The ChromatogramExtractor extracts chromatograms from a spectra file. More...
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
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typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates | ExtractionCoordinates |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Public Member Functions | |
template<typename ExperimentT > | |
void | extractChromatograms (const ExperimentT &input, ExperimentT &output, OpenMS::TargetedExperiment &transition_exp, double mz_extraction_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... | |
void | extractChromatograms (const OpenSwath::SpectrumAccessPtr input, std::vector< OpenSwath::ChromatogramPtr > &output, std::vector< ExtractionCoordinates > extraction_coordinates, double mz_extraction_window, bool ppm, String filter) |
Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates. More... | |
void | prepare_coordinates (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ExtractionCoordinates > &coordinates, OpenMS::TargetedExperiment &transition_exp, const double rt_extraction_window, const bool ms1) const |
Prepare the extraction coordinates from a TargetedExperiment. 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) |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. 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... | |
Static Public Member Functions | |
template<typename TransitionExpT > | |
static void | return_chromatogram (std::vector< OpenSwath::ChromatogramPtr > &chromatograms, std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, TransitionExpT &transition_exp_used, SpectrumSettings settings, std::vector< OpenMS::MSChromatogram<> > &output_chromatograms, bool ms1) |
This converts the ChromatogramPtr to MSChromatogram and adds meta-information. 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) |
int | getFilterNr_ (String filter) |
void | populatePeptideRTMap_ (OpenMS::TargetedExperiment &transition_exp, double rt_extraction_window) |
Private Attributes | |
std::map< OpenMS::String, double > | PeptideRTMap_ |
Additional Inherited Members | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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static int | recursion_depth_ |
The ChromatogramExtractor extracts chromatograms from a spectra file.
It will take as input a set of transitions coordinates and will extract the signal of the provided map at the product ion m/z and retention time (rt) values specified by the extraction coordinates. There are two interfaces, the old interface will take a full TargetedExperiment and assume that one wants to extract at the m/z of the transitions present in the TargetedExperiment. The new interface (see also the ChromatogramExtractorAlgorithm class) only expects a set of coordinates which are up to the user to fill but a convenient prepare_coordinates function is provided to create the coordinates for the most common case of an MS2 and MS1 extraction.
In the case of MS2 extraction, the map is assumed to originate from a SWATH (data-independent acquisition or DIA) experiment.
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Extract chromatograms defined by the TargetedExperiment from the input map and write them to the output map.
mz_extraction_window | Extracts a window of this size in m/z dimension (e.g. a window of 50 ppm means an extraction of 25 ppm on either side) |
rt_extraction_window | Extracts a window of this size in RT dimension (e.g. a window of 600 seconds means an extraction of 300 seconds on either side) |
References TargetedExperiment::getTransitions(), TransformationDescription::invert(), OpenMS::Constants::k, and TargetedExperiment::sortTransitionsByProductMZ().
Referenced by OpenSwathWorkflow::performExtraction(), and OpenSwathWorkflow::simpleExtractChromatograms().
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Extract chromatograms at the m/z and RT defined by the ExtractionCoordinates.
References ChromatogramExtractorAlgorithm::extractChromatograms().
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void prepare_coordinates | ( | std::vector< OpenSwath::ChromatogramPtr > & | output_chromatograms, |
std::vector< ExtractionCoordinates > & | coordinates, | ||
OpenMS::TargetedExperiment & | transition_exp, | ||
const double | rt_extraction_window, | ||
const bool | ms1 | ||
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Prepare the extraction coordinates from a TargetedExperiment.
Will fill the coordinates vector with the appropriate extraction coordinates (transitions for MS2 extraction, peptide m/z for MS1 extraction). The output will be sorted by m/z.
output_chromatograms | An empty vector which will be initialized correctly |
coordinates | An empty vector which will be filled with the appropriate extraction coordinates in m/z and rt and sorted by m/z (to be used as input to extractChromatograms) |
transition_exp | The transition experiment used as input (is constant) |
rt_extraction_window | Full RT extraction window (rt_end - rt_start will equal this window size). Enforces the presence of retention times if larger than zero (throws an exception), if less than zero, rt_end will be set to -1 and rt_start to 0. |
ms1 | Whether to extract for MS1 (peptide level) or MS2 (transition level) |
Referenced by OpenSwathWorkflow::simpleExtractChromatograms().
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This populates the chromatograms vector with empty chromatograms (but sets their meta-information)
It extracts 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) Copy the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition
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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This converts the ChromatogramPtr to MSChromatogram and adds meta-information.
It sets 1) the target m/z 2) the isolation window (upper/lower) 3) the peptide sequence 4) the fragment m/z 5) the meta-data, e.g. InstrumentSettings, AcquisitionInfo, sourceFile and DataProcessing 6) the native ID from the transition
References ChromatogramSettings::BASEPEAK_CHROMATOGRAM, OpenSwathDataAccessHelper::convertToOpenMSChromatogram(), SpectrumSettings::getAcquisitionInfo(), ChromatogramSettings::getDataProcessing(), SpectrumSettings::getDataProcessing(), SpectrumSettings::getInstrumentSettings(), SpectrumSettings::getPrecursors(), SpectrumSettings::getSourceFile(), ChromatogramExtractorAlgorithm::ExtractionCoordinates::id, ChromatogramExtractorAlgorithm::ExtractionCoordinates::mz, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, ChromatogramSettings::setAcquisitionInfo(), ChromatogramSettings::setChromatogramType(), ChromatogramSettings::setInstrumentSettings(), Precursor::setIsolationWindowLowerOffset(), Precursor::setIsolationWindowUpperOffset(), MetaInfoInterface::setMetaValue(), Product::setMZ(), Peak1D::setMZ(), ChromatogramSettings::setNativeID(), ChromatogramSettings::setPrecursor(), ChromatogramSettings::setProduct(), and ChromatogramSettings::setSourceFile().
Referenced by OpenSwathWorkflow::performExtraction(), and OpenSwathWorkflow::simpleExtractChromatograms().
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OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |