OpenMS  3.0.0
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  pasef_(false),
116  threads_outer_loop_(-1)
117  {
118  }
119 
132  OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop) :
133  use_ms1_traces_(use_ms1_traces),
134  use_ms1_ion_mobility_(use_ms1_ion_mobility),
135  prm_(prm),
136  pasef_(pasef),
137  threads_outer_loop_(threads_outer_loop)
138  {
139  }
140 
154  void MS1Extraction_(const OpenSwath::SpectrumAccessPtr ms1_map,
155  const std::vector< OpenSwath::SwathMap > & swath_maps,
156  std::vector< MSChromatogram >& ms1_chromatograms,
157  Interfaces::IMSDataConsumer * chromConsumer,
158  const ChromExtractParams & cp,
159  const OpenSwath::LightTargetedExperiment& transition_exp,
160  const TransformationDescription& trafo_inverse,
161  bool ms1only = false,
162  int ms1_isotopes = 0);
163 
181  void prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
182  std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > & coordinates,
183  const OpenSwath::LightTargetedExperiment & transition_exp_used,
184  const TransformationDescription trafo_inverse,
185  const ChromExtractParams & cp,
186  const bool ms1 = false,
187  const int ms1_isotopes = -1) const;
188 
189 
197  OpenSwath::SpectrumAccessPtr ms1_map_ = nullptr;
198 
201 
204 
213  bool prm_;
214 
223  bool pasef_;
224 
235 
236 };
237 
254  class OPENMS_DLLAPI OpenSwathCalibrationWorkflow :
255  public OpenSwathWorkflowBase
256  {
257  public:
258 
261  {
262  }
263 
264  explicit OpenSwathCalibrationWorkflow(bool use_ms1_traces) :
265  OpenSwathWorkflowBase(use_ms1_traces, false, false, false, -1)
266  {
267  }
268 
293  TransformationDescription performRTNormalization(const OpenSwath::LightTargetedExperiment & irt_transitions,
294  std::vector< OpenSwath::SwathMap > & swath_maps,
295  TransformationDescription& im_trafo,
296  double min_rsq,
297  double min_coverage,
298  const Param & feature_finder_param,
299  const ChromExtractParams & cp_irt,
300  const Param& irt_detection_param,
301  const Param& calibration_param,
302  const String& irt_mzml_out,
303  Size debug_level,
304  bool sonar = false,
305  bool load_into_memory = false);
306 
307  public:
308 
338  TransformationDescription doDataNormalization_(const OpenSwath::LightTargetedExperiment& transition_exp_,
339  const std::vector< OpenMS::MSChromatogram >& chromatograms,
340  TransformationDescription& im_trafo,
341  std::vector< OpenSwath::SwathMap > & swath_maps,
342  double min_rsq,
343  double min_coverage,
344  const Param& default_ffparam,
345  const Param& irt_detection_param,
346  const Param& calibration_param);
347 
359  void simpleExtractChromatograms_(const std::vector< OpenSwath::SwathMap > & swath_maps,
360  const OpenSwath::LightTargetedExperiment & irt_transitions,
361  std::vector< OpenMS::MSChromatogram > & chromatograms,
362  const TransformationDescription& trafo,
363  const ChromExtractParams & cp,
364  bool sonar,
365  bool load_into_memory);
366 
373  static void addChromatograms(MSChromatogram& base_chrom, const MSChromatogram& newchrom);
374 
375  };
376 
405  class OPENMS_DLLAPI OpenSwathWorkflow :
406  public OpenSwathWorkflowBase
407  {
410 
411  public:
412 
427  OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop) :
428  OpenSwathWorkflowBase(use_ms1_traces, use_ms1_ion_mobility, prm, pasef, threads_outer_loop)
429  {
430  }
431 
457  void performExtraction(const std::vector< OpenSwath::SwathMap > & swath_maps,
458  const TransformationDescription trafo,
459  const ChromExtractParams & chromatogram_extraction_params,
460  const ChromExtractParams & ms1_chromatogram_extraction_params,
461  const Param & feature_finder_param,
462  const OpenSwath::LightTargetedExperiment& assay_library,
463  FeatureMap& result_featureFile,
464  bool store_features_in_featureFile,
465  OpenSwathTSVWriter & result_tsv,
466  OpenSwathOSWWriter & result_osw,
467  Interfaces::IMSDataConsumer * result_chromatograms,
468  int batchSize,
469  int ms1_isotopes,
470  bool load_into_memory);
471 
472  protected:
473 
474 
489  void writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > & chromatograms,
490  const FeatureMap & featureFile,
491  FeatureMap& out_featureFile,
492  bool store_features,
493  Interfaces::IMSDataConsumer * chromConsumer);
494 
531  void scoreAllChromatograms_(
532  const std::vector< OpenMS::MSChromatogram > & ms2_chromatograms,
533  const std::vector< OpenMS::MSChromatogram > & ms1_chromatograms,
534  const std::vector< OpenSwath::SwathMap >& swath_maps,
535  const OpenSwath::LightTargetedExperiment& transition_exp,
536  const Param& feature_finder_param,
538  const double rt_extraction_window,
539  FeatureMap& output,
540  OpenSwathTSVWriter & tsv_writer,
541  OpenSwathOSWWriter & osw_writer,
542  int nr_ms1_isotopes = 0,
543  bool ms1only = false) const;
544 
560  void selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment& transition_exp_used_all,
561  OpenSwath::LightTargetedExperiment& transition_exp_used, int batch_size, size_t batch_idx);
562 
573  void copyBatchTransitions_(const std::vector<OpenSwath::LightCompound>& used_compounds,
574  const std::vector<OpenSwath::LightTransition>& all_transitions,
575  std::vector<OpenSwath::LightTransition>& output);
576  };
577 
603  class OPENMS_DLLAPI OpenSwathWorkflowSonar :
604  public OpenSwathWorkflow
605  {
606 
607  public:
608 
609  explicit OpenSwathWorkflowSonar(bool use_ms1_traces) :
610  OpenSwathWorkflow(use_ms1_traces, false, false, false, -1)
611  {
612  }
613 
635  void performExtractionSonar(const std::vector< OpenSwath::SwathMap > & swath_maps,
636  const TransformationDescription trafo,
637  const ChromExtractParams & cp,
638  const ChromExtractParams & cp_ms1,
639  const Param & feature_finder_param,
640  const OpenSwath::LightTargetedExperiment& transition_exp,
641  FeatureMap& out_featureFile,
642  bool store_features,
643  OpenSwathTSVWriter & tsv_writer,
644  OpenSwathOSWWriter & osw_writer,
645  Interfaces::IMSDataConsumer * chromConsumer,
646  int batchSize,
647  bool load_into_memory);
648 
652  void computeSonarWindows_(const std::vector< OpenSwath::SwathMap > & swath_maps,
653  double & sonar_winsize,
654  double & sonar_start,
655  double & sonar_end,
656  int & sonar_total_win);
657 
661  void performSonarExtraction_(const std::vector< OpenSwath::SwathMap > & used_maps,
662  const std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
663  std::vector< OpenSwath::ChromatogramPtr > & chrom_list,
664  const ChromExtractParams & cp);
665 
673  };
674 
675 }
676 
677 
MSDataTransformingConsumer.h
OpenMS::UniqueIdInterface::ensureUniqueId
Size ensureUniqueId()
Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was cha...
OpenMS::TransitionTSVFile
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:144
OpenMS::ChromExtractParams::extraction_function
String extraction_function
The extraction function in mass space.
Definition: OpenSwathWorkflow.h:93
OpenMS::ChromExtractParams::extra_rt_extract
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
LinearResamplerAlign.h
OpenMS::FileTypes::SQMASS
SqLite format for mass and chromatograms, see SqMassFile.
Definition: FileTypes.h:101
FileHandler.h
FileTypes.h
OpenMS::OpenSwathCalibrationWorkflow::simpleExtractChromatograms_
void simpleExtractChromatograms_(const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram > &chromatograms, const TransformationDescription &trafo, const ChromExtractParams &cp, bool sonar, bool load_into_memory)
Simple method to extract chromatograms (for the RT-normalization peptides)
Size
OpenMS::OpenSwathWorkflowBase::prm_
bool prm_
Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.
Definition: OpenSwathWorkflow.h:213
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
TransitionTSVFile.h
OpenSwathWorkflow.h
SwathMap.h
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:89
SwathMapMassCorrection.h
OpenMS::OpenSwathCalibrationWorkflow::OpenSwathCalibrationWorkflow
OpenSwathCalibrationWorkflow(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:264
OpenMS::ChromExtractParams::min_upper_edge_dist
double min_upper_edge_dist
Whether to not extract anything closer than this (in Da) from the upper edge.
Definition: OpenSwathWorkflow.h:85
OpenMS::OpenSwathTSVWriter
Class to write out an OpenSwath TSV output (mProphet input).
Definition: OpenSwathTSVWriter.h:129
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::String
A more convenient string class.
Definition: String.h:58
MSDataSqlConsumer.h
OpenMS::OpenSwathOSWWriter
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:115
OpenMS::MSDataTransformingConsumer::setSpectraProcessingFunc
virtual void setSpectraProcessingFunc(std::function< void(SpectrumType &)> f_spec)
Sets the lambda function to be called for every spectrum which is passed to this interface.
MzMLFile.h
TransitionExperiment.h
ISpectrumAccess.h
OpenMS::OpenSwathWorkflow
Execute all steps in an OpenSwath analysis.
Definition: OpenSwathWorkflow.h:405
OpenMS::OpenSwathWorkflowBase::OpenSwathWorkflowBase
OpenSwathWorkflowBase()
Default constructor.
Definition: OpenSwathWorkflow.h:111
SimpleOpenMSSpectraAccessFactory.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
FeatureXMLFile.h
DataStructures.h
OpenMS::ChromExtractParams::mz_extraction_window
double mz_extraction_window
Extraction window in Da or ppm (e.g. 50ppm means extraction +/- 25ppm)
Definition: OpenSwathWorkflow.h:87
IMSDataConsumer.h
OpenMS::TOPPOpenSwathBase
Definition: OpenSwathBase.h:84
OpenMS::ChromExtractParams::rt_extraction_window
double rt_extraction_window
The retention time extraction window.
Definition: OpenSwathWorkflow.h:95
ChromatogramExtractor.h
OpenMS::ChromExtractParams
ChromatogramExtractor parameters.
Definition: OpenSwathWorkflow.h:82
SpectrumAccessOpenMS.h
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenMS::Param::setMaxFloat
void setMaxFloat(const std::string &key, double max)
Sets the maximum value for the floating point or floating point list parameter key.
OpenMS::OpenSwathWorkflow::OpenSwathWorkflow
OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:427
OpenMS::TransformationDescription::invert
void invert()
Computes an (approximate) inverse of the transformation.
OpenSwath::SwathQC
Quality Control function for OpenSwath.
Definition: SwathQC.h:63
OpenMS::SwathWindowLoader::readSwathWindows
static void readSwathWindows(const std::string &filename, std::vector< double > &swath_prec_lower, std::vector< double > &swath_prec_upper)
Reading a tab delimited file specifying the SWATH windows.
SwathWindowLoader.h
OpenSwathHelper.h
UInt64
SwathFile.h
OpenSwath::LightTargetedExperiment::getProteins
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:250
SpectrumAccessOpenMSInMemory.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenSwath::LightTargetedExperiment::getCompounds
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:240
MRMRTNormalizer.h
OpenSwath::LightTargetedExperiment::getTransitions
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:230
SwathQC.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::OpenSwathWorkflowBase::use_ms1_ion_mobility_
bool use_ms1_ion_mobility_
Whether to use ion mobility extraction on MS1 traces.
Definition: OpenSwathWorkflow.h:203
MRMFeatureFinderScoring.h
OpenSwathBase.h
TransformationXMLFile.h
OpenMS::OpenSwathWorkflowSonar::OpenSwathWorkflowSonar
OpenSwathWorkflowSonar(bool use_ms1_traces)
Definition: OpenSwathWorkflow.h:609
OpenMS::Param::setMinInt
void setMinInt(const std::string &key, int min)
Sets the minimum value for the integer or integer list parameter key.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::OpenSwathCalibrationWorkflow::doDataNormalization_
TransformationDescription doDataNormalization_(const OpenSwath::LightTargetedExperiment &transition_exp_, const std::vector< OpenMS::MSChromatogram > &chromatograms, TransformationDescription &im_trafo, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, const Param &calibration_param)
Perform retention time and m/z calibration.
SpectrumAccessTransforming.h
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::ChromExtractParams::ppm
bool ppm
Whether the extraction window is given in ppm or Da.
Definition: OpenSwathWorkflow.h:91
OpenMS::MSDataTransformingConsumer
Transforming consumer of MS data.
Definition: MSDataTransformingConsumer.h:58
OpenMS::TransformationDescription::apply
double apply(double value) const
Applies the transformation to value.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::OpenSwathWorkflow::TransitionType
OpenSwath::LightTransition TransitionType
Definition: OpenSwathWorkflow.h:408
OpenMS::OpenSwathWorkflowBase::OpenSwathWorkflowBase
OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)
Constructor.
Definition: OpenSwathWorkflow.h:132
OpenMS::UniqueIdGenerator::getUniqueId
static UInt64 getUniqueId()
Returns a new unique id.
OpenMS::OpenSwathWorkflowBase::pasef_
bool pasef_
Whether data is diaPASEF data.
Definition: OpenSwathWorkflow.h:223
OpenMS::OpenSwathCalibrationWorkflow
Execute all steps for retention time and m/z calibration of SWATH-MS data.
Definition: OpenSwathWorkflow.h:254
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::OpenSwathCalibrationWorkflow::OpenSwathCalibrationWorkflow
OpenSwathCalibrationWorkflow()
Definition: OpenSwathWorkflow.h:259
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::ParamValue::toString
std::string toString(bool full_precision=true) const
Convert ParamValue to string.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::Param::setMinFloat
void setMinFloat(const std::string &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
OpenMS::OpenSwathWorkflowBase::use_ms1_traces_
bool use_ms1_traces_
Whether to use the MS1 traces.
Definition: OpenSwathWorkflow.h:200
DataAccessHelper.h
OpenMS::SwathMapMassCorrection
A class containing correction functions for Swath MS maps.
Definition: SwathMapMassCorrection.h:52
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FileTypes::PQP
OpenSWATH Peptide Query Parameter (PQP) SQLite DB, see TransitionPQPFile.
Definition: FileTypes.h:102
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::OpenSwathWorkflowBase
Definition: OpenSwathWorkflow.h:100
OpenMS::OpenSwathWorkflow::MRMTransitionGroupType
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: OpenSwathWorkflow.h:409
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
OpenMS::MRMTransitionGroup
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
MRMTransitionGroupPicker.h
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenSwathOSWWriter.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::ChromExtractParams::im_extraction_window
double im_extraction_window
Extraction window in ion mobility.
Definition: OpenSwathWorkflow.h:89
OpenMS::OpenSwathWorkflowBase::threads_outer_loop_
int threads_outer_loop_
How many threads should be used for the outer loop.
Definition: OpenSwathWorkflow.h:234
OpenMS::OpenSwathWorkflowSonar
Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)
Definition: OpenSwathWorkflow.h:603
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenMS::String::ensureLastChar
String & ensureLastChar(char end)
Makes sure the string ends with the character end.
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
TransitionPQPFile.h
MSDataWritingConsumer.h
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenSwath::LightTransition
Definition: TransitionExperiment.h:45
OpenSwathTSVWriter.h
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
OpenMS::Param::remove
void remove(const std::string &key)
Remove the entry key or a section key (when suffix is ':')
OpenMS::MSDataTransformingConsumer::setExperimentalSettingsFunc
virtual void setExperimentalSettingsFunc(std::function< void(const OpenMS::ExperimentalSettings &)> f_exp_settings)
Sets the lambda function to be called when setExperimentalSettings is called via this interface.
OpenMS::Param::setValidStrings
void setValidStrings(const std::string &key, const std::vector< std::string > &strings)
Sets the valid strings for the parameter key.
File.h
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.