NucleicAcidSearchEngine Class Reference

Inheritance diagram for NucleicAcidSearchEngine:

Collaboration diagram for NucleicAcidSearchEngine:

Classes
struct	AnnotatedHit
class	HasInvalidLength
struct	PrecursorInfo

Public Member Functions
	NucleicAcidSearchEngine ()
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 Types
typedef multimap< double, AnnotatedHit, greater< double > >	HitsByScore

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...
set< ConstRibonucleotidePtr >	getModifications_ (const set< String > &mod_names)
AdductInfo	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	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	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...
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...

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...
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...

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 , 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...
Static Protected Attributes inherited from TOPPBase
static String	topp_ini_file_
	.TOPP.ini file for storing system default parameters More...

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Class Documentation

NucleicAcidSearchEngine::AnnotatedHit

struct NucleicAcidSearchEngine::AnnotatedHit

Collaboration diagram for 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::applyToObservationMatches(), IDFilter::filterObservationMatchesByScore(), IdentificationData::findScoreType(), DefaultParamHandler::getDefaults(), IdentificationData::getObservationMatches(), IdentificationData::getObservations(), 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::getObservationMatches(), 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(), ScoredProcessingResult::addProcessingStep(), MSExperiment::addSpectrum(), NucleicAcidSearchEngine::AnnotatedHit::annotations, ModifiedNASequenceGenerator::applyVariableModifications(), ProcessingSoftware::assigned_scores, OpenMS::IdentificationDataInternal::AVERAGE, File::basename(), 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, IdentificationData::getCurrentProcessingStep(), IdentificationData::getDBSearchParams(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getEnzyme(), IdentificationData::getIdentifiedOligos(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getInstance(), AdductInfo::getMassShift(), NucleicAcidSpectrumGenerator::getMultipleSpectra(), MSExperiment::getNrSpectra(), MzTab::getNucleicAcidSectionRows(), IdentificationData::getObservations(), MzTab::getOligonucleotideSectionRows(), MzTab::getOSMSectionRows(), DefaultParamHandler::getParameters(), IdentificationData::getParentSequences(), MSExperiment::getPrimaryMSRunPath(), MSSpectrum::getRT(), FileTypes::IDXML, IdentificationDataConverter::importSequences(), OMSFile::load(), FASTAFile::load(), FileHandler::loadExperiment(), DBSearchParam::mass_type, DBSearchParam::max_length, DBSearchParam::min_length, DBSearchParam::missed_cleavages, DBSearchParam::molecule_type, OpenMS::IdentificationDataInternal::MONOISOTOPIC, FileTypes::MZML, 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, InputFile::primary_files, IdentificationData::registerAdduct(), IdentificationData::registerDBSearchParam(), IdentificationData::registerInputFile(), IdentificationData::registerParentSequence(), IdentificationData::registerProcessingSoftware(), IdentificationData::registerProcessingStep(), IdentificationData::registerScoreType(), OpenMS::IdentificationDataInternal::RNA, NucleicAcidSearchEngine::AnnotatedHit::sequence, IdentificationData::setCurrentProcessingStep(), RNaseDigestion::setEnzyme(), ProgressLogger::setLogType(), EnzymaticDigestion::setMissedCleavages(), MSSpectrum::setName(), FileHandler::setOptions(), DefaultParamHandler::setParameters(), ProgressLogger::setProgress(), MSSpectrum::setRT(), Param::setValue(), Software::setVersion(), MSExperiment::size(), MSExperiment::sortSpectra(), ProgressLogger::startProgress(), OMSFile::store(), MzTabFile::store(), FileHandler::storeExperiment(), FileHandler::storeIdentifications(), NASequence::toString(), and DBSearchParam::variable_mods.

parseAdduct_()

AdductInfo 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

References ScoredProcessingResult::addScore(), NucleicAcidSearchEngine::PrecursorInfo::adduct, ObservationMatch::adduct_opt, NucleicAcidSearchEngine::AnnotatedHit::annotations, NucleicAcidSearchEngine::PrecursorInfo::charge, IdentificationData::cleanup(), IdentificationData::getCurrentProcessingStep(), IdentificationData::getInputFiles(), SpectrumSettings::getNativeID(), SpectrumSettings::getPrecursors(), MSSpectrum::getRT(), IdentificationData::getScoreTypes(), NucleicAcidSearchEngine::PrecursorInfo::isotope, NucleicAcidSearchEngine::AnnotatedHit::oligo_ref, OPENMS_LOG_DEBUG, ObservationMatch::peak_annotations, NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm, OpenMS::Constants::UserParam::PRECURSOR_ERROR_PPM_USERPARAM, NucleicAcidSearchEngine::AnnotatedHit::precursor_ref, IdentificationData::registerIdentifiedOligo(), IdentificationData::registerObservation(), IdentificationData::registerObservationMatch(), IdentifiedSequence< SeqType >::sequence, NucleicAcidSearchEngine::AnnotatedHit::sequence, MetaInfoInterface::setMetaValue(), and NASequence::toString().

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().

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.

Implements TOPPBase.

References DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getAllNames(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getInstance(), RibonucleotideDB::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