OpenMS::DIAHelpers Namespace Reference

Functions
void	getBYSeries (const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
	Helper functions for the DIA scoring of OpenSWATH. More...
void	getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
	for SWATH – get the theoretical b and y series masses for a sequence More...
void	getAveragineIsotopeDistribution (const double product_mz, std::vector< std::pair< double, double > > &isotopesSpec, const double charge=1., const int nr_isotopes=4, const double mannmass=1.00048)
	get averagine distribution given mass More...
void	simulateSpectrumFromAASequence (const AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, TheoreticalSpectrumGenerator const *g, double charge=1.)
	simulate spectrum from AASequence More...
void	modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.)
	modify masses by charge More...
void	addPreisotopeWeights (const std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeSpec, UInt nrpeaks=2, double preIsotopePeaksWeight=-0.5, double mannmass=1.000482, double charge=1.)
	add negative pre-isotope weights to spectrum More...
void	addIsotopes2Spec (const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)
	given an experimental spectrum add isotope pattern. More...
void	sortByFirst (std::vector< std::pair< double, double > > &tmp)
	sorts vector of pairs by first More...
void	extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
	extract first from vector of pairs More...
void	extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
	extract second from vector of pairs More...

Function Documentation

addIsotopes2Spec()

void OpenMS::DIAHelpers::addIsotopes2Spec	(	const std::vector< std::pair< double, double > > &	spec,
		std::vector< std::pair< double, double > > &	isotopeMasses,
		double	charge = 1.
	)

given an experimental spectrum add isotope pattern.

addPreisotopeWeights()

void OpenMS::DIAHelpers::addPreisotopeWeights	(	const std::vector< double > &	firstIsotopeMasses,
		std::vector< std::pair< double, double > > &	isotopeSpec,
		UInt	nrpeaks = 2,
		double	preIsotopePeaksWeight = -0.5,
		double	mannmass = 1.000482,
		double	charge = 1.
	)

add negative pre-isotope weights to spectrum

extractFirst()

void OpenMS::DIAHelpers::extractFirst	(	const std::vector< std::pair< double, double > > &	peaks,
		std::vector< double > &	mass
	)

extract first from vector of pairs

extractSecond()

void OpenMS::DIAHelpers::extractSecond	(	const std::vector< std::pair< double, double > > &	peaks,
		std::vector< double > &	mass
	)

extract second from vector of pairs

getAveragineIsotopeDistribution()

void OpenMS::DIAHelpers::getAveragineIsotopeDistribution	(	const double	product_mz,
		std::vector< std::pair< double, double > > &	isotopesSpec,
		const double	charge = 1.,
		const int	nr_isotopes = 4,
		const double	mannmass = 1.00048
	)

get averagine distribution given mass

getBYSeries()

void OpenMS::DIAHelpers::getBYSeries	(	const AASequence &	a,
		std::vector< double > &	bseries,
		std::vector< double > &	yseries,
		TheoreticalSpectrumGenerator const *	g,
		UInt	charge = 1u
	)

Helper functions for the DIA scoring of OpenSWATH.

compute the b and y series masses for a given AASequence

getTheorMasses()

void OpenMS::DIAHelpers::getTheorMasses	(	const AASequence &	a,
		std::vector< double > &	masses,
		TheoreticalSpectrumGenerator const *	g,
		UInt	charge = 1u
	)

for SWATH – get the theoretical b and y series masses for a sequence

modifyMassesByCharge()

void OpenMS::DIAHelpers::modifyMassesByCharge	(	const std::vector< std::pair< double, double > > &	masses,
		std::vector< std::pair< double, double > > &	modmass,
		double	charge = 1.
	)

modify masses by charge

Parameters

[in]

modmass

[out]

simulateSpectrumFromAASequence()

void OpenMS::DIAHelpers::simulateSpectrumFromAASequence	(	const AASequence &	aa,
		std::vector< double > &	firstIsotopeMasses,
		std::vector< std::pair< double, double > > &	isotopeMasses,
		TheoreticalSpectrumGenerator const *	g,
		double	charge = 1.
	)

simulate spectrum from AASequence

sortByFirst()

void OpenMS::DIAHelpers::sortByFirst

(

std::vector< std::pair< double, double > > &

tmp

)

sorts vector of pairs by first