OpenMS
SwathFile Class Reference

File adapter for Swath files. More...

#include <OpenMS/FORMAT/SwathFile.h>

Inheritance diagram for SwathFile:
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Collaboration diagram for SwathFile:
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Public Member Functions

std::vector< OpenSwath::SwathMaploadSplit (StringList file_list, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal")
 Loads a Swath run from a list of split mzML files. More...
 
std::vector< OpenSwath::SwathMaploadMzML (const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal", Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
 Loads a Swath run from a single mzML file. More...
 
std::vector< OpenSwath::SwathMaploadMzXML (const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal")
 Loads a Swath run from a single mzXML file. More...
 
std::vector< OpenSwath::SwathMaploadSqMass (const String &file, boost::shared_ptr< ExperimentalSettings > &)
 Loads a Swath run from a single sqMass file. More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
virtual ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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 setLogger (ProgressLoggerImpl *logger)
 Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 

Protected Member Functions

OpenSwath::SpectrumAccessPtr doCacheFile_ (const String &in, const String &tmp, const String &tmp_fname, const boost::shared_ptr< PeakMap > &experiment_metadata)
 Cache a file to disk. More...
 
boost::shared_ptr< PeakMappopulateMetaData_ (const String &file)
 Only read the meta data from a file and use it to populate exp_meta. More...
 
void countScansInSwath_ (const std::vector< MSSpectrum > &exp, std::vector< int > &swath_counter, int &nr_ms1_spectra, std::vector< OpenSwath::SwathMap > &known_window_boundaries, double TOLERANCE=1e-6)
 Counts the number of scans in a full Swath file (e.g. concatenated non-split file) More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD , GUI , NONE }
 Possible log types. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

File adapter for Swath files.

This class can load SWATH files in different storage versions. The most convenient file is a single MzML file which contains one experiment. However, also the loading of a list of files is supported (loadSplit) where it is assumed that each individual file only contains scans from one precursor isolation window (one SWATH). Finally, experimental support for mzXML is available but needs to be selected with a specific compile flag (this is not for everyday use).

Member Function Documentation

◆ countScansInSwath_()

void countScansInSwath_ ( const std::vector< MSSpectrum > &  exp,
std::vector< int > &  swath_counter,
int &  nr_ms1_spectra,
std::vector< OpenSwath::SwathMap > &  known_window_boundaries,
double  TOLERANCE = 1e-6 
)
protected

Counts the number of scans in a full Swath file (e.g. concatenated non-split file)

◆ doCacheFile_()

OpenSwath::SpectrumAccessPtr doCacheFile_ ( const String in,
const String tmp,
const String tmp_fname,
const boost::shared_ptr< PeakMap > &  experiment_metadata 
)
protected

Cache a file to disk.

◆ loadMzML()

std::vector<OpenSwath::SwathMap> loadMzML ( const String file,
const String tmp,
boost::shared_ptr< ExperimentalSettings > &  exp_meta,
const String readoptions = "normal",
Interfaces::IMSDataConsumer plugin_consumer = nullptr 
)

Loads a Swath run from a single mzML file.

Using the plugin_consumer, you can provide a custom consumer which will be chained into the process of loading the data and making it available (depending on readoptions). This is useful if you want to modify the data a priori or extract some other information using MSDataTransformingConsumer (for example). Make sure it leaves the data intact, such that the returned SwathMaps are actually useful.

Parameters
[in]fileInput filename
[in]tmpTemporary directory (for cached data)
[out]exp_metaExperimental metadata from mzML file
[in]readoptionsHow are spectra accessed after reading - tradeoff between memory usage and time (disk caching)
[in]plugin_consumerAn intermediate custom consumer
Returns
Swath maps for MS2 and MS1 (unless readoptions == split, which returns no data)

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ loadMzXML()

std::vector<OpenSwath::SwathMap> loadMzXML ( const String file,
const String tmp,
boost::shared_ptr< ExperimentalSettings > &  exp_meta,
const String readoptions = "normal" 
)

Loads a Swath run from a single mzXML file.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ loadSplit()

std::vector<OpenSwath::SwathMap> loadSplit ( StringList  file_list,
const String tmp,
boost::shared_ptr< ExperimentalSettings > &  exp_meta,
const String readoptions = "normal" 
)

Loads a Swath run from a list of split mzML files.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ loadSqMass()

std::vector<OpenSwath::SwathMap> loadSqMass ( const String file,
boost::shared_ptr< ExperimentalSettings > &   
)

Loads a Swath run from a single sqMass file.

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

◆ populateMetaData_()

boost::shared_ptr< PeakMap > populateMetaData_ ( const String file)
protected

Only read the meta data from a file and use it to populate exp_meta.