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

#include <OpenMS/CHEMISTRY/NucleicAcidSpectrumGenerator.h>

Inheritance diagram for NucleicAcidSpectrumGenerator:

Collaboration 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...

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
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< 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.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
add_metainfo	string	false	true, false	Adds the type of peaks as meta information to the peaks, e.g. c1, y2, a3-B
add_precursor_peaks	string	false	true, false	Adds peaks of the unfragmented precursor ion to the spectrum
add_all_precursor_charges	string	false	true, false	Adds precursor peaks with all charges in the given range
add_first_prefix_ion	string	false	true, false	If set to true a1, b1, ..., z1 ions are added
add_a_ions	string	false	true, false	Add peaks of a-ions to the spectrum
add_b_ions	string	true	true, false	Add peaks of b-ions to the spectrum
add_c_ions	string	false	true, false	Add peaks of c-ions to the spectrum
add_d_ions	string	false	true, false	Add peaks of d-ions to the spectrum
add_w_ions	string	false	true, false	Add peaks of w-ions to the spectrum
add_x_ions	string	false	true, false	Add peaks of x-ions to the spectrum
add_y_ions	string	true	true, false	Add peaks of y-ions to the spectrum
add_z_ions	string	false	true, false	Add peaks of z-ions to the spectrum
add_a-B_ions	string	false	true, false	Add peaks of a-B-ions to the spectrum
a_intensity	float	1.0		Intensity of the a-ions
b_intensity	float	1.0		Intensity of the b-ions
c_intensity	float	1.0		Intensity of the c-ions
d_intensity	float	1.0		Intensity of the d-ions
w_intensity	float	1.0		Intensity of the w-ions
x_intensity	float	1.0		Intensity of the x-ions
y_intensity	float	1.0		Intensity of the y-ions
z_intensity	float	1.0		Intensity of the z-ions
a-B_intensity	float	1.0		Intensity of the a-B-ions
precursor_intensity	float	1.0		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]

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

Public Member Functions

Acessors

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NucleicAcidSpectrumGenerator() [1/2]

◆ NucleicAcidSpectrumGenerator() [2/2]

◆ ~NucleicAcidSpectrumGenerator()

Member Function Documentation

◆ addAMinusBPeaks_()

◆ addChargedSpectrum_()

◆ addFragmentPeaks_()

◆ getMultipleSpectra()

◆ getSpectrum()

◆ getUnchargedSpectrum_()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ a_intensity_

◆ aB_intensity_

◆ add_a_ions_

◆ add_aB_ions_

◆ add_all_precursor_charges_

◆ add_b_ions_

◆ add_c_ions_

◆ add_d_ions_

◆ add_first_prefix_ion_

◆ add_metainfo_

◆ add_precursor_peaks_

◆ add_w_ions_

◆ add_x_ions_

◆ add_y_ions_

◆ add_z_ions_

◆ b_intensity_

◆ c_intensity_

◆ d_intensity_

◆ precursor_intensity_

◆ w_intensity_

◆ x_intensity_

◆ y_intensity_

◆ z_intensity_