OpenSwath Namespace Reference

Namespaces
namespace	Scoring
	Scoring functions used by MRMScoring.
Classes
class	MRMScoring
	This class implements different scores for peaks found in SRM/MRM. More...
struct	mySqrt
class	mean_and_stddev
	functor to compute the mean and stddev of sequence using the std::foreach algorithm More...
struct	IDataFrameWriter
struct	DataMatrix
struct	CSVWriter
struct	BinaryDataArray
	The datastructures used by the OpenSwath interfaces. More...
struct	ChromatogramMeta
	Identifying information for a chromatogram. More...
struct	Chromatogram
	A single chromatogram. More...
struct	SpectrumMeta
	Identifying information for a spectrum. More...
struct	Spectrum
	The structure that captures the generation of a peak list (including the underlying acquisitions). More...
class	ISpectrumAccess
	The interface of a mass spectrometry experiment. More...
class	IFeature
class	IMRMFeature
struct	ITransitionGroup
struct	ISignalToNoise
class	MockFeature
	Mock object implementing IFeature. More...
class	MockMRMFeature
	Mock object implementing IMRMFeature. More...
class	MockTransitionGroup
	Mock object implementing ITransitionGroup. More...
class	MockSignalToNoise
	Mock object implementing ISignalToNoise. More...
struct	LightTransition
struct	LightModification
struct	LightPeptide
struct	LightProtein
struct	LightTargetedExperiment
struct	TransitionHelper
struct	Peptide
struct	Protein
struct	TargetedExperiment
Functions
OPENSWATHALGO_DLLAPI void	normalize (const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
	Normalize intensities in vector by normalization_factor.
template<typename T >
double	norm (T beg, T end)
	compute the norm of the vector
template<typename Texp , typename Ttheo >
double	dotProd (Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
	compute dotprod of vecotrs
OPENSWATHALGO_DLLAPI double	dotprodScoring (std::vector< double > intExp, std::vector< double > theorint)
	the dot product scoring
template<typename Texp , typename Ttheo >
double	manhattanDist (Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
	compute manhattan distance between Exp and Theo
OPENSWATHALGO_DLLAPI double	manhattanScoring (std::vector< double > intExp, std::vector< double > theorint)
	manhattan scoring
template<typename TInputIterator , typename TInputIteratorY >
std::iterator_traits < TInputIterator >::value_type	cor_pearson (TInputIterator xBeg, TInputIterator xEnd, TInputIteratorY yBeg)
	compute prearson correlation of vector x and y
OPENSWATHALGO_DLLAPI bool	integrateWindow (const OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &mz, double &intensity, bool centroided=false)
	Integrate intensity in a spectrum from start to end.
OPENSWATHALGO_DLLAPI void	integrateWindows (const OpenSwath::SpectrumPtr spectrum, const std::vector< double > &windowsCenter, double width, std::vector< double > &integratedWindowsIntensity, std::vector< double > &integratedWindowsMZ, bool remZero=false)
	Integrate intensities in a spectrum from start to end.
Variables
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr < BinaryDataArray >	BinaryDataArrayPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr < ChromatogramMeta >	ChromatogramMetaPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr < Chromatogram >	ChromatogramPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum >	SpectrumPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr < ISpectrumAccess >	SpectrumAccessPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr < ISignalToNoise >	ISignalToNoisePtr

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Function Documentation

std::iterator_traits<TInputIterator>::value_type OpenSwath::cor_pearson	(	TInputIterator	xBeg,
		TInputIterator	xEnd,
		TInputIteratorY	yBeg
	)

compute prearson correlation of vector x and y

double OpenSwath::dotProd	(	Texp	intExpBeg,
		Texp	intExpEnd,
		Ttheo	intTheo
	)

compute dotprod of vecotrs

References OpenMS::Math::sum().

OPENSWATHALGO_DLLAPI double OpenSwath::dotprodScoring	(	std::vector< double >	intExp,
		std::vector< double >	theorint
	)

the dot product scoring

sqrt data, normalize by vector norm compute dotprod

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

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

OPENSWATHALGO_DLLAPI void OpenSwath::integrateWindows	(	const OpenSwath::SpectrumPtr	spectrum,
		const std::vector< double > &	windowsCenter,
		double	width,
		std::vector< double > &	integratedWindowsIntensity,
		std::vector< double > &	integratedWindowsMZ,
		bool	remZero = false
	)

Integrate intensities in a spectrum from start to end.

Parameters:

[in]	spectrum	Spectrum
[in]	windowsCenter	center location

double OpenSwath::manhattanDist	(	Texp	itExpBeg,
		Texp	itExpEnd,
		Ttheo	itTheo
	)

compute manhattan distance between Exp and Theo

References OpenMS::Math::sum().

OPENSWATHALGO_DLLAPI double OpenSwath::manhattanScoring	(	std::vector< double >	intExp,
		std::vector< double >	theorint
	)

manhattan scoring

sqrt intensities normalize vector by TIC compute manhattan score

double OpenSwath::norm	(	T	beg,
		T	end
	)

compute the norm of the vector

Referenced by GaussFilter::integrate_().

OPENSWATHALGO_DLLAPI void OpenSwath::normalize	(	const std::vector< double > &	intensities,
		double	normalization_factor,
		std::vector< double > &	normalized_intensities
	)

Normalize intensities in vector by normalization_factor.

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

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Variable Documentation

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr

Referenced by Spectrum::initvec(), and Chromatogram::initvec().

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Chromatogram> ChromatogramPtr

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr

OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Spectrum> SpectrumPtr

Referenced by MRMFeatureFinderScoring::calculateSwathScores_(), and MRMFeatureFinderScoring::getAddedSpectra_().