The ChromatogramExtractor extracts chromatograms from a mzML file. More...
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
Public Member Functions | |
| ChromatogramExtractor () | |
| Constructor. More... | |
| ~ChromatogramExtractor () | |
| Destructor. More... | |
| 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. More... | |
| 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) |
Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
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) More... | |
| bool | outsideExtractionWindow_ (const ReactionMonitoringTransition &transition, double current_rt, const TransformationDescription &trafo, double rt_extraction_window) |
Private Attributes | |
| std::map< OpenMS::String, double > | PeptideRTMap_ |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. More... | |
Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| SignedSize | begin_ |
| SignedSize | end_ |
| SignedSize | value_ |
| QProgressDialog * | dlg_ |
| StopWatch | stop_watch_ |
| time_t | last_invoke_ |
Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
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.
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Constructor.
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Destructor.
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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().
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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().
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |