The ChromatogramExtractor extracts chromatograms from a spectra file. More...
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
Public Types | |
typedef ChromatogramExtractorAlgorithm::ExtractionCoordinates | ExtractionCoordinates |
Public Types inherited from ProgressLogger | |
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, const 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) |
Public Member Functions inherited from ProgressLogger | |
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) |
Static Private Member Functions | |
template<typename TransitionExpT > | |
static String | extract_id_ (TransitionExpT &transition_exp_used, String id) |
Extracts id (peptide sequence or compound name) for a compound. More... | |
Private Attributes | |
std::map< OpenMS::String, double > | PeptideRTMap_ |
Additional Inherited Members | |
Static Protected Member Functions inherited from ProgressLogger | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
Protected Attributes inherited from ProgressLogger | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
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.
Extracts id (peptide sequence or compound name) for a compound.
transition_exp | The transition experiment used as input (is constant) and either of type LightTargetedExperiment or TargetedExperiment |
id | The identifier of the compound or peptide |
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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().
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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, | ||
const 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 | If non-negative, full RT extraction window, centered on the first RT value (rt_end - rt_start will equal this window size). If negative, rt_end will be set to -1 and rt_start to 0 (i.e. full RT range). If NaN, exactly two RT entries are expected
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ms1 | Whether to extract for MS1 (peptide level) or MS2 (transition level) |
Exception::IllegalArgument | if RT values are expected (depending on rt_extraction_window ) but not provided |
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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::getCompoundRef(), TargetedExperiment::getCompounds(), ReactionMonitoringTransition::getNativeID(), ReactionMonitoringTransition::getPeptideRef(), TargetedExperiment::getPeptides(), ReactionMonitoringTransition::getPrecursorMZ(), ReactionMonitoringTransition::getProductMZ(), TargetedExperiment::getTransitions(), Compound::id, 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().
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OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:07 using doxygen 1.8.13 |