Namespaces
	Scoring
	Scoring functions used by MRMScoring.

Classes
struct	CSVWriter

struct	DataMatrix

struct	IDataFrameWriter

class	IFeature

class	IMRMFeature

struct	ISignalToNoise

class	ISpectrumAccess
	The interface of a mass spectrometry experiment. More...

struct	ITransitionGroup

struct	LightCompound

struct	LightModification

struct	LightProtein

struct	LightTargetedExperiment

struct	LightTransition

class	mean_and_stddev
	functor to compute the mean and stddev of sequence using the std::foreach algorithm More...

class	MockFeature
	Mock object implementing IFeature. More...

class	MockMRMFeature
	Mock object implementing IMRMFeature. More...

class	MockSignalToNoise
	Mock object implementing ISignalToNoise. More...

class	MockTransitionGroup
	Mock object implementing ITransitionGroup. More...

class	MRMScoring
	This class implements different scores for peaks found in SRM/MRM. More...

struct	mySqrt

struct	OSBinaryDataArray
	The datastructures used by the OpenSwath interfaces. More...

struct	OSChromatogram
	A single chromatogram. More...

struct	OSChromatogramMeta
	Identifying information for a chromatogram. More...

struct	OSSpectrum
	The structure that captures the generation of a peak list (including the underlying acquisitions) More...

struct	OSSpectrumMeta
	Identifying information for a spectrum. More...

struct	Peptide

struct	Protein

struct	SwathMap
	Data structure to hold one SWATH map with information about upper / lower isolation window and whether the map is MS1 or MS2. More...

struct	TargetedExperiment

struct	TransitionHelper

Typedefs
typedef OSBinaryDataArray	BinaryDataArray

typedef boost::shared_ptr< BinaryDataArray >	BinaryDataArrayPtr

typedef OSChromatogramMeta	ChromatogramMeta

typedef boost::shared_ptr< ChromatogramMeta >	ChromatogramMetaPtr

typedef OSChromatogram	Chromatogram

typedef boost::shared_ptr< Chromatogram >	ChromatogramPtr

typedef OSSpectrumMeta	SpectrumMeta

typedef boost::shared_ptr< SpectrumMeta >	SpectrumMetaPtr

typedef OSSpectrum	Spectrum

typedef boost::shared_ptr< Spectrum >	SpectrumPtr

typedef boost::shared_ptr< ISpectrumAccess >	SpectrumAccessPtr

typedef boost::shared_ptr< ISignalToNoise >	ISignalToNoisePtr

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. More...

template<typename T >
double	norm (T beg, T end)
	compute the norm of the vector More...

template<typename Texp , typename Ttheo >
double	dotProd (Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
	compute dotprod of vectors More...

OPENSWATHALGO_DLLAPI double	dotprodScoring (std::vector< double > intExp, std::vector< double > theorint)
	the dot product scoring More...

template<typename Texp , typename Ttheo >
double	manhattanDist (Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
	compute manhattan distance between Exp and Theo More...

OPENSWATHALGO_DLLAPI double	manhattanScoring (std::vector< double > intExp, std::vector< double > theorint)
	manhattan scoring More...

template<typename TInputIterator , typename TInputIteratorY >
std::iterator_traits< TInputIterator >::value_type	cor_pearson (TInputIterator xBeg, TInputIterator xEnd, TInputIteratorY yBeg)
	compute pearson correlation of vector x and y More...

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. More...

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. More...

Typedef Documentation

◆ BinaryDataArray

typedef OSBinaryDataArray BinaryDataArray

◆ BinaryDataArrayPtr

typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr

◆ Chromatogram

typedef OSChromatogram Chromatogram

◆ ChromatogramMeta

typedef OSChromatogramMeta ChromatogramMeta

◆ ChromatogramMetaPtr

typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr

◆ ChromatogramPtr

typedef boost::shared_ptr<Chromatogram> ChromatogramPtr

◆ ISignalToNoisePtr

typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr

◆ Spectrum

typedef OSSpectrum Spectrum

◆ SpectrumAccessPtr

typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr

◆ SpectrumMeta

typedef OSSpectrumMeta SpectrumMeta

◆ SpectrumMetaPtr

typedef boost::shared_ptr<SpectrumMeta> SpectrumMetaPtr

◆ SpectrumPtr

typedef boost::shared_ptr<Spectrum> SpectrumPtr

Function Documentation

◆ cor_pearson()

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

compute pearson correlation of vector x and y

◆ dotProd()

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

compute dotprod of vectors

References dotprodScoring(), and OpenMS::Math::sum().

◆ dotprodScoring()

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

Referenced by dotProd().

◆ integrateWindow()

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

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

◆ integrateWindows()

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

◆ manhattanDist()

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

compute manhattan distance between Exp and Theo

References manhattanScoring(), and OpenMS::Math::sum().

◆ manhattanScoring()

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

manhattan scoring

sqrt intensities normalize vector by TIC compute manhattan score

Referenced by manhattanDist().

◆ norm()

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

compute the norm of the vector

Referenced by GaussFilterAlgorithm::integrate_().

◆ normalize()

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 PSLPFormulation::VariableIndexLess::operator()(), and IMSIsotopeDistribution::setNominalMass().

Namespaces

Classes

Typedefs

Functions