NucleicAcidSpectrumGenerator Class Reference

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

#include <OpenMS/CHEMISTRY/NucleicAcidSpectrumGenerator.h>

Inheritance diagram for NucleicAcidSpectrumGenerator:

Public Member Functions
Constructors and Destructors
	NucleicAcidSpectrumGenerator ()
	default constructor More...
	NucleicAcidSpectrumGenerator (const NucleicAcidSpectrumGenerator &source)
	copy constructor More...
	~NucleicAcidSpectrumGenerator () override
	destructor More...
NucleicAcidSpectrumGenerator &	operator= (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...
virtual DefaultParamHandler &	operator= (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 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_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
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< 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 for nucleic acid sequences.

Constructor & Destructor Documentation

NucleicAcidSpectrumGenerator() [1/2]

NucleicAcidSpectrumGenerator

(

)

default constructor

NucleicAcidSpectrumGenerator() [2/2]

NucleicAcidSpectrumGenerator

(

const NucleicAcidSpectrumGenerator &

source

)

copy constructor

~NucleicAcidSpectrumGenerator()

~NucleicAcidSpectrumGenerator ( )

override

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

spectra	Output spectra
oligo	Target oligonucleotide sequence
charges	Set of charge states to generate
base_charge	Minimum 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=()

NucleicAcidSpectrumGenerator& operator=

(

const NucleicAcidSpectrumGenerator &

source

)

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