| OpenMS 2.5.0

Namespaces | Classes | Typedefs | Functions
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 | 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...
class | SwathQC
| Quality Control function for OpenSwath. 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...

## Class Documentation

## ◆ OpenSwath::LightModification

struct OpenSwath::LightModification

Class Members
int | location |
int | unimod_id |

## ◆ OpenSwath::LightProtein

struct OpenSwath::LightProtein

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 intensityThe structure into which encoded binary data goes.

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

Class Members
string | id |
vector< Peptide > | peptides |
string | sequence |

## ◆ OpenSwath::TargetedExperiment

struct OpenSwath::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

## 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 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.