#include <OpenMS/APPLICATIONS/OpenSwathBase.h>

Inheritance diagram for TOPPOpenSwathBase:

Collaboration diagram for TOPPOpenSwathBase:

Public Member Functions
	TOPPOpenSwathBase (String name, String description, bool official=true)

Public Member Functions inherited from TOPPBase
	TOPPBase ()=delete
	No default constructor. More...

	TOPPBase (const TOPPBase &)=delete
	No default copy constructor. More...

	TOPPBase (const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)
	Constructor. More...

virtual	~TOPPBase ()
	Destructor. More...

ExitCodes	main (int argc, const char **argv)
	Main routine of all TOPP applications. More...

String	getToolPrefix () const
	Returns the prefix used to identify the tool. More...

String	getDocumentationURL () const
	Returns a link to the documentation of the tool (accessible on our servers and only after inclusion in the nightly branch or a release). 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 prm, const bool pasef, 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, const UInt64 run_id)
	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 pasef, 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
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	registerOutputPrefix_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output file prefix used for tools with multiple file output. More...

void	registerOutputDir_ (const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false)
	Registers an output directory used for tools with multiple output files which are not an output file list, i.e. do not correspond to the number of input files. 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, const 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, const 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, const 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, const 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, const 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 (use `getOutputDirOption()` for output directories) More...

String	getOutputDirOption (const String &name) const
	Returns the value of a previously registered output_dir 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_ (const StringList &param_value, const String &param_name, const ParameterInformation &p) const
	checks if files of an input file list exist More...

void	fileParamValidityCheck_ (String &param_value, 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	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...

void	writeLogInfo_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_INFO. More...

void	writeLogWarn_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_WARN. More...

void	writeLogError_ (const String &text) const
	Writes a string to the log file and to OPENMS_LOG_ERROR. More...

void	writeDebug_ (const String &text, UInt min_level) const
	Writes a string to the log file and to OPENMS_LOG_DEBUG 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 OPENMS_LOG_DEBUG if the debug level is at least `min_level`. More...

ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, const QString &workdir="") const
	Runs an external process via ExternalProcess and prints its stderr output on failure or if debug_level > 4. More...

ExitCodes	runExternalProcess_ (const QString &executable, const QStringList &arguments, String &proc_stdout, String &proc_stderr, const QString &workdir="") const

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	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...

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...

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...

template<typename Writer >
void	writeToolDescription_ (Writer &writer, std::string write_type, std::string fileExtension)
	Helper function avoiding repeated code between CTD, JSON and CWL. 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 , EXTERNAL_PROGRAM_NOTFOUND }
	Exit codes. More...

Static Public Member Functions inherited from TOPPBase
static void	setMaxNumberOfThreads (int num_threads)
	Sets the maximal number of usable threads. More...

Static Public Attributes inherited from TOPPBase
static const char *	TAG_OUTPUT_FILE = "output file"

static const char *	TAG_INPUT_FILE = "input file"

static const char *	TAG_OUTPUT_DIR = "output dir"

static const char *	TAG_OUTPUT_PREFIX = "output prefix"

static const char *	TAG_ADVANCED = "advanced"

static const char *	TAG_REQUIRED = "required"

static const Citation	cite_openms
	The latest and greatest OpenMS citation. 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...

bool	toolhandler_test_
	Enable the ToolHandler tests. 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...

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	prm,
		const bool	pasef,
		Interfaces::IMSDataConsumer *	plugin_consumer = `nullptr`
	)

inlineprotected

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)
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
prm	Whether data is in prm format; allows for overlap
pasef	Whether data is in PASEF format; allows for overlap
plugin_consumer	Intermediate consumer for mzML input. See SwathFile::loadMzML() for details.

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
	)

inlineprivate

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
	)

inlineprotected

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(), FileHandler::loadTransitions(), 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	pasef,
		bool	load_into_memory,
		const String &	irt_trafo_out,
		const String &	irt_mzml_out
	)

inlineprotected

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)
pasef	whether the data is PASEF data with possible overlapping m/z windows (with different ion mobility). In this case, the "best" SWATH window (with precursor cetntered around IM) is chosen.
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_(), LightTargetedExperiment::getTransitions(), FileHandler::getType(), Param::getValue(), OpenMS::Constants::k, FileHandler::loadTransformations(), TOPPOpenSwathBase::loadTransitionList(), TOPPBase::log_type_, OpenSwathCalibrationWorkflow::performRTNormalization(), ProgressLogger::setLogType(), Param::setValue(), FileHandler::storeTransformations(), ParamValue::toString(), and FileTypes::TRANSFORMATIONXML.

◆ prepareChromOutput()

void prepareChromOutput	(	Interfaces::IMSDataConsumer **	chromatogramConsumer,
		const boost::shared_ptr< ExperimentalSettings > &	exp_meta,
		const OpenSwath::LightTargetedExperiment &	transition_exp,
		const String &	out_chrom,
		const UInt64	run_id
	)

inlineprotected

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
run_id	Unique identifier which links the sqMass and OSW file

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.

Public Member Functions

Protected Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ TOPPOpenSwathBase()

Member Function Documentation

◆ loadSwathFiles()

◆ loadSwathFiles_()

◆ loadTransitionList()

◆ performCalibration()

◆ prepareChromOutput()