()

void getSpectrum ( MSSpectrum spectrum,
const NASequence oligo,
Int  min_charge,
Int  max_charge 
) const

Generates a spectrum for an oligonucleotide sequence, with the ion types that are set in the tool parameters.

◆ getUnchargedSpectrum_()

MSSpectrum getUnchargedSpectrum_ ( const NASequence oligo) const
protected

Generates a spectrum containing peaks for uncharged fragment masses.

◆ operator=()

assignment operator

◆ updateMembers_()

void updateMembers_ ( )
overridevirtual

overwrite

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ a_intensity_

double a_intensity_
protected

◆ aB_intensity_

double aB_intensity_
protected

◆ add_a_ions_

bool add_a_ions_
protected

◆ add_aB_ions_

bool add_aB_ions_
protected

◆ add_all_precursor_charges_

bool add_all_precursor_charges_
protected

◆ add_b_ions_

bool add_b_ions_
protected

◆ add_c_ions_

bool add_c_ions_
protected

◆ add_d_ions_

bool add_d_ions_
protected

◆ add_first_prefix_ion_

bool add_first_prefix_ion_
protected

◆ add_metainfo_

bool add_metainfo_
protected

◆ add_precursor_peaks_

bool add_precursor_peaks_
protected

◆ add_w_ions_

bool add_w_ions_
protected

◆ add_x_ions_

bool add_x_ions_
protected

◆ add_y_ions_

bool add_y_ions_
protected

◆ add_z_ions_

bool add_z_ions_
protected

◆ b_intensity_

double b_intensity_
protected

◆ c_intensity_

double c_intensity_
protected

◆ d_intensity_

double d_intensity_
protected

◆ precursor_intensity_

double precursor_intensity_
protected

◆ w_intensity_

double w_intensity_
protected

◆ x_intensity_

double x_intensity_
protected

◆ y_intensity_

double y_intensity_
protected

◆ z_intensity_

double z_intensity_
protected