| OpenMS 2.5.0

Public Member Functions | List of all members
OpenSwathWorkflowSonar Class Reference

Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data) More...

`#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>`

Inheritance diagram for OpenSwathWorkflowSonar:

## Public Member Functions

| OpenSwathWorkflowSonar (bool use_ms1_traces)
void | performExtractionSonar (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &cp, const ChromExtractParams &cp_ms1, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, Interfaces::IMSDataConsumer *chromConsumer, int batchSize, bool load_into_memory)
| Execute OpenSWATH analysis on a set of SONAR SwathMaps and transitions. More...
void | computeSonarWindows_ (const std::vector< OpenSwath::SwathMap > &swath_maps, double &sonar_winsize, double &sonar_start, double &sonar_end, int &sonar_total_win)
| Compute start, end and total number of (virtual) SONAR windows. More...
void | performSonarExtraction_ (const std::vector< OpenSwath::SwathMap > &used_maps, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, std::vector< OpenSwath::ChromatogramPtr > &chrom_list, const ChromExtractParams &cp)
| Perform extraction from multiple SONAR windows. More...
OpenSwath::ChromatogramPtr | addChromatograms (OpenSwath::ChromatogramPtr base_chrom, OpenSwath::ChromatogramPtr newchrom)
| Add two chromatograms. More...
Public Member Functions inherited from OpenSwathWorkflow
| OpenSwathWorkflow (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
| Constructor. More...
void | performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &chromatogram_extraction_params, const ChromExtractParams &ms1_chromatogram_extraction_params, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &assay_library, FeatureMap &result_featureFile, bool store_features_in_featureFile, OpenSwathTSVWriter &result_tsv, OpenSwathOSWWriter &result_osw, Interfaces::IMSDataConsumer *result_chromatograms, int batchSize, int ms1_isotopes, bool load_into_memory)
| Execute OpenSWATH analysis on a set of SwathMaps and transitions. More...
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...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) More...

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. More...
Protected Member Functions inherited from OpenSwathWorkflow
void | writeOutFeaturesAndChroms_ (std::vector< OpenMS::MSChromatogram > &chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)
| Write output features and chromatograms. More...
void | scoreAllChromatograms_ (const std::vector< OpenMS::MSChromatogram > &ms2_chromatograms, const std::vector< OpenMS::MSChromatogram > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, int nr_ms1_isotopes=0, bool ms1only=false) const
| Perform scoring on a set of chromatograms. More...
void | selectCompoundsForBatch_ (const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t batch_idx)
| Select which compounds to analyze in the next batch (and copy to output) More...
void | copyBatchTransitions_ (const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)
| Helper function for selectCompoundsForBatch_() More...
Protected Member Functions inherited from OpenSwathWorkflowBase
| OpenSwathWorkflowBase ()
| Default constructor. More...
| OpenSwathWorkflowBase (bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop)
| Constructor. More...
void | MS1Extraction_ (const OpenSwath::SpectrumAccessPtr ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1only=false, int ms1_isotopes=0)
| Perform MS1 extraction and store result in ms1_chromatograms. More...
void | prepareExtractionCoordinates_ (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const TransformationDescription trafo_inverse, const ChromExtractParams &cp, const bool ms1=false, const int ms1_isotopes=-1) const
| Function to prepare extraction coordinates that also correctly handles RT transformations. More...
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 OpenSwathWorkflowBase
OpenSwath::SpectrumAccessPtr | ms1_map_ = nullptr
| Spectrum Access to the MS1 map (note that this is *not* threadsafe!) More...
bool | use_ms1_traces_
| Whether to use the MS1 traces. More...
bool | use_ms1_ion_mobility_
| Whether to use ion mobility extraction on MS1 traces. More...
bool | prm_
| Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows. More...
int | threads_outer_loop_
| How many threads should be used for the outer loop. 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_

## Detailed Description

Execute all steps in an OpenEcho analysis (OpenSwath for SONAR data)

The workflow will perform a complete OpenSWATH analysis, using scanning SWATH data (SONAR data) instead of regular data. In this case, each fragment ion may appear in multiple SWATH windows and thus needs to be extracted from multiple maps.

The overall execution flow in this class is as follows (see performExtractionSonar() function)

- Obtain precursor ion chromatograms (if enabled) through MS1Extraction_()
- Compute SONAR windows using computeSonarWindows_()
- Iterate through each SONAR window:
  - Select which transitions to extract (proceed in batches) using OpenSwathHelper::selectSwathTransitions()
  - Identify which SONAR windows to use for current set of transitions
  - Iterate through each batch of transitions:
    - Extract current batch of transitions from current SONAR window:
      - Select transitions for current batch (see OpenSwathWorkflow::selectCompoundsForBatch_())
      - Prepare transition extraction (see OpenSwathWorkflow::prepareExtractionCoordinates_())
      - Extract transitions using performSonarExtraction_()
      - Convert data to OpenMS format using ChromatogramExtractor::return_chromatogram()
    - Score extracted transitions (see scoreAllChromatograms_())
    - Write scored chromatograms and peak groups to disk (see writeOutFeaturesAndChroms_())

## Constructor & Destructor Documentation

## ◆ OpenSwathWorkflowSonar()

OpenSwathWorkflowSonar | ( | bool | use_ms1_traces | ) |

inline explicit

## Member Function Documentation

## ◆ addChromatograms()

OpenSwath::ChromatogramPtr addChromatograms | ( | OpenSwath::ChromatogramPtr | base_chrom,
|  | OpenSwath::ChromatogramPtr | newchrom
| ) |  |

Add two chromatograms.

Parameters

  base_chrom | The base chromatogram to which we will add intensity
  newchrom | The chromatogram to be added

## ◆ computeSonarWindows_()

void computeSonarWindows_ | ( | const std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | double & | sonar_winsize,
|  | double & | sonar_start,
|  | double & | sonar_end,
|  | int & | sonar_total_win
| ) |  |

Compute start, end and total number of (virtual) SONAR windows.

## ◆ performExtractionSonar()

void performExtractionSonar | ( | const std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | const TransformationDescription | trafo,
|  | const ChromExtractParams & | cp,
|  | const ChromExtractParams & | cp_ms1,
|  | const Param & | feature_finder_param,
|  | const OpenSwath::LightTargetedExperiment & | transition_exp,
|  | FeatureMap & | out_featureFile,
|  | bool | store_features,
|  | OpenSwathTSVWriter & | tsv_writer,
|  | OpenSwathOSWWriter & | osw_writer,
|  | Interfaces::IMSDataConsumer * | chromConsumer,
|  | int | batchSize,
|  | bool | load_into_memory
| ) |  |

Execute OpenSWATH analysis on a set of SONAR SwathMaps and transitions.

See OpenSwathWorkflowSonar class for a detailed description of this function.

Note
  Given that these are scanning SWATH maps, for each transition multiple maps will be used for chromatogram extraction and scoring.

Parameters

  swath_maps | The raw data, expected to be scanning SWATH maps (SONAR)
  trafo | Transformation description (translating this runs' RT to normalized RT space)
  cp | Parameter set for the chromatogram extraction
  feature_finder_param | Parameter set for the feature finding in chromatographic dimension
  transition_exp | The set of assays to be extracted and scored
  out_featureFile | Output feature map to store identified features
  store_features | Whether features should be appended to the output feature map (if this is false, then out_featureFile will be empty)
  tsv_writer | TSV Writer object to store identified features in csv format (set store_features to false if using this option)
  osw_writer | OSW Writer object to store identified features in SQLite format (set store_features to false if using this option)
  chromConsumer | Chromatogram consumer object to store the extracted chromatograms
  batchSize | Size of the batches which should be extracted and scored
  load_into_memory | Whether to cache the current SONAR map(s) in memory

## ◆ performSonarExtraction_()

void performSonarExtraction_ | ( | const std::vector< OpenSwath::SwathMap > & | used_maps,
|  | const std::vector< ChromatogramExtractor::ExtractionCoordinates > & | coordinates,
|  | std::vector< OpenSwath::ChromatogramPtr > & | chrom_list,
|  | const ChromExtractParams & | cp
| ) |  |

Perform extraction from multiple SONAR windows.