OpenMS  2.5.0
OpenSwathWorkflow.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 // Interfaces
42 
43 #include <OpenMS/FORMAT/MzMLFile.h> // debug file store only
44 
45 // Kernel and implementations
51 
52 // Helpers
54 // #include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>
58 
59 // Algorithms
66 
67 #include <cassert>
68 #include <limits>
69 
70 // #define OPENSWATH_WORKFLOW_DEBUG
71 
72 // The workflow class
73 namespace OpenMS
74 {
75 
83  {
91  bool ppm;
98  };
99 
100  class OPENMS_DLLAPI OpenSwathWorkflowBase :
101  public ProgressLogger
102  {
103 
104 protected:
105 
112  use_ms1_traces_(false),
113  use_ms1_ion_mobility_(false),
114  prm_(false),
115  threads_outer_loop_(-1)
116  {
117  }
118 
131  OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop) :
132  use_ms1_traces_(use_ms1_traces),
133  use_ms1_ion_mobility_(use_ms1_ion_mobility),
134  prm_(prm),
135  threads_outer_loop_(threads_outer_loop)
136  {
137  }
138 
152  void MS1Extraction_(const OpenSwath::SpectrumAccessPtr ms1_map,
153  const std::vector< OpenSwath::SwathMap > & swath_maps,
154  std::vector< MSChromatogram >& ms1_chromatograms,
155  Interfaces::IMSDataConsumer * chromConsumer,
156  const ChromExtractParams & cp,
157  const OpenSwath::LightTargetedExperiment& transition_exp,
158  const TransformationDescription& trafo_inverse,
159  bool ms1only = false,
160  int ms1_isotopes = 0);
161 
179  void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
180  std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
181  const OpenSwath::LightTargetedExperiment & transition_exp_used,
182  const TransformationDescription trafo_inverse,
183  const ChromExtractParams & cp,
184  const bool ms1 = false,
185  const int ms1_isotopes = -1) const;
186 
187 
195  OpenSwath::SpectrumAccessPtr ms1_map_ = nullptr;
196 
199 
202 
204  bool prm_;
205 
216 
217 };
218 
235  class OPENMS_DLLAPI OpenSwathCalibrationWorkflow :
236  public OpenSwathWorkflowBase
237  {
238  public:
239 
242  {
243  }
244 
245  explicit OpenSwathCalibrationWorkflow(bool use_ms1_traces) :
246  OpenSwathWorkflowBase(use_ms1_traces, false, false, -1)
247  {
248  }
249 
274  TransformationDescription performRTNormalization(const OpenSwath::LightTargetedExperiment & irt_transitions,
275  std::vector< OpenSwath::SwathMap > & swath_maps,
276  TransformationDescription& im_trafo,
277  double min_rsq,
278  double min_coverage,
279  const Param & feature_finder_param,
280  const ChromExtractParams & cp_irt,
281  const Param& irt_detection_param,
282  const Param& calibration_param,
283  const String& irt_mzml_out,
284  Size debug_level,
285  bool sonar = false,
286  bool load_into_memory = false);
287 
288  public:
289 
319  TransformationDescription doDataNormalization_(const OpenSwath::LightTargetedExperiment& transition_exp_,
320  const std::vector< OpenMS::MSChromatogram >& chromatograms,
321  TransformationDescription& im_trafo,
322  std::vector< OpenSwath::SwathMap > & swath_maps,
323  double min_rsq,
324  double min_coverage,
325  const Param& default_ffparam,
326  const Param& irt_detection_param,
327  const Param& calibration_param);
328 
340  void simpleExtractChromatograms_(const std::vector< OpenSwath::SwathMap > & swath_maps,
341  const OpenSwath::LightTargetedExperiment & irt_transitions,
342  std::vector< OpenMS::MSChromatogram > & chromatograms,
343  const TransformationDescription& trafo,
344  const ChromExtractParams & cp,
345  bool sonar,
346  bool load_into_memory);
347 
354  static void addChromatograms(MSChromatogram& base_chrom, const MSChromatogram& newchrom);
355 
356  };
357 
382  class OPENMS_DLLAPI OpenSwathWorkflow :
383  public OpenSwathWorkflowBase
384  {
387 
388  public:
389 
404  OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop) :
405  OpenSwathWorkflowBase(use_ms1_traces, use_ms1_ion_mobility, prm, threads_outer_loop)
406  {
407  }
408 
434  void performExtraction(const std::vector< OpenSwath::SwathMap > & swath_maps,
435  const TransformationDescription trafo,
436  const ChromExtractParams & chromatogram_extraction_params,
437  const ChromExtractParams & ms1_chromatogram_extraction_params,
438  const Param & feature_finder_param,
439  const OpenSwath::LightTargetedExperiment& assay_library,
440  FeatureMap& result_featureFile,
441  bool store_features_in_featureFile,
442  OpenSwathTSVWriter & result_tsv,
443  OpenSwathOSWWriter & result_osw,
444  Interfaces::IMSDataConsumer * result_chromatograms,
445  int batchSize,
446  int ms1_isotopes,
447  bool load_into_memory);
448 
449  protected:
450 
451 
466  void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
467  const FeatureMap & featureFile,
468  FeatureMap& out_featureFile,
469  bool store_features,
470  Interfaces::IMSDataConsumer * chromConsumer);
471 
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,
512  const OpenSwath::LightTargetedExperiment& transition_exp,
513  const Param& feature_finder_param,
515  const double rt_extraction_window,
516  FeatureMap& output,
517  OpenSwathTSVWriter & tsv_writer,
518  OpenSwathOSWWriter & osw_writer,
519  int nr_ms1_isotopes = 0,
520  bool ms1only = false) const;
521 
537  void selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment& transition_exp_used_all,
538  OpenSwath::LightTargetedExperiment& transition_exp_used, int batch_size, size_t batch_idx);
539 
550  void copyBatchTransitions_(const std::vector<OpenSwath::LightCompound>& used_compounds,
551  const std::vector<OpenSwath::LightTransition>& all_transitions,
552  std::vector<OpenSwath::LightTransition>& output);
553 
554  };
555 
581  class OPENMS_DLLAPI OpenSwathWorkflowSonar :
582  public OpenSwathWorkflow
583  {
584 
585  public:
586 
587  explicit OpenSwathWorkflowSonar(bool use_ms1_traces) :
588  OpenSwathWorkflow(use_ms1_traces, false, false, -1)
589  {
590  }
591 
613  void performExtractionSonar(const std::vector< OpenSwath::SwathMap > & swath_maps,
614  const TransformationDescription trafo,
615  const ChromExtractParams & cp,
616  const ChromExtractParams & cp_ms1,
617  const Param & feature_finder_param,
618  const OpenSwath::LightTargetedExperiment& transition_exp,
619  FeatureMap& out_featureFile,
620  bool store_features,
621  OpenSwathTSVWriter & tsv_writer,
622  OpenSwathOSWWriter & osw_writer,
623  Interfaces::IMSDataConsumer * chromConsumer,
624  int batchSize,
625  bool load_into_memory);
626 
630  void computeSonarWindows_(const std::vector< OpenSwath::SwathMap > & swath_maps,
631  double & sonar_winsize,
632  double & sonar_start,
633  double & sonar_end,
634  int & sonar_total_win);
635 
639  void performSonarExtraction_(const std::vector< OpenSwath::SwathMap > & used_maps,
640  const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
641  std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
642  const ChromExtractParams & cp);
643 
651  };
652 
653 }
654 
655 
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