Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation. More...

#include <OpenMS/ANALYSIS/TOPDOWN/FLASHHelperClasses.h>

Collaboration diagram for FLASHHelperClasses::PrecalculatedAveragine:

[legend]

Public Member Functions
	PrecalculatedAveragine ()=default
	default constructor

	PrecalculatedAveragine (double min_mass, double max_mass, double delta, CoarseIsotopePatternGenerator &generator, bool use_RNA_averagine, double decoy_iso_distance=-1)
	constructor with parameters such as mass ranges and bin size.

	PrecalculatedAveragine (const PrecalculatedAveragine &)=default
	copy constructor

	PrecalculatedAveragine (PrecalculatedAveragine &&other) noexcept=default
	move constructor

PrecalculatedAveragine &	operator= (const PrecalculatedAveragine &pc)=default
	copy assignment operator

PrecalculatedAveragine &	operator= (PrecalculatedAveragine &&pc) noexcept=default
	move assignment operator

	~PrecalculatedAveragine ()=default
	destructor

IsotopeDistribution	get (double mass) const
	get distribution for input mass. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

size_t	getMaxIsotopeIndex () const
	get max isotope index

void	setMaxIsotopeIndex (int index)
	set max isotope index

Size	getLeftCountFromApex (double mass) const

Size	getRightCountFromApex (double mass) const

Size	getApexIndex (double mass) const
	get index of most abundant isotope. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

Size	getLastIndex (double mass) const
	get index of last isotope. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

double	getAverageMassDelta (double mass) const

double	getMostAbundantMassDelta (double mass) const

double	getSNRMultiplicationFactor (double mass) const
	get the SNR multiplication factor - used for quick SNR calculation

Private Member Functions
Size	massToIndex_ (double mass) const
	calculate the mass bin index from mass

Private Attributes
std::vector< IsotopeDistribution >	isotopes_
	isotope distributions for different (binned) masses

std::vector< double >	norms_
	L2 norms_ for masses - for quick isotope cosine calculation.

std::vector< double >	average_mono_mass_difference_
	mass differences between average mass and monoisotopic mass

std::vector< double >	abundant_mono_mass_difference_
	mass differences between most abundant mass and monoisotopic mass

std::vector< double >	snr_mul_factor_

std::vector< int >	left_count_from_apex_
	Isotope start indices: isotopes of the indices less than them have very low intensities.

std::vector< int >	right_count_from_apex_
	Isotope end indices: isotopes of the indices larger than them have very low intensities.

std::vector< Size >	apex_index_
	most abundant isotope index

Size	max_isotope_index_
	max isotope index

double	mass_interval_
	mass interval for calculation

double	min_mass_
	min mass for calculation

Detailed Description

Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine calculation.

Constructor & Destructor Documentation

◆ PrecalculatedAveragine() [1/4]

PrecalculatedAveragine ( )

default

default constructor

◆ PrecalculatedAveragine() [2/4]

PrecalculatedAveragine	(	double	min_mass,
		double	max_mass,
		double	delta,
		CoarseIsotopePatternGenerator &	generator,
		bool	use_RNA_averagine,
		double	decoy_iso_distance = `-1`
	)

constructor with parameters such as mass ranges and bin size.

Parameters

[in]	min_mass	the averagine distributions will be calculated from this min_mass
[in]	max_mass	to the max_mass
[in]	delta	with the bin size delta
[in]	generator	this generates (calculates) the distributions
[in]	use_RNA_averagine	if set, nucleotide-based isotope patters are calculated
[in]	decoy_iso_distance	if set to a positive value, nonsensical isotope patterns are generated - the distance between isotope = decoy_iso_distance * normal distance.

◆ PrecalculatedAveragine() [3/4]

PrecalculatedAveragine ( const PrecalculatedAveragine & )

default

copy constructor

◆ PrecalculatedAveragine() [4/4]

PrecalculatedAveragine ( PrecalculatedAveragine && other )

defaultnoexcept

move constructor

◆ ~PrecalculatedAveragine()

~PrecalculatedAveragine ( )

default

destructor

Member Function Documentation

◆ get()

IsotopeDistribution get ( double mass ) const

get distribution for input mass. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getApexIndex()

Size getApexIndex ( double mass ) const

get index of most abundant isotope. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getAverageMassDelta()

double getAverageMassDelta ( double mass ) const

get mass difference between avg and mono masses. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getLastIndex()

Size getLastIndex ( double mass ) const

get index of last isotope. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getLeftCountFromApex()

Size getLeftCountFromApex ( double mass ) const

get isotope distance (from apex to the left direction) to consider. This is specified in the constructor. index. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getMaxIsotopeIndex()

size_t getMaxIsotopeIndex ( ) const

get max isotope index

◆ getMostAbundantMassDelta()

double getMostAbundantMassDelta ( double mass ) const

get mass difference between most abundant mass and mono masses. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getRightCountFromApex()

Size getRightCountFromApex ( double mass ) const

get isotope distance (from apex to the right direction) to consider. This is specified in the constructor. index. If input mass exceeds the maximum mass (specified in constructor), output for the maximum mass

◆ getSNRMultiplicationFactor()

double getSNRMultiplicationFactor ( double mass ) const

get the SNR multiplication factor - used for quick SNR calculation

◆ massToIndex_()

Size massToIndex_ ( double mass ) const

private

calculate the mass bin index from mass

◆ operator=() [1/2]

PrecalculatedAveragine & operator= ( const PrecalculatedAveragine & pc )

default

copy assignment operator

◆ operator=() [2/2]

PrecalculatedAveragine & operator= ( PrecalculatedAveragine && pc )

defaultnoexcept

move assignment operator

◆ setMaxIsotopeIndex()

void setMaxIsotopeIndex ( int index )

set max isotope index

Member Data Documentation

◆ abundant_mono_mass_difference_

std::vector<double> abundant_mono_mass_difference_

private

mass differences between most abundant mass and monoisotopic mass

◆ apex_index_

std::vector<Size> apex_index_

private

most abundant isotope index

◆ average_mono_mass_difference_

std::vector<double> average_mono_mass_difference_

private

mass differences between average mass and monoisotopic mass

◆ isotopes_

std::vector<IsotopeDistribution> isotopes_

private

isotope distributions for different (binned) masses

◆ left_count_from_apex_

std::vector<int> left_count_from_apex_

private

Isotope start indices: isotopes of the indices less than them have very low intensities.

◆ mass_interval_

double mass_interval_

private

mass interval for calculation

◆ max_isotope_index_

Size max_isotope_index_

private

max isotope index

◆ min_mass_

double min_mass_

private

min mass for calculation

◆ norms_

std::vector<double> norms_

private

L2 norms_ for masses - for quick isotope cosine calculation.

◆ right_count_from_apex_

std::vector<int> right_count_from_apex_

private

Isotope end indices: isotopes of the indices larger than them have very low intensities.

◆ snr_mul_factor_

std::vector<double> snr_mul_factor_

private

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PrecalculatedAveragine() [1/4]

◆ PrecalculatedAveragine() [2/4]

◆ PrecalculatedAveragine() [3/4]

◆ PrecalculatedAveragine() [4/4]

◆ ~PrecalculatedAveragine()

Member Function Documentation

◆ get()

◆ getApexIndex()

◆ getAverageMassDelta()

◆ getLastIndex()

◆ getLeftCountFromApex()

◆ getMaxIsotopeIndex()

◆ getMostAbundantMassDelta()

◆ getRightCountFromApex()

◆ getSNRMultiplicationFactor()

◆ massToIndex_()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ setMaxIsotopeIndex()

Member Data Documentation

◆ abundant_mono_mass_difference_

◆ apex_index_

◆ average_mono_mass_difference_

◆ isotopes_

◆ left_count_from_apex_

◆ mass_interval_

◆ max_isotope_index_

◆ min_mass_

◆ norms_

◆ right_count_from_apex_

◆ snr_mul_factor_