Functions

bool	integrateWindow (const OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &mz, double &intensity, bool centroided=false)
	Helper functions for the DIA scoring of OpenSWATH. More...

void	integrateWindows (const OpenSwath::SpectrumPtr spectrum, const std::vector< double > &windows_center, double width, std::vector< double > &integrated_windows_intensity, std::vector< double > &integrated_windows_mz, bool remove_zero=false)
	Integrate intensities in a spectrum from start to end. More...

void	integrateDriftSpectrum (OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &im, double &intensity, double drift_start, double drift_end)
	Integrate intensity in an ion mobility spectrum from start to end. More...

void	adjustExtractionWindow (double &right, double &left, const double &mz_extract_window, const bool &mz_extraction_ppm)
	Adjust left/right window based on window and whether its ppm or not. More...

void	getBYSeries (const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
	compute the b and y series masses for a given AASequence 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

◆ adjustExtractionWindow()

void OpenMS::DIAHelpers::adjustExtractionWindow	(	double &	right,
		double &	left,
		const double &	mz_extract_window,
		const bool &	mz_extraction_ppm
	)

Adjust left/right window based on window and whether its ppm or not.

◆ 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`
	)

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

◆ integrateDriftSpectrum()

void OpenMS::DIAHelpers::integrateDriftSpectrum	(	OpenSwath::SpectrumPtr	spectrum,
		double	mz_start,
		double	mz_end,
		double &	im,
		double &	intensity,
		double	drift_start,
		double	drift_end
	)

Integrate intensity in an ion mobility spectrum from start to end.

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted drift time value.

Note: If there is no signal, mz will be set to -1 and intensity to 0

◆ integrateWindow()

bool OpenMS::DIAHelpers::integrateWindow	(	const OpenSwath::SpectrumPtr	spectrum,
		double	mz_start,
		double	mz_end,
		double &	mz,
		double &	intensity,
		bool	centroided = `false`
	)

Helper functions for the DIA scoring of OpenSWATH.

Integrate intensity in a spectrum from start to end

This function will integrate the intensity in a spectrum between mz_start and mz_end, returning the total intensity and an intensity-weighted m/z value.

Note: If there is no signal, mz will be set to -1 and intensity to 0

Returns: Returns true if a signal was found (and false if no signal was found)

◆ integrateWindows()

void OpenMS::DIAHelpers::integrateWindows	(	const OpenSwath::SpectrumPtr	spectrum,
		const std::vector< double > &	windows_center,
		double	width,
		std::vector< double > &	integrated_windows_intensity,
		std::vector< double > &	integrated_windows_mz,
		bool	remove_zero = `false`
	)

Integrate intensities in a spectrum from start to end.

Parameters

[in]	spectrum	Spectrum
[in]	windows_center	center location

◆ 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

Functions