| OpenMS 2.5.0

Protected Member Functions | Protected Attributes | List of all members
OpenSwathWorkflowBase Class Reference

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

Inheritance diagram for OpenSwathWorkflowBase:

## Protected Member Functions

| 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...

## Protected Attributes

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_

## Additional Inherited Members

Public Types inherited from ProgressLogger
enum | LogType { CMD, GUI, NONE }
| Possible log types. 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...
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...
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Constructor & Destructor Documentation

## ◆ OpenSwathWorkflowBase() [1/2]

OpenSwathWorkflowBase | ( |  | ) |

inline protected

Default constructor.

Will not use any ms1 traces and use all threads in the outer loop.

## ◆ OpenSwathWorkflowBase() [2/2]

OpenSwathWorkflowBase | ( | bool | use_ms1_traces,
|  | bool | use_ms1_ion_mobility,
|  | bool | prm,
|  | int | threads_outer_loop
| ) |  |

inline protected

Constructor.

Parameters

  use_ms1_traces | Whether to use MS1 data
  threads_outer_loop | How many threads should be used for the outer loop (-1 will use all threads in the outer loop)

Note
  The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).

## Member Function Documentation

## ◆ MS1Extraction_()

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`
| ) |  |

protected

Perform MS1 extraction and store result in ms1_chromatograms.

Parameters

  swath_maps | The raw data (swath maps)
  ms1_chromatograms | Output vector for MS1 chromatograms
  chromConsumer | Chromatogram consumer object to store the extracted chromatograms
  cp | Parameter set for the chromatogram extraction
  transition_exp | The set of assays to be extracted and scored
  trafo_inverse | Inverse transformation function
  load_into_memory | Whether to cache the current SWATH map in memory
  ms1only | If true, will only score on MS1 level and ignore MS2 level

## ◆ prepareExtractionCoordinates_()

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

protected

Function to prepare extraction coordinates that also correctly handles RT transformations.

Creates a set of (empty) chromatograms and extraction coordinates with the correct ids, m/z and retention time start/end points to be extracted by the ChromatogramExtractor.

Handles rt extraction windows by calculating the correct transformation for each coordinate.

Parameters

  chrom_list | Output of chromatograms (will be filled with empty chromatogram ptrs)
  coordinates | Output of extraction coordinates (will be filled with matching extraction coordinates)
  transition_exp_used | The transition experiment used to create the coordinates
  ms1 | Whether to perform MS1 (precursor ion) or MS2 (fragment ion) extraction
  trafo_inverse | Inverse transformation function
  cp | Parameter set for the chromatogram extraction

## Member Data Documentation

## ◆ ms1_map_

OpenSwath::SpectrumAccessPtr ms1_map_ = nullptr

protected

Spectrum Access to the MS1 map (note that this is *not* threadsafe!)

Note
  This pointer is not threadsafe, please use the lightClone() function to create a copy for each thread
  This pointer may be NULL if use_ms1_traces_ is set to false

## ◆ prm_

bool prm_

protected

Whether data is acquired in targeted DIA (e.g. PRM mode) with potentially overlapping windows.

## ◆ threads_outer_loop_

int threads_outer_loop_

protected

How many threads should be used for the outer loop.

Note
  A value of -1 will use all threads in the outer loop
  The total number of threads should be divisible by this number (e.g. use 8 in outer loop if you have 24 threads in total and 3 will be used for the inner loop).

## ◆ use_ms1_ion_mobility_

bool use_ms1_ion_mobility_

protected

Whether to use ion mobility extraction on MS1 traces.

## ◆ use_ms1_traces_

bool use_ms1_traces_

protected

Whether to use the MS1 traces.