OpenSwath Namespace Reference

Namespaces
	Scoring
	Scoring functions used by MRMScoring.

Classes
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	OSBinaryDataArray
	The datastructures used by the OpenSwath interfaces. More...
struct	OSChromatogramMeta
	Identifying information for a chromatogram. More...
struct	OSChromatogram
	A single chromatogram. More...
struct	OSSpectrumMeta
	Identifying information for a spectrum. More...
struct	OSSpectrum
	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	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	LightTransition
struct	LightModification
struct	LightCompound
struct	LightProtein
struct	LightTargetedExperiment
struct	TransitionHelper
struct	Peptide
struct	Protein
struct	TargetedExperiment
class	MRMScoring
	This class implements different scores for peaks found in SRM/MRM. More...
class	SwathQC
	Quality Control function for OpenSwath. More...

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
using	SpectrumSequence = OpenMS::SpectrumSequence
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 Euclidean 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...

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Class Documentation

OpenSwath::OSBinaryDataArray

struct OpenSwath::OSBinaryDataArray

The datastructures used by the OpenSwath interfaces.

Many of them are closely related to Proteowizard data structures, originally written by Darren Kessner and released under the Apache 2.0 licence.

Original author: Darren Kessner darre.nosp@m.n@pr.nosp@m.oteow.nosp@m.izar.nosp@m.d.org

Copyright 2007 Spielberg Family Center for Applied Proteomics Cedars-Sinai Medical Center, Los Angeles, California 90048

The following datastructures are used :

• BinaryDataArray : a struct that holds a std::vector<double> with the data
• ChromatogramMeta : meta information of a chromatogram (index)
• Chromatogram : chromatogram data. Contains a vector of pointers to BinaryDataArray, the first one is time array (RT), the second one is intensity
• SpectrumMeta : meta information of a spectrum (index, identifier, RT, ms_level)
• Spectrum : spectrum data. Contains a vector of pointers to BinaryDataArray, the first one is mz array, the second one is intensity The structure into which encoded binary data goes.

Collaboration diagram for OSBinaryDataArray:

Class Members
vector< double >	data	this optional attribute may reference the 'id' attribute of the appropriate dataProcessing. the binary data.
string	description	(optional) data description for non-standard arrays.

OpenSwath::LightModification

struct OpenSwath::LightModification

Collaboration diagram for LightModification:

Class Members
int	location
int	unimod_id

OpenSwath::LightProtein

struct OpenSwath::LightProtein

Collaboration diagram for LightProtein:

Class Members
string	id
string	sequence

OpenSwath::Protein

struct OpenSwath::Protein

Collaboration diagram for Protein:

Class Members
string	id
vector< Peptide >	peptides
string	sequence

OpenSwath::TargetedExperiment

struct OpenSwath::TargetedExperiment

Collaboration diagram for TargetedExperiment:

Class Members
vector< Protein >	proteins

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

SpectrumSequence

using SpectrumSequence = OpenMS::SpectrumSequence

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 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

manhattanDist()

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

compute manhattan distance between Exp and Theo

References 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

norm()

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

compute the Euclidean 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.