Inheritance diagram for NucleicAcidSearchEngine:

Classes
struct	AnnotatedHit

class	HasInvalidLength

struct	PrecursorInfo

Public Member Functions
	NucleicAcidSearchEngine ()

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 Types
typedef multimap< double, AnnotatedHit, greater< double > >	HitsByScore

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

set< ConstRibonucleotidePtr >	getModifications_ (const set< String > &mod_names)

EmpiricalFormula	parseAdduct_ (const String &adduct)

void	deisotopeAndSingleChargeMSSpectrum_ (MSSpectrum &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)

void	preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool negative_mode, Int min_charge, Int max_charge, bool include_unknown_charge)

double	calculatePrecursorMass_ (double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)

void	resolveAmbiguousMods_ (HitsByScore &hits)

void	postProcessHits_ (const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)

void	registerIDMetaData_ (IdentificationData &id_data, const String &in_mzml, const vector< String > &primary_files, const IdentificationData::DBSearchParam &search_param)

void	calculateAndFilterFDR_ (IdentificationData &id_data, bool only_top_hits)

void	generateLFQInput_ (IdentificationData &id_data, const String &out_file)

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...

Protected Attributes
vector< String >	fragment_ion_codes_

map< String, String >	ambiguous_mods_

bool	resolve_ambiguous_mods_

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...

Private Types
using	ConstRibonucleotidePtr = const Ribonucleotide *

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...

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...

Class Documentation

◆ NucleicAcidSearchEngine::AnnotatedHit

struct NucleicAcidSearchEngine::AnnotatedHit

Class Members
vector< PeakAnnotation >	annotations
IdentifiedOligoRef	oligo_ref
double	precursor_error_ppm
const PrecursorInfo *	precursor_ref
NASequence	sequence

Member Typedef Documentation

◆ ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide*

private

◆ HitsByScore

typedef multimap<double, AnnotatedHit, greater<double> > HitsByScore

protected

Constructor & Destructor Documentation

◆ NucleicAcidSearchEngine()

NucleicAcidSearchEngine ( )

inline

Member Function Documentation

◆ calculateAndFilterFDR_()

void calculateAndFilterFDR_	(	IdentificationData &	id_data,
		bool	only_top_hits
	)

inlineprotected

References FalseDiscoveryRate::applyToQueryMatches(), IDFilter::filterQueryMatchesByScore(), IdentificationData::findScoreType(), IdentificationData::getDataQueries(), DefaultParamHandler::getDefaults(), IdentificationData::getMoleculeQueryMatches(), OPENMS_LOG_INFO, IDFilter::removeDecoys(), DefaultParamHandler::setParameters(), and Param::setValue().

◆ calculatePrecursorMass_()

double calculatePrecursorMass_	(	double	mz,
		Int	charge,
		Int	isotope,
		double	adduct_mass,
		bool	negative_mode
	)

inlineprotected

References OpenMS::Constants::C13C12_MASSDIFF_U, and OpenMS::Constants::PROTON_MASS_U.

◆ deisotopeAndSingleChargeMSSpectrum_()

void deisotopeAndSingleChargeMSSpectrum_	(	MSSpectrum &	in,
		Int	min_charge,
		Int	max_charge,
		double	fragment_tolerance,
		bool	fragment_unit_ppm,
		bool	keep_only_deisotoped = `false`,
		Size	min_isopeaks = `3`,
		Size	max_isopeaks = `10`,
		bool	make_single_charged = `true`
	)

inlineprotected

References OpenMS::Constants::C13C12_MASSDIFF_U, MSSpectrum::clear(), MSSpectrum::findNearest(), Peak1D::getMZ(), OpenMS::Constants::PROTON_MASS_U, Peak1D::setMZ(), and MSSpectrum::sortByPosition().

◆ generateLFQInput_()

void generateLFQInput_	(	IdentificationData &	id_data,
		const String &	out_file
	)

inlineprotected

References ListUtils::concatenate(), IdentificationData::getMoleculeQueryMatches(), OpenMS::Math::median(), and SVOutStream::modifyStrings().

◆ getModifications_()

set<ConstRibonucleotidePtr> getModifications_ ( const set< String > & mod_names )

inlineprotected

References RibonucleotideDB::getInstance(), and Ribonucleotide::isAmbiguous().

◆ main_()

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

inlineoverrideprotectedvirtual

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

Implements TOPPBase.

References PeakFileOptions::addMSLevel(), NucleicAcidSearchEngine::AnnotatedHit::annotations, ModifiedNASequenceGenerator::applyVariableModifications(), OpenMS::IdentificationDataInternal::AVERAGE, MSExperiment::begin(), IdentificationData::calculateCoverages(), DBSearchParam::charges, PeakFileOptions::clearMSLevels(), MetaboliteSpectralMatching::computeHyperScore(), DBSearchParam::database, RNaseDigestion::digest(), DBSearchParam::digestion_enzyme, MSExperiment::end(), ProgressLogger::endProgress(), IdentificationDataConverter::exportIDs(), IdentificationDataConverter::exportMzTab(), DBSearchParam::fragment_mass_tolerance, DBSearchParam::fragment_tolerance_ppm, EmpiricalFormula::getAverageWeight(), IdentificationData::getDataQueries(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getEnzyme(), IdentificationData::getIdentifiedOligos(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getInstance(), EmpiricalFormula::getMonoWeight(), NucleicAcidSpectrumGenerator::getMultipleSpectra(), MSExperiment::getNrSpectra(), MzTab::getNucleicAcidSectionRows(), MzTab::getOligonucleotideSectionRows(), MzMLFile::getOptions(), MzTab::getOSMSectionRows(), DefaultParamHandler::getParameters(), MSExperiment::getPrimaryMSRunPath(), IdentificationDataConverter::importSequences(), MzMLFile::load(), FASTAFile::load(), DBSearchParam::mass_type, DBSearchParam::max_length, DBSearchParam::min_length, DBSearchParam::missed_cleavages, DBSearchParam::molecule_type, OpenMS::IdentificationDataInternal::MONOISOTOPIC, NucleicAcidSearchEngine::AnnotatedHit::oligo_ref, OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, OPENMS_LOG_INFO, OPENMS_LOG_WARN, NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm, DBSearchParam::precursor_mass_tolerance, NucleicAcidSearchEngine::AnnotatedHit::precursor_ref, DBSearchParam::precursor_tolerance_ppm, OpenMS::IdentificationDataInternal::RNA, NucleicAcidSearchEngine::AnnotatedHit::sequence, RNaseDigestion::setEnzyme(), ProgressLogger::setLogType(), EnzymaticDigestion::setMissedCleavages(), MSSpectrum::setName(), DefaultParamHandler::setParameters(), ProgressLogger::setProgress(), Param::setValue(), MSExperiment::size(), MSExperiment::sortSpectra(), ProgressLogger::startProgress(), MzTabFile::store(), IdXMLFile::store(), MzMLFile::store(), NASequence::toString(), and DBSearchParam::variable_mods.

◆ parseAdduct_()

EmpiricalFormula parseAdduct_ ( const String & adduct )

inlineprotected

References OPENMS_LOG_DEBUG, and String::split().

◆ postProcessHits_()

void postProcessHits_	(	const PeakMap &	exp,
		vector< HitsByScore > &	annotated_hits,
		IdentificationData &	id_data,
		bool	negative_mode
	)

inlineprotected

◆ preprocessSpectra_()

void preprocessSpectra_	(	PeakMap &	exp,
		double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		bool	single_charge_spectra,
		bool	negative_mode,
		Int	min_charge,
		Int	max_charge,
		bool	include_unknown_charge
	)

inlineprotected

References ThresholdMower::filterPeakMap(), Normalizer::filterPeakMap(), NLargest::filterPeakSpectrum(), WindowMower::filterPeakSpectrum(), SpectrumSettings::getNativeID(), DefaultParamHandler::getParameters(), SpectrumSettings::getPrecursors(), OPENMS_LOG_DEBUG, OPENMS_LOG_ERROR, OPENMS_LOG_INFO, OPENMS_LOG_WARN, Precursor::setCharge(), DefaultParamHandler::setParameters(), SpectrumSettings::setPrecursors(), Param::setValue(), MSExperiment::size(), MSSpectrum::sortByPosition(), and MSExperiment::sortSpectra().

◆ registerIDMetaData_()

void registerIDMetaData_	(	IdentificationData &	id_data,
		const String &	in_mzml,
		const vector< String > &	primary_files,
		const IdentificationData::DBSearchParam &	search_param
	)

inlineprotected

References DataProcessingSoftware::assigned_scores, File::basename(), IdentificationData::registerDataProcessingSoftware(), IdentificationData::registerDataProcessingStep(), IdentificationData::registerDBSearchParam(), IdentificationData::registerInputFile(), IdentificationData::registerScoreType(), IdentificationData::setCurrentProcessingStep(), and Software::setVersion().

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )

inlineprotectedvirtual

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.

Implements TOPPBase.

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getAllNames(), RibonucleotideDB::getInstance(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getInstance(), and String::remove().

◆ resolveAmbiguousMods_()

void resolveAmbiguousMods_ ( HitsByScore & hits )

inlineprotected

References NASequence::empty(), RibonucleotideDB::getInstance(), OPENMS_PRECONDITION, and NASequence::size().

Member Data Documentation

◆ ambiguous_mods_

map<String, String> ambiguous_mods_

protected

◆ fragment_ion_codes_

vector<String> fragment_ion_codes_

protected

◆ resolve_ambiguous_mods_

bool resolve_ambiguous_mods_

protected

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Types

Additional Inherited Members

Class Documentation

◆ NucleicAcidSearchEngine::AnnotatedHit

Member Typedef Documentation

◆ ConstRibonucleotidePtr

◆ HitsByScore

Constructor & Destructor Documentation

◆ NucleicAcidSearchEngine()

Member Function Documentation

◆ calculateAndFilterFDR_()

◆ calculatePrecursorMass_()

◆ deisotopeAndSingleChargeMSSpectrum_()

◆ generateLFQInput_()

◆ getModifications_()

◆ main_()

◆ parseAdduct_()

◆ postProcessHits_()

◆ preprocessSpectra_()

◆ registerIDMetaData_()

◆ registerOptionsAndFlags_()

◆ resolveAmbiguousMods_()

Member Data Documentation

◆ ambiguous_mods_

◆ fragment_ion_codes_

◆ resolve_ambiguous_mods_