OpenSwath Namespace Reference

Namespaces
namespace	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	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...
class	SwathQC
	Quality Control function for OpenSwath. More...
struct	TargetedExperiment
struct	TransitionFlags
	Packed boolean flags for transitions Reduces memory from 4 bytes (4 separate bools) to 1 byte. More...
struct	TransitionHelper

Typedefs
typedef OSBinaryDataArray	BinaryDataArray
typedef std::shared_ptr< BinaryDataArray >	BinaryDataArrayPtr
typedef OSChromatogramMeta	ChromatogramMeta
typedef std::shared_ptr< ChromatogramMeta >	ChromatogramMetaPtr
typedef OSChromatogram	Chromatogram
typedef std::shared_ptr< Chromatogram >	ChromatogramPtr
typedef OSSpectrumMeta	SpectrumMeta
typedef std::shared_ptr< SpectrumMeta >	SpectrumMetaPtr
typedef OSSpectrum	Spectrum
typedef std::shared_ptr< Spectrum >	SpectrumPtr
using	SpectrumSequence = OpenMS::SpectrumSequence
typedef std::shared_ptr< ISpectrumAccess >	SpectrumAccessPtr
typedef std::shared_ptr< ISignalToNoise >	ISignalToNoisePtr

Enumerations
enum class	FragmentIonType : uint8_t {   Unknown = 0 , AIon , BIon , CIon ,   XIon , YIon , ZIon , ZPrimeIon ,   ZDotIon , Precursor , BMinusH2O , YMinusH2O ,   BMinusNH3 , YMinusNH3 , Empty = 255 }
	Compact enum for fragment ion types (replaces string storage) Reduces memory from ~32 bytes (std::string) to 1 byte. More...

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 Euclidean norm of the vector
template<typename Texp , typename Ttheo >
double	dotProd (Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
	compute dotprod of vectors
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 pearson correlation of vector x and y
FragmentIonType	stringToFragmentIonType (const std::string &s)
	Convert fragment ion type string to enum.
std::string	fragmentIonTypeToString (FragmentIonType t)
	Convert fragment ion type enum to string.

---

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::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 std::shared_ptr<BinaryDataArray> BinaryDataArrayPtr

Chromatogram

typedef OSChromatogram Chromatogram

ChromatogramMeta

typedef OSChromatogramMeta ChromatogramMeta

ChromatogramMetaPtr

typedef std::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr

ChromatogramPtr

typedef std::shared_ptr<Chromatogram> ChromatogramPtr

ISignalToNoisePtr

typedef std::shared_ptr<ISignalToNoise> ISignalToNoisePtr

Spectrum

typedef OSSpectrum Spectrum

SpectrumAccessPtr

typedef std::shared_ptr<ISpectrumAccess> SpectrumAccessPtr

SpectrumMeta

typedef OSSpectrumMeta SpectrumMeta

SpectrumMetaPtr

typedef std::shared_ptr<SpectrumMeta> SpectrumMetaPtr

SpectrumPtr

typedef std::shared_ptr<Spectrum> SpectrumPtr

SpectrumSequence

using SpectrumSequence = OpenMS::SpectrumSequence

Enumeration Type Documentation

FragmentIonType

enum class FragmentIonType : uint8_t

strong

Compact enum for fragment ion types (replaces string storage) Reduces memory from ~32 bytes (std::string) to 1 byte.

Enumerator
Unknown
AIon	a-ion
BIon	b-ion
CIon	c-ion
XIon	x-ion
YIon	y-ion
ZIon	z-ion
ZPrimeIon	z'-ion (z prime)
ZDotIon	z.-ion (z dot)
Precursor	Precursor ion.
BMinusH2O	b-ion with water loss
YMinusH2O	y-ion with water loss
BMinusNH3	b-ion with ammonia loss
YMinusNH3	y-ion with ammonia loss
Empty	No fragment type set.

Function Documentation

cor_pearson()

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

dotProd()

template<typename Texp , typename Ttheo >

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

compute dotprod of vectors

dotprodScoring()

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

the dot product scoring

sqrt data, normalize by vector norm compute dotprod

fragmentIonTypeToString()

std::string fragmentIonTypeToString ( FragmentIonType  t )

inline

Convert fragment ion type enum to string.

Parameters

t	FragmentIonType enum value

Returns

Fragment type string (e.g. "y", "b", "prec")

References AIon, BIon, BMinusH2O, BMinusNH3, CIon, Empty, Precursor, Unknown, XIon, YIon, YMinusH2O, YMinusNH3, ZDotIon, ZIon, and ZPrimeIon.

Referenced by LightTransition::getAnnotation(), and LightTransition::getFragmentType().

manhattanDist()

template<typename Texp , typename Ttheo >

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

compute manhattan distance between Exp and Theo

manhattanScoring()

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

manhattan scoring

sqrt intensities normalize vector by TIC compute manhattan score

norm()

template<typename T >

double norm	(	T	beg,
		T	end
	)

compute the Euclidean norm of the vector

normalize()

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

Normalize intensities in vector by normalization_factor.

stringToFragmentIonType()

FragmentIonType stringToFragmentIonType ( const std::string &  s )

inline

Convert fragment ion type string to enum.

Parameters

s	Fragment type string (e.g. "y", "b", "prec")

Returns

Corresponding FragmentIonType enum value

References AIon, BIon, BMinusH2O, BMinusNH3, CIon, Empty, Precursor, Unknown, XIon, YIon, YMinusH2O, YMinusNH3, ZDotIon, ZIon, and ZPrimeIon.

Referenced by LightTransition::setFragmentType().