| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | List of all members
SwathFile Class Reference

File adapter for Swath files. More...

`#include <OpenMS/FORMAT/SwathFile.h>`

Inheritance diagram for SwathFile:

## Public Member Functions

std::vector< OpenSwath::SwathMap > | loadSplit (StringList file_list, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
| Loads a Swath run from a list of split mzML files. More...
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. More...
std::vector< OpenSwath::SwathMap > | loadMzXML (String file, String tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, String readoptions="normal")
| Loads a Swath run from a single mzXML file. More...
std::vector< OpenSwath::SwathMap > | loadSqMass (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...
| ~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...

## Protected Member Functions

OpenSwath::SpectrumAccessPtr | doCacheFile_ (const String &in, const String &tmp, const String &tmp_fname, boost::shared_ptr< PeakMap > experiment_metadata)
| Cache a file to disk. More...
boost::shared_ptr< PeakMap > | populateMetaData_ (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)
| 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...
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 ProgressLogger
LogType | type_
time_t | last_invoke_
ProgressLoggerImpl * | current_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
| ) |  |

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,
|  | 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] | file Input filename
  [IN] | tmp Temporary directory (for cached data)
  [OUT] | exp_meta Experimental metadata from mzML file
  [IN] | readoptions How are spectra accessed after reading - tradeoff between memory usage and time (disk caching)
  [IN] | plugin_consumer An 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 | ( | String | file,
|  | String | tmp,
|  | boost::shared_ptr< ExperimentalSettings > & | exp_meta,
|  | 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,
|  | String | tmp,
|  | boost::shared_ptr< ExperimentalSettings > & | exp_meta,
|  | String | readoptions = `"normal"`
| ) |  |

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

Referenced by TOPPOpenSwathBase::loadSwathFiles_().

## ◆ loadSqMass()

std::vector<OpenSwath::SwathMap> loadSqMass | ( | 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.