| 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 |