OpenMS
2.5.0
|
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... | |
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 n@pr oteow izar d.org
Copyright 2007 Spielberg Family Center for Applied Proteomics Cedars-Sinai Medical Center, Los Angeles, California 90048
The following datastructures are used :
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. |
struct OpenSwath::Protein |
Class Members | ||
---|---|---|
string | id | |
vector< Peptide > | peptides | |
string | sequence |
struct OpenSwath::TargetedExperiment |
Class Members | ||
---|---|---|
vector< Protein > | proteins |
typedef OSBinaryDataArray BinaryDataArray |
typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr |
typedef OSChromatogram Chromatogram |
typedef OSChromatogramMeta ChromatogramMeta |
typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr |
typedef boost::shared_ptr<Chromatogram> ChromatogramPtr |
typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr |
typedef OSSpectrum Spectrum |
typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr |
typedef OSSpectrumMeta SpectrumMeta |
typedef boost::shared_ptr<SpectrumMeta> SpectrumMetaPtr |
typedef boost::shared_ptr<Spectrum> SpectrumPtr |
std::iterator_traits<TInputIterator>::value_type OpenSwath::cor_pearson | ( | TInputIterator | xBeg, |
TInputIterator | xEnd, | ||
TInputIteratorY | yBeg | ||
) |
compute pearson correlation of vector x and y
double OpenSwath::dotProd | ( | Texp | intExpBeg, |
Texp | intExpEnd, | ||
Ttheo | intTheo | ||
) |
compute dotprod of vectors
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
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 | ( | T | beg, |
T | end | ||
) |
compute the norm of the vector
Referenced by GaussFilterAlgorithm::integrate_().