Inheritance diagram for UTILProteomicsLFQ:

Public Member Functions
	UTILProteomicsLFQ ()

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
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...

map< String, String >	mapMzML2Ids_ (StringList &in, StringList &in_ids)

map< String, String >	mapId2MzMLs_ (const map< String, String > &m2i)

ExitCodes	centroidAndCorrectPrecursors_ (const String &mz_file, MSExperiment &ms_centroided)

void	recalibrateMasses_ (MSExperiment &ms_centroided, vector< PeptideIdentification > &peptide_ids, const String &id_file_abs_path)

double	estimateMedianChromatographicFWHM_ (MSExperiment &ms_centroided)

void	calculateSeeds_ (const MSExperiment &ms_centroided, FeatureMap &seeds, double median_fwhm)

double	align_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)

void	transform_ (vector< FeatureMap > &feature_maps, vector< TransformationDescription > &transformations)

void	link_ (vector< FeatureMap > &feature_maps, double median_fwhm, double max_alignment_diff, ConsensusMap &consensus_fraction)

double	alignAndLink_ (vector< FeatureMap > &feature_maps, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, const double median_fwhm)

map< pair< String, UInt >, vector< int > >	getPeptideOccurrence_ (const ConsensusMap &cons)

multimap< Size, PeptideIdentification >	transferIDsBetweenSameFraction_ (const ConsensusMap &consensus_fraction, Size min_occurrence=3)

ExitCodes	quantifyFraction_ (const pair< unsigned int, std::vector< String > > &ms_files, const map< String, String > &mzfile2idfile, double median_fwhm, const multimap< Size, PeptideIdentification > &transfered_ids, ConsensusMap &consensus_fraction, vector< TransformationDescription > &transformations, double &max_alignment_diff, set< String > &fixed_modifications, set< String > &variable_modifications)

ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main(). More...

Protected Member Functions inherited from TOPPBase
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	printUsage_ ()
	Prints the tool-specific command line options and appends the common options. 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...

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...

bool	writeCTD_ ()
	Write common tool description (CTD) file. More...

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

◆ UTILProteomicsLFQ()

UTILProteomicsLFQ ( )

inline

Member Function Documentation

◆ align_()

double align_	(	vector< FeatureMap > &	feature_maps,
		vector< TransformationDescription > &	transformations
	)

inlineprotected

References MapAlignmentAlgorithmIdentification::align(), ListUtils::concatenate(), Param::copy(), Param::getValue(), OpenMS::OpenMS_Log_debug, OPENMS_LOG_INFO, ProgressLogger::setLogType(), and DefaultParamHandler::setParameters().

◆ alignAndLink_()

double alignAndLink_	(	vector< FeatureMap > &	feature_maps,
		ConsensusMap &	consensus_fraction,
		vector< TransformationDescription > &	transformations,
		const double	median_fwhm
	)

inlineprotected

References DataProcessing::ALIGNMENT, MapConversion::convert(), and DataProcessing::FEATURE_GROUPING.

◆ calculateSeeds_()

void calculateSeeds_	(	const MSExperiment &	ms_centroided,
		FeatureMap &	seeds,
		double	median_fwhm
	)

inlineprotected

References MSExperiment::addSpectrum(), ThresholdMower::filterPeakMap(), FeatureFinderMultiplexAlgorithm::getFeatureMap(), DefaultParamHandler::getParameters(), OPENMS_LOG_INFO, FeatureFinderMultiplexAlgorithm::run(), DefaultParamHandler::setParameters(), and Param::setValue().

◆ centroidAndCorrectPrecursors_()

ExitCodes centroidAndCorrectPrecursors_	(	const String &	mz_file,
		MSExperiment &	ms_centroided
	)

inlineprotected

References MSExperiment::clear(), MSExperiment::clearMetaDataArrays(), Param::copy(), PrecursorCorrection::correctToHighestIntensityMS1Peak(), MSExperiment::empty(), OpenMS::Math::getPPM(), OpenMS::Math::getPPMAbs(), MzMLFile::load(), OpenMS::Math::MAD(), OpenMS::Math::median(), OPENMS_LOG_WARN, PeakPickerHiRes::pickExperiment(), ProgressLogger::setLogType(), DefaultParamHandler::setParameters(), and MSExperiment::size().

◆ estimateMedianChromatographicFWHM_()

double estimateMedianChromatographicFWHM_ ( MSExperiment & ms_centroided )

inlineprotected

References DefaultParamHandler::getParameters(), OpenMS::Math::median(), OPENMS_LOG_INFO, and MassTraceDetection::run().

◆ getPeptideOccurrence_()

map<pair<String, UInt>, vector<int> > getPeptideOccurrence_ ( const ConsensusMap & cons )

inlineprotected

References ConsensusMap::getColumnHeaders().

◆ link_()

void link_	(	vector< FeatureMap > &	feature_maps,
		double	median_fwhm,
		double	max_alignment_diff,
		ConsensusMap &	consensus_fraction
	)

inlineprotected

References Param::copy(), FeatureGroupingAlgorithmQT::group(), OPENMS_LOG_INFO, DefaultParamHandler::setParameters(), and Param::setValue().

◆ main_()

ExitCodes main_	(	int	argc,
		const char **	argv
	)

inlineoverrideprotectedvirtual

The actual "main" method. main_() is invoked by main().

Implements TOPPBase.

References File::absolutePath(), PeptideAndProteinQuant::annotateQuantificationsToProteins(), ConsensusMap::appendColumns(), FalseDiscoveryRate::applyBasic(), PeptideProteinResolution::buildGraph(), ConsensusMap::clear(), Param::copy(), PeptideIndexing::DATABASE_EMPTY, PeptideIndexing::EXECUTION_OK, File::exists(), MzTab::exportConsensusMapToMzTab(), IDFilter::filterHitsByScore(), ExperimentalDesign::MSFileSectionEntry::fraction, ExperimentalDesign::MSFileSectionEntry::fraction_group, ExperimentalDesign::getFractionToMSFilesMapping(), ExperimentalDesign::getNumberOfFractionGroups(), DefaultParamHandler::getParameters(), ConsensusMap::getProteinIdentifications(), PeptideAndProteinQuant::getProteinResults(), BayesianProteinInferenceAlgorithm::inferPosteriorProbabilities(), IDFilter::keepUniquePeptidesPerProtein(), ExperimentalDesign::MSFileSectionEntry::label, IdXMLFile::load(), ExperimentalDesignFile::load(), OPENMS_LOG_FATAL_ERROR, OPENMS_LOG_INFO, OPENMS_LOG_WARN, OPENMS_POSTCONDITION, ExperimentalDesign::MSFileSectionEntry::path, PeptideIndexing::PEPTIDE_IDS_EMPTY, PeptideAndProteinQuant::quantifyPeptides(), PeptideAndProteinQuant::quantifyProteins(), PeptideAndProteinQuant::readQuantData(), IDFilter::removeUnreferencedProteins(), UniqueIdIndexer< RandomAccessContainer >::resolveUniqueIdConflicts(), BasicProteinInferenceAlgorithm::run(), PeptideIndexing::run(), ExperimentalDesign::MSFileSectionEntry::sample, ExperimentalDesign::setMSFileSection(), DefaultParamHandler::setParameters(), Param::setValue(), ConsensusMap::sortByPosition(), ConsensusMap::sortPeptideIdentificationsByMapIndex(), MzTabFile::store(), ConsensusXMLFile::store(), IdXMLFile::store(), MSstatsFile::storeLFQ(), PeptideIndexing::UNEXPECTED_RESULT, IDFilter::updateProteinGroups(), and IDFilter::updateProteinReferences().

◆ mapId2MzMLs_()

map<String, String> mapId2MzMLs_ ( const map< String, String > & m2i )

inlineprotected

◆ mapMzML2Ids_()

map<String, String> mapMzML2Ids_	(	StringList &	in,
		StringList &	in_ids
	)

inlineprotected

References File::absolutePath(), and File::exists().

◆ quantifyFraction_()

ExitCodes quantifyFraction_	(	const pair< unsigned int, std::vector< String > > &	ms_files,
		const map< String, String > &	mzfile2idfile,
		double	median_fwhm,
		const multimap< Size, PeptideIdentification > &	transfered_ids,
		ConsensusMap &	consensus_fraction,
		vector< TransformationDescription > &	transformations,
		double &	max_alignment_diff,
		set< String > &	fixed_modifications,
		set< String > &	variable_modifications
	)

inlineprotected

References File::absolutePath(), SpectrumMetaDataLookup::addMissingSpectrumReferences(), ConsensusMap::applyMemberFunction(), Param::copy(), ConsensusMap::getColumnHeaders(), FeatureFinderIdentificationAlgorithm::getMSData(), FeatureFinderIdentificationAlgorithm::getProgressLogger(), IdXMLFile::load(), ConsensusMapNormalizerAlgorithmMedian::NM_SCALE, ConsensusMapNormalizerAlgorithmMedian::normalizeMaps(), OPENMS_LOG_DEBUG, OPENMS_LOG_FATAL_ERROR, OPENMS_LOG_WARN, OPENMS_PRECONDITION, IDFilter::removeDecoyHits(), IDFilter::removeEmptyIdentifications(), IDFilter::removeUnreferencedProteins(), IDConflictResolverAlgorithm::resolve(), FeatureFinderIdentificationAlgorithm::run(), ProgressLogger::setLogType(), DefaultParamHandler::setParameters(), FeatureMap::setPrimaryMSRunPath(), UniqueIdInterface::setUniqueId(), Param::setValue(), ConsensusMap::sortPeptideIdentificationsByMapIndex(), ConsensusXMLFile::store(), FeatureXMLFile::store(), MSExperiment::swap(), and MapAlignmentTransformer::transformRetentionTimes().

◆ recalibrateMasses_()

void recalibrateMasses_	(	MSExperiment &	ms_centroided,
		vector< PeptideIdentification > &	peptide_ids,
		const String &	id_file_abs_path
	)

inlineprotected

References File::basename(), InternalCalibration::calibrate(), InternalCalibration::fillCalibrants(), InternalCalibration::getCalibrationPoints(), MZTrafoModel::LINEAR, OPENMS_LOG_WARN, MZTrafoModel::setCoefficientLimits(), ProgressLogger::setLogType(), MZTrafoModel::setRANSACParams(), and CalibrationData::size().

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )

inlineoverrideprotectedvirtual

Sets the valid command line options (with argument) and flags (without argument).

The options '-ini' '-log' '-instance' '-debug' and the flag '–help' are automatically registered.

TODO: think about export of quality control files (qcML?)

Implements TOPPBase.

References DefaultParamHandler::getDefaults(), Param::insert(), and Param::setValue().

◆ transferIDsBetweenSameFraction_()

multimap<Size, PeptideIdentification> transferIDsBetweenSameFraction_	(	const ConsensusMap &	consensus_fraction,
		Size	min_occurrence = `3`
	)

inlineprotected

References OpenMS::Constants::c, and OPENMS_LOG_INFO.

◆ transform_()

void transform_	(	vector< FeatureMap > &	feature_maps,
		vector< TransformationDescription > &	transformations
	)

inlineprotected

References BaseException::getMessage(), OPENMS_LOG_WARN, TransformationXMLFile::store(), and MapAlignmentTransformer::transformRetentionTimes().

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ UTILProteomicsLFQ()

Member Function Documentation

◆ align_()

◆ alignAndLink_()

◆ calculateSeeds_()

◆ centroidAndCorrectPrecursors_()

◆ estimateMedianChromatographicFWHM_()

◆ getPeptideOccurrence_()

◆ link_()

◆ main_()

◆ mapId2MzMLs_()

◆ mapMzML2Ids_()

◆ quantifyFraction_()

◆ recalibrateMasses_()

◆ registerOptionsAndFlags_()

◆ transferIDsBetweenSameFraction_()

◆ transform_()