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

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

Collaboration diagram for FLASHDeconvHelperStructs::PrecalculatedAveragine:

[legend]

Public Member Functions
	PrecalculatedAveragine ()=default
	default constructor More...

	PrecalculatedAveragine (const double min_mass, const double max_mass, const double delta, CoarseIsotopePatternGenerator *generator, const bool use_RNA_averagine)
	constructor with parameters such as mass ranges and bin size. More...

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

int	getMaxIsotopeIndex () const
	get max isotope index More...

void	setMaxIsotopeIndex (const int index)
	set max isotope index More...

Size	getLeftCountFromApex (const 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 More...

Size	getRightCountFromApex (const double mass) const
	get isotope distance (from apex to the rigth 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 More...

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

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

double	getAverageMassDelta (const 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 More...

double	getMostAbundantMassDelta (const 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 More...

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

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

std::vector< double >	norms_
	L2 norms_ for masses. More...

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

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

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

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

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

Size	max_isotope_index_
	max isotope index More...

double	mass_interval_
	mass interval for calculation More...

double	min_mass_
	min mass for calculation More...

Detailed Description

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

Constructor & Destructor Documentation

◆ PrecalculatedAveragine() [1/2]

PrecalculatedAveragine ( )

default

default constructor

◆ PrecalculatedAveragine() [2/2]

PrecalculatedAveragine	(	const double	min_mass,
		const double	max_mass,
		const double	delta,
		CoarseIsotopePatternGenerator *	generator,
		const bool	use_RNA_averagine
	)

constructor with parameters such as mass ranges and bin size.

Parameters

min_mass	the averagine distributions will be calculated from this min_mass
max_mass	to the max_mass
delta	with the bin size delta
generator	this generates (calculates) the distributions
use_RNA_averagine	if set, nucleotide-based isotope patters are calculated

Member Function Documentation

◆ get()

IsotopeDistribution get ( const 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 ( const 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 ( const 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 ( const double mass ) const

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

Referenced by TOPPFLASHDeconv::main_().

◆ getLeftCountFromApex()

Size getLeftCountFromApex ( const 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()

int getMaxIsotopeIndex ( ) const

get max isotope index

◆ getMostAbundantMassDelta()

double getMostAbundantMassDelta ( const 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 ( const double mass ) const

get isotope distance (from apex to the rigth 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

◆ massToIndex_()

Size massToIndex_ ( double const mass ) const

private

calculate the mass bin index from mass

◆ setMaxIsotopeIndex()

void setMaxIsotopeIndex ( const 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.

◆ 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.

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PrecalculatedAveragine() [1/2]

◆ PrecalculatedAveragine() [2/2]

Member Function Documentation

◆ get()

◆ getApexIndex()

◆ getAverageMassDelta()

◆ getLastIndex()

◆ getLeftCountFromApex()

◆ getMaxIsotopeIndex()

◆ getMostAbundantMassDelta()

◆ getRightCountFromApex()

◆ massToIndex_()

◆ 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_