OpenMS  3.0.0
OpenSwath Namespace Reference

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  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  TransitionHelper
 

Typedefs

typedef OSBinaryDataArray BinaryDataArray
 
typedef boost::shared_ptr< BinaryDataArrayBinaryDataArrayPtr
 
typedef OSChromatogramMeta ChromatogramMeta
 
typedef boost::shared_ptr< ChromatogramMetaChromatogramMetaPtr
 
typedef OSChromatogram Chromatogram
 
typedef boost::shared_ptr< ChromatogramChromatogramPtr
 
typedef OSSpectrumMeta SpectrumMeta
 
typedef boost::shared_ptr< SpectrumMetaSpectrumMetaPtr
 
typedef OSSpectrum Spectrum
 
typedef boost::shared_ptr< SpectrumSpectrumPtr
 
typedef boost::shared_ptr< ISpectrumAccessSpectrumAccessPtr
 
typedef boost::shared_ptr< ISignalToNoiseISignalToNoisePtr
 

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...
 

Class Documentation

◆ OpenSwath::LightModification

struct OpenSwath::LightModification
Collaboration diagram for LightModification:
[legend]
Class Members
int location
int unimod_id

◆ OpenSwath::LightProtein

struct OpenSwath::LightProtein
Collaboration diagram for LightProtein:
[legend]
Class Members
string id
string sequence

◆ 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:
[legend]
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:
[legend]
Class Members
string id
vector< Peptide > peptides
string sequence

◆ OpenSwath::TargetedExperiment

struct OpenSwath::TargetedExperiment
Collaboration diagram for TargetedExperiment:
[legend]
Class Members
vector< Protein > proteins

Typedef Documentation

◆ BinaryDataArray

◆ BinaryDataArrayPtr

typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr

◆ Chromatogram

◆ ChromatogramMeta

◆ ChromatogramMetaPtr

typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr

◆ ChromatogramPtr

typedef boost::shared_ptr<Chromatogram> ChromatogramPtr

◆ ISignalToNoisePtr

typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr

◆ Spectrum

◆ SpectrumAccessPtr

typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr

◆ 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 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 ( beg,
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.