| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
TOPPOpenSwathBase Class Reference

`#include <OpenMS/APPLICATIONS/OpenSwathBase.h>`

Inheritance diagram for TOPPOpenSwathBase:

## Public Member Functions

| TOPPOpenSwathBase (String name, String description, bool official=true)
Public Member Functions inherited from TOPPBase
| TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={})
| Constructor. More...
virtual | ~TOPPBase ()
| Destructor. More...
ExitCodes | main (int argc, const char **argv)
| Main routine of all TOPP applications. More...

## Protected Member Functions

bool | loadSwathFiles (const StringList &file_list, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, const bool split_file, const String &tmp, const String &readoptions, const String &swath_windows_file, const double min_upper_edge_dist, const bool force, const bool sort_swath_maps, const bool sonar, const bool prm, Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
| Load the DIA files into internal data structures. More...
void | prepareChromOutput (Interfaces::IMSDataConsumer **chromatogramConsumer, const boost::shared_ptr< ExperimentalSettings > &exp_meta, const OpenSwath::LightTargetedExperiment &transition_exp, const String &out_chrom)
| Prepare chromatogram output. More...
OpenSwath::LightTargetedExperiment | loadTransitionList (const FileTypes::Type &tr_type, const String &tr_file, const Param &tsv_reader_param)
| Loads transition list from TraML / TSV or PQP. More...
TransformationDescription | performCalibration (String trafo_in, String irt_tr_file, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, Size debug_level, bool sonar, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out)
| Perform retention time and m/z calibration. More...
Protected Member Functions inherited from TOPPBase
const String & | getIniLocation_ () const
| Returns the location of the ini file where parameters are taken from. E.g. if the command line was `TOPPTool -instance 17`, then this will be `"TOPPTool:17:"`. Note the ':' at the end. More...
const String & | toolName_ () const
| Returns the tool name. More...
void | printUsage_ ()
| Prints the tool-specific command line options and appends the common options. More...
virtual ExitCodes | main_ (int argc, const char **argv)=0
| The actual "main" method. main_() is invoked by main(). More...
bool | parseRange_ (const String &text, double &low, double &high) const
| Parses a range string ([a]:[b]) into two variables (doubles) More...
bool | parseRange_ (const String &text, Int &low, Int &high) const
| Parses a range string ([a]:[b]) into two variables (integers) More...
bool | writeCTD_ ()
| Write common tool description (CTD) file. More...
virtual void | registerOptionsAndFlags_ ()=0
| Sets the valid command line options (with argument) and flags (without argument). More...
String | getParamArgument_ (const Param::ParamEntry &entry) const
| Utility function that determines a suitable argument value for the given Param::ParamEntry. More...
std::vector< ParameterInformation > | paramToParameterInformation_ (const Param &param) const
| Translates the given parameter object into a vector of ParameterInformation, that can be utilized for cl parsing. More...
ParameterInformation | paramEntryToParameterInformation_ (const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const
| Transforms a ParamEntry object to command line parameter (ParameterInformation). More...
void | registerParamSubsectionsAsTOPPSubsections_ (const Param &param)
void | registerFullParam_ (const Param &param)
| Register command line parameters for all entries in a Param object. More...
void | registerStringOption_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
| Registers a string option. More...
void | setValidStrings_ (const String &name, const std::vector< String > &strings)
| Sets the valid strings for a string option or a whole string list. More...
void | setValidStrings_ (const String &name, const std::string vstrings[], int count)
| Sets the valid strings for a string option or a whole string list. More...
void | registerInputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
| Registers an input file option. More...
void | registerOutputFile_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
| Registers an output file option. More...
void | setValidFormats_ (const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true)
| Sets the formats for a input/output file option or for all members of an input/output file lists. More...
void | registerDoubleOption_ (const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false)
| Registers a double option. More...
void | setMinInt_ (const String &name, Int min)
| Sets the minimum value for the integer parameter(can be a list of integers,too) `name`. More...
void | setMaxInt_ (const String &name, Int max)
| Sets the maximum value for the integer parameter(can be a list of integers,too) `name`. More...
void | setMinFloat_ (const String &name, double min)
| Sets the minimum value for the floating point parameter(can be a list of floating points,too) `name`. More...
void | setMaxFloat_ (const String &name, double max)
| Sets the maximum value for the floating point parameter(can be a list of floating points,too) `name`. More...
void | registerIntOption_ (const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false)
| Registers an integer option. More...
void | registerIntList_ (const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false)
| Registers a list of integers option. More...
void | registerDoubleList_ (const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false)
| Registers a list of doubles option. More...
void | registerStringList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
| Registers a list of strings option. More...
void | registerInputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList())
| Registers a list of input files option. More...
void | registerOutputFileList_ (const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false)
| Registers a list of output files option. More...
void | registerFlag_ (const String &name, const String &description, bool advanced=false)
| Registers a flag. More...
void | registerSubsection_ (const String &name, const String &description)
| Registers an allowed subsection in the INI file (usually from OpenMS algorithms). More...
void | registerTOPPSubsection_ (const String &name, const String &description)
| Registers an allowed subsection in the INI file originating from the TOPP tool itself. More...
void | addEmptyLine_ ()
| Adds an empty line between registered variables in the documentation. More...
String | getStringOption_ (const String &name) const
| Returns the value of a previously registered string option. More...
double | getDoubleOption_ (const String &name) const
| Returns the value of a previously registered double option. More...
Int | getIntOption_ (const String &name) const
| Returns the value of a previously registered integer option. More...
StringList | getStringList_ (const String &name) const
| Returns the value of a previously registered StringList. More...
IntList | getIntList_ (const String &name) const
| Returns the value of a previously registered IntList. More...
DoubleList | getDoubleList_ (const String &name) const
| Returns the value of a previously registered DoubleList. More...
bool | getFlag_ (const String &name) const
| Returns the value of a previously registered flag. More...
const ParameterInformation & | findEntry_ (const String &name) const
| Finds the entry in the parameters_ array that has the name `name`. More...
Param const & | getParam_ () const
| Return all parameters relevant to this TOPP tool. More...
void | checkParam_ (const Param &param, const String &filename, const String &location) const
| Checks top-level entries of `param` according to the information during registration. More...
void | fileParamValidityCheck_ (String &filename, const String &param_name, const ParameterInformation &p) const
| checks if an input file exists (respecting the flags) More...
void | checkIfIniParametersAreApplicable_ (const Param &ini_params)
| Checks if the parameters of the provided ini file are applicable to this tool. More...
void | writeLog_ (const String &text) const
| Writes a string to the log file and to std::cout. More...
void | writeDebug_ (const String &text, UInt min_level) const
| Writes a `text` to the log file and to std::cout if the debug level is at least `min_level`. More...
void | writeDebug_ (const String &text, const Param &param, UInt min_level) const
| Writes a String followed by a Param to the log file and to std::cout if the debug level is at least `min_level`. More...
String | makeTempDirectory_ () const
| Creates a unique temporary directory and returns its name (you have to clean it up yourself) More...
String | makeAutoRemoveTempDirectory_ (Int keep_debug=2)
| Creates a unique temporary directory and returns its name (will be cleaned up automatically if debug level is high enough) More...
void | removeTempDirectory_ (const String &dirname, Int keep_debug=2) const
| Removes a (temporary) directory. More...
ExitCodes | runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
| Runs an external process via QProcess and reports its status in the logs. More...
void | inputFileReadable_ (const String &filename, const String &param_name) const
| Checks if an input file exists, is readable and is not empty. More...
void | outputFileWritable_ (const String &filename, const String &param_name) const
| Checks if an output file is writable. More...
void | addDataProcessing_ (ConsensusMap &map, const DataProcessing &dp) const
| Data processing setter for consensus maps. More...
void | addDataProcessing_ (FeatureMap &map, const DataProcessing &dp) const
| Data processing setter for feature maps. More...
void | addDataProcessing_ (PeakMap &map, const DataProcessing &dp) const
| Data processing setter for peak maps. More...
DataProcessing | getProcessingInfo_ (DataProcessing::ProcessingAction action) const
| Returns the data processing information. More...
DataProcessing | getProcessingInfo_ (const std::set< DataProcessing::ProcessingAction > &actions) const
| Returns the data processing information. More...

## Private Member Functions

void | loadSwathFiles_ (const StringList &file_list, const bool split_file, const String &tmp, const String &readoptions, boost::shared_ptr< ExperimentalSettings > &exp_meta, std::vector< OpenSwath::SwathMap > &swath_maps, Interfaces::IMSDataConsumer *plugin_consumer)

## Additional Inherited Members

Public Types inherited from TOPPBase
enum | ExitCodes { EXECUTION_OK, INPUT_FILE_NOT_FOUND, INPUT_FILE_NOT_READABLE, INPUT_FILE_CORRUPT, INPUT_FILE_EMPTY, CANNOT_WRITE_OUTPUT_FILE, ILLEGAL_PARAMETERS, MISSING_PARAMETERS, UNKNOWN_ERROR, EXTERNAL_PROGRAM_ERROR, PARSE_ERROR, INCOMPATIBLE_INPUT_DATA, INTERNAL_ERROR, UNEXPECTED_RESULT
}
| Exit codes. More...
Static Public Member Functions inherited from TOPPBase
static void | setMaxNumberOfThreads (int num_threads)
| Sets the maximal number of usable threads. More...
Protected Attributes inherited from TOPPBase
String | version_
| Version string (if empty, the OpenMS/TOPP version is printed) More...
String | verboseVersion_
| Version string including additional revision/date time information. Note: This differs from version_ only if not provided by the user. More...
bool | official_
| Flag indicating if this an official TOPP tool. More...
std::vector< Citation > | citations_
| Papers, specific for this tool (will be shown in '–help') More...
ProgressLogger::LogType | log_type_
| Type of progress logging. More...
bool | test_mode_
| Test mode. More...
Int | debug_level_
| Debug level set by -debug. More...
Static Protected Attributes inherited from TOPPBase
static String | topp_ini_file_
| .TOPP.ini file for storing system default parameters More...
static const Citation | cite_openms_
| The OpenMS citation. More...

## Constructor & Destructor Documentation

## ◆ TOPPOpenSwathBase()

TOPPOpenSwathBase | ( | String | name,
|  | String | description,
|  | bool | official = `true`
| ) |  |

inline

## Member Function Documentation

## ◆ loadSwathFiles()

bool loadSwathFiles | ( | const StringList & | file_list,
|  | boost::shared_ptr< ExperimentalSettings > & | exp_meta,
|  | std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | const bool | split_file,
|  | const String & | tmp,
|  | const String & | readoptions,
|  | const String & | swath_windows_file,
|  | const double | min_upper_edge_dist,
|  | const bool | force,
|  | const bool | sort_swath_maps,
|  | const bool | sonar,
|  | const bool | prm,
|  | Interfaces::IMSDataConsumer * | plugin_consumer = `nullptr`
| ) |  |

inline protected

Load the DIA files into internal data structures.

Loads SWATH files into the provided OpenSwath::SwathMap data structures. It uses the SwathFile class to load files from either mzML, mzXML or SqMass. The files will be either loaded into memory or cached to disk (depending on the readoptions parameter).

Parameters

  file_list | The input file(s)
  exp_meta | The output (meta data about experiment)
  swath_maps | The output (ptr to raw data)
  file_list | The input file(s)
  split_file | If loading a single file that contains a single SWATH window
  tmp | Temporary directory
  readoptions | Description on how to read the data ("normal", "cache")
  swath_windows_file | Provided file containing the SWATH windows which will be mapped to the experimental windows
  min_upper_edge_dist | Distance for each assay to the upper edge of the SWATH window
  force | Whether to override the sanity check
  sort_swath_maps | Whether to sort the provided windows first before mapping
  sonar | Whether data is in sonar format

Returns
  Returns whether loading and sanity check was successful

References SwathWindowLoader::annotateSwathMapsFromFile(), TOPPOpenSwathBase::loadSwathFiles_(), OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, and OPENMS_LOG_WARN.

## ◆ loadSwathFiles_()

void loadSwathFiles_ | ( | const StringList & | file_list,
|  | const bool | split_file,
|  | const String & | tmp,
|  | const String & | readoptions,
|  | boost::shared_ptr< ExperimentalSettings > & | exp_meta,
|  | std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | Interfaces::IMSDataConsumer * | plugin_consumer
| ) |  |

inline private

References FileHandler::getTypeByFileName(), SwathFile::loadMzML(), SwathFile::loadMzXML(), SwathFile::loadSplit(), SwathFile::loadSqMass(), TOPPBase::log_type_, FileTypes::MZML, FileTypes::MZXML, ProgressLogger::setLogType(), and FileTypes::SQMASS.

Referenced by TOPPOpenSwathBase::loadSwathFiles().

## ◆ loadTransitionList()

OpenSwath::LightTargetedExperiment loadTransitionList | ( | const FileTypes::Type & | tr_type,
|  | const String & | tr_file,
|  | const Param & | tsv_reader_param
| ) |  |

inline protected

Loads transition list from TraML / TSV or PQP.

Parameters

  tr_type | Input file type
  tr_file | Input file name
  tsv_reader_param | Parameters on how to interpret spectral data

References TransitionPQPFile::convertPQPToTargetedExperiment(), OpenSwathDataAccessHelper::convertTargetedExp(), TransitionTSVFile::convertTSVToTargetedExperiment(), ProgressLogger::endProgress(), TraMLFile::load(), TOPPBase::log_type_, OPENMS_LOG_ERROR, FileTypes::PQP, ProgressLogger::setLogType(), DefaultParamHandler::setParameters(), ProgressLogger::startProgress(), FileTypes::TRAML, and FileTypes::TSV.

Referenced by TOPPOpenSwathBase::performCalibration().

## ◆ performCalibration()

TransformationDescription performCalibration | ( | String | trafo_in,
|  | String | irt_tr_file,
|  | std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | double | min_rsq,
|  | double | min_coverage,
|  | const Param & | feature_finder_param,
|  | const ChromExtractParams & | cp_irt,
|  | const Param & | irt_detection_param,
|  | const Param & | calibration_param,
|  | Size | debug_level,
|  | bool | sonar,
|  | bool | load_into_memory,
|  | const String & | irt_trafo_out,
|  | const String & | irt_mzml_out
| ) |  |

inline protected

Perform retention time and m/z calibration.

This function will create the retention time transformation either by loading a provided .trafoXML file or determine it from the data itself by extracting the transitions specified in the irt_tr_file TraML file. It will also perform the m/z calibration.

Note
  Internally, the retention time and `m/z` calibration are performed by OpenMS::OpenSwathCalibrationWorkflow::performRTNormalization

Parameters

  trafo_in | Input trafoXML file (if not empty, transformation will be loaded from this file)
  irt_tr_file | Input TraML file containing transitions (if trafo_in is empty, this file will be loaded and transitions will be extracted)
  swath_maps | The raw data (swath maps)
  min_rsq | Minimal R^2 value that is expected for the RT regression
  min_coverage | Minimal coverage of the chromatographic space that needs to be achieved
  feature_finder_param | Parameter set for the feature finding in chromatographic dimension
  cp_irt | Parameter set for the chromatogram extraction
  irt_detection_param | Parameter set for the detection of the iRTs (outlier detection, peptides per bin etc)
  calibration_param | Parameter for the m/z and im calibration (see SwathMapMassCorrection)
  debug_level | Debug level (writes out the RT normalization chromatograms if larger than 1)
  sonar | Whether the data is SONAR data
  load_into_memory | Whether to cache the current SWATH map in memory
  irt_trafo_out | Output trafoXML file (if not empty and no input trafoXML file is given, the transformation parameters will be stored in this file)
  irt_mzml_out | Output Chromatogram mzML containing the iRT peptides (if not empty, iRT chromatograms will be stored in this file)

References Param::copy(), TransformationDescription::fitModel(), DefaultParamHandler::getDefaults(), TOPPBase::getParam_(), FileHandler::getType(), Param::getValue(), TransformationXMLFile::load(), TOPPOpenSwathBase::loadTransitionList(), TOPPBase::log_type_, OpenSwathCalibrationWorkflow::performRTNormalization(), ProgressLogger::setLogType(), Param::setValue(), and TransformationXMLFile::store().

## ◆ prepareChromOutput()

void prepareChromOutput | ( | Interfaces::IMSDataConsumer ** | chromatogramConsumer,
|  | const boost::shared_ptr< ExperimentalSettings > & | exp_meta,
|  | const OpenSwath::LightTargetedExperiment & | transition_exp,
|  | const String & | out_chrom
| ) |  |

inline protected

Prepare chromatogram output.

Sets up the chromatogram output, either sqMass or mzML (using numpress lossy compression). This assumes that 0.05 accuracy in RT is sufficient for all purposes.

Parameters

  chromatogramConsumer | The consumer to process chromatograms
  exp_meta | meta data about experiment
  transition_exp | The spectral library
  out_chrom | The output file for the chromatograms

References MSDataWritingConsumer::addDataProcessing(), MSNumpressCoder::NumpressConfig::estimate_fixed_point, MzMLHandler::getOptions(), TOPPBase::getProcessingInfo_(), String::hasSuffix(), MSNumpressCoder::NumpressConfig::linear_fp_mass_acc, MSNumpressCoder::NumpressConfig::numpressErrorTolerance, PeakFileOptions::setCompression(), MSNumpressCoder::NumpressConfig::setCompression(), MSDataWritingConsumer::setExpectedSize(), MSDataWritingConsumer::setExperimentalSettings(), PeakFileOptions::setNumpressConfigurationIntensity(), PeakFileOptions::setNumpressConfigurationMassTime(), PeakFileOptions::setWriteIndex(), DataProcessing::SMOOTHING, String::toLower(), and LightTargetedExperiment::transitions.