112 use_ms1_traces_(false),
113 use_ms1_ion_mobility_(false),
115 threads_outer_loop_(-1)
132 use_ms1_traces_(use_ms1_traces),
133 use_ms1_ion_mobility_(use_ms1_ion_mobility),
135 threads_outer_loop_(threads_outer_loop)
153 const std::vector< OpenSwath::SwathMap > & swath_maps,
154 std::vector< MSChromatogram >& ms1_chromatograms,
159 bool ms1only =
false,
160 int ms1_isotopes = 0);
179 void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
180 std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
184 const bool ms1 =
false,
185 const int ms1_isotopes = -1)
const;
275 std::vector< OpenSwath::SwathMap > & swath_maps,
279 const Param & feature_finder_param,
281 const Param& irt_detection_param,
282 const Param& calibration_param,
283 const String& irt_mzml_out,
286 bool load_into_memory =
false);
320 const std::vector< OpenMS::MSChromatogram >& chromatograms,
322 std::vector< OpenSwath::SwathMap > & swath_maps,
325 const Param& default_ffparam,
326 const Param& irt_detection_param,
327 const Param& calibration_param);
340 void simpleExtractChromatograms_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
342 std::vector< OpenMS::MSChromatogram > & chromatograms,
346 bool load_into_memory);
404 OpenSwathWorkflow(
bool use_ms1_traces,
bool use_ms1_ion_mobility,
bool prm,
int threads_outer_loop) :
434 void performExtraction(
const std::vector< OpenSwath::SwathMap > & swath_maps,
438 const Param & feature_finder_param,
441 bool store_features_in_featureFile,
447 bool load_into_memory);
466 void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
508 void scoreAllChromatograms_(
509 const std::vector< OpenMS::MSChromatogram > & ms2_chromatograms,
510 const std::vector< OpenMS::MSChromatogram > & ms1_chromatograms,
511 const std::vector< OpenSwath::SwathMap >& swath_maps,
513 const Param& feature_finder_param,
515 const double rt_extraction_window,
519 int nr_ms1_isotopes = 0,
520 bool ms1only =
false)
const;
550 void copyBatchTransitions_(
const std::vector<OpenSwath::LightCompound>& used_compounds,
551 const std::vector<OpenSwath::LightTransition>& all_transitions,
552 std::vector<OpenSwath::LightTransition>& output);
613 void performExtractionSonar(
const std::vector< OpenSwath::SwathMap > & swath_maps,
617 const Param & feature_finder_param,
625 bool load_into_memory);
630 void computeSonarWindows_(
const std::vector< OpenSwath::SwathMap > & swath_maps,
631 double & sonar_winsize,
632 double & sonar_start,
634 int & sonar_total_win);
639 void performSonarExtraction_(
const std::vector< OpenSwath::SwathMap > & used_maps,
640 const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
641 std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
A more convenient string class.
Definition: String.h:58
The representation of a chromatogram.
Definition: MSChromatogram.h:54
bool use_ms1_ion_mobility_
Whether to use ion mobility extraction on MS1 traces.
Definition: OpenSwathWorkflow.h:201
OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:404
ChromatogramExtractor parameters.
Definition: OpenSwathWorkflow.h:82
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
The representation of a group of transitions in a targeted proteomics experiment. ...
Definition: MRMTransitionGroup.h:67
String extraction_function
The extraction function in mass space.
Definition: OpenSwathWorkflow.h:93
A container for features.
Definition: FeatureMap.h:95
OpenSwathWorkflowSonar(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:587
Execute all steps in an OpenSwath analysis.
Definition: OpenSwathWorkflow.h:382
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
bool use_ms1_traces_
Whether to use the MS1 traces.
Definition: OpenSwathWorkflow.h:198
double extra_rt_extract
Whether to extract some extra in the retention time (can be useful if one wants to look at the chroma...
Definition: OpenSwathWorkflow.h:97
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:115
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double im_extraction_window
Extraction window in ion mobility.
Definition: OpenSwathWorkflow.h:89
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenSwathWorkflowBase()
Default constructor.
Definition: OpenSwathWorkflow.h:111
Execute all steps for retention time and m/z calibration of SWATH-MS data.
Definition: OpenSwathWorkflow.h:235
Class to write out an OpenSwath TSV output (mProphet input).
Definition: OpenSwathTSVWriter.h:129
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
Definition: TransitionExperiment.h:207
int threads_outer_loop_
How many threads should be used for the outer loop.
Definition: OpenSwathWorkflow.h:215
Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)
Definition: OpenSwathWorkflow.h:581
bool prm_
Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows...
Definition: OpenSwathWorkflow.h:204
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenSwathCalibrationWorkflow(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:245
Definition: OpenSwathWorkflow.h:100
Definition: TransitionExperiment.h:46
double min_upper_edge_dist
Whether to not extract anything closer than this (in Da) from the upper edge.
Definition: OpenSwathWorkflow.h:85
double rt_extraction_window
The retention time extraction window.
Definition: OpenSwathWorkflow.h:95
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: OpenSwathWorkflow.h:386
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenSwathCalibrationWorkflow()
Definition: OpenSwathWorkflow.h:240
OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:131
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double mz_extraction_window
Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
Definition: OpenSwathWorkflow.h:87
OpenSwath::LightTransition TransitionType
Definition: OpenSwathWorkflow.h:385
bool ppm
Whether the extraction window is given in ppm or Da.
Definition: OpenSwathWorkflow.h:91