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OpenSwath Namespace Reference

Namespaces

 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. 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 vecotrs 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 prearson 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...
 

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
 

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]spectrumSpectrum
[in]windowsCentercenter 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 ( beg,
end 
)

compute the norm of the vector

Referenced by GaussFilterAlgorithm::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_().

Variable Documentation

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<ISignalToNoise> ISignalToNoisePtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Spectrum> SpectrumPtr

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:38 using doxygen 1.8.5