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 |
| 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.
| 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.
| [in] | spectrum | Spectrum |
| [in] | windowsCenter | center 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 | ( | T | beg, |
| T | 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_().
| OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr |
Referenced by Chromatogram::initvec(), and Spectrum::initvec().
| OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr |
| OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Chromatogram> ChromatogramPtr |
| OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr |
Referenced by MRMFeatureFinderScoring::scorePeakgroups_().
| OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ISpectrumAccess> SpectrumAccessPtr |
Referenced by MRMFeatureFinderScoring::pickExperiment().
| 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 |