The ChromatogramExtractor extracts chromatograms from a mzML file. More...
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
Public Member Functions | |
| ChromatogramExtractor () | |
| Constructor. | |
| ~ChromatogramExtractor () | |
| Destructor. | |
| template<typename ExperimentT > | |
| void | extractChromatograms (const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double extract_window, bool ppm, TransformationDescription trafo, double rt_extraction_window, String filter) |
| Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map. | |
| template<typename SpectrumT > | |
| void | extract_value_tophat (const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm) |
| template<typename SpectrumT > | |
| void | extract_value_bartlett (const SpectrumT &input, const double &mz, Size &peak_idx, double &integrated_intensity, const double &extract_window, const bool ppm) |
| void | extract_value_tophat (const std::vector< double >::const_iterator &mz_start, std::vector< double >::const_iterator &mz_it, const std::vector< double >::const_iterator &mz_end, std::vector< double >::const_iterator &int_it, const double &mz, double &integrated_intensity, double &extract_window, bool ppm) |
Private Member Functions | |
| template<class SpectrumSettingsT , class ChromatogramT > | |
| void | prepareSpectra_ (SpectrumSettingsT &settings, std::vector< ChromatogramT > &chromatograms, OpenMS::TargetedExperiment &transition_exp) |
| This populates the chromatograms vector with empty chromatograms (but sets their meta-information). | |
| bool | outsideExtractionWindow_ (const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window) |
Private Attributes | |
| std::map< OpenMS::String, double > | PeptideRTMap_ |
Detailed Description
The ChromatogramExtractor extracts chromatograms from a mzML file.
It will take as input a set of (TraML) transitions and will extract the signal of the provided map at the product ion m/z values specified by the transitions. The map is thus assumed to be an MS2 map from a SWATH / DIA experiment.
Constructor & Destructor Documentation
| ChromatogramExtractor | ( | ) | [inline] |
Constructor.
| ~ChromatogramExtractor | ( | ) | [inline] |
Destructor.
Member Function Documentation
| void extract_value_bartlett | ( | const SpectrumT & | input, | |
| const double & | mz, | |||
| Size & | peak_idx, | |||
| double & | integrated_intensity, | |||
| const double & | extract_window, | |||
| const bool | ppm | |||
| ) | [inline] |
| void extract_value_tophat | ( | const std::vector< double >::const_iterator & | mz_start, | |
| std::vector< double >::const_iterator & | mz_it, | |||
| const std::vector< double >::const_iterator & | mz_end, | |||
| std::vector< double >::const_iterator & | int_it, | |||
| const double & | mz, | |||
| double & | integrated_intensity, | |||
| double & | extract_window, | |||
| bool | ppm | |||
| ) | [inline] |
| void extract_value_tophat | ( | const SpectrumT & | input, | |
| const double & | mz, | |||
| Size & | peak_idx, | |||
| double & | integrated_intensity, | |||
| const double & | extract_window, | |||
| const bool | ppm | |||
| ) | [inline] |
| void extractChromatograms | ( | const ExperimentT & | input, | |
| ExperimentT & | output, | |||
| OpenMS::TargetedExperiment & | transition_exp, | |||
| double | extract_window, | |||
| bool | ppm, | |||
| TransformationDescription | trafo, | |||
| double | rt_extraction_window, | |||
| String | filter | |||
| ) | [inline] |
Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map.
References TargetedExperiment::getPeptides(), TargetedExperiment::getTransitions(), Peptide::id, TransformationDescription::invert(), OpenMS::Constants::k, Peptide::rts, and TargetedExperiment::sortTransitionsByProductMZ().
| bool outsideExtractionWindow_ | ( | const ReactionMonitoringTransition & | transition, | |
| double | current_rt, | |||
| const TransformationDescription & | trafo, | |||
| double | rt_extraction_window | |||
| ) | [inline, private] |
| void prepareSpectra_ | ( | SpectrumSettingsT & | settings, | |
| std::vector< ChromatogramT > & | chromatograms, | |||
| OpenMS::TargetedExperiment & | transition_exp | |||
| ) | [inline, private] |
This populates the chromatograms vector with empty chromatograms (but sets their meta-information).
References ReactionMonitoringTransition::getNativeID(), ReactionMonitoringTransition::getPeptideRef(), TargetedExperiment::getPeptides(), ReactionMonitoringTransition::getPrecursorMZ(), ReactionMonitoringTransition::getProductMZ(), TargetedExperiment::getTransitions(), Peptide::id, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, Peptide::sequence, Precursor::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), Product::setMZ(), and Peak1D::setMZ().
Member Data Documentation
std::map<OpenMS::String, double> PeptideRTMap_ [private] |
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1 |