RNPxlSearch Class Reference

Inheritance diagram for RNPxlSearch:

Classes
struct	AnnotatedHit
	Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More...
struct	FragmentAdductDefinition_
struct	MS2AdductsOfSinglePrecursorAdduct
class	RNPxlFragmentIonGenerator
struct	RNPxlParameterParsing

Public Member Functions
	RNPxlSearch ()
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
using	NucleotideToFeasibleFragmentAdducts = pair< char, vector< FragmentAdductDefinition_ > >

Protected Member Functions
void	registerOptionsAndFlags_ () override
	Sets the valid command line options (with argument) and flags (without argument). More...
void	preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge=false)
void	postScoreHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide, const TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts &all_feasible_adducts)
void	postProcessHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide)
	Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information. More...
void	mapPrecursorMassesToScans (const Int min_precursor_charge, const Int max_precursor_charge, const IntList &precursor_isotopes, const double small_peptide_mass_filter_threshold, const Size peptide_min_size, const PeakMap &spectra, multimap< double, pair< Size, int >> &multimap_mass_2_scan_index) const
void	initializeSpectrumGenerators (TheoreticalSpectrumGenerator &total_loss_spectrum_generator, TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, TheoreticalSpectrumGenerator &a_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &immonium_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &precursor_ion_sub_score_spectrum_generator) const
ExitCodes	main_ (int, const char **) override
	The actual "main" method. main_() is invoked by main(). More...
void	scoreTotalLossFragments_ (const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &a_ion_sub_score_spectrum, const PeakSpectrum &precursor_sub_score_spectrum, const PeakSpectrum &immonium_sub_score_spectrum, float &total_loss_score, float &tlss_MIC, float &tlss_err, float &tlss_Morph, float &immonium_sub_score, float &precursor_sub_score, float &a_ion_sub_score) const
void	scorePartialLossFragments_ (const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &partial_loss_spectrum_z1, const PeakSpectrum &partial_loss_spectrum_z2, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, float &plss_err, float &plss_Morph) const
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...
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...
ExitCodes	writeWSDL_ (const String &filename)
	Write WSDL file and validate it. Returns EXECUTION_OK or INTERNAL_ERROR (if validation failed) 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	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...

Static Protected Attributes
static constexpr const char *	ANNOTATIONS_MARKER_ION_PREFIX = "MI:"
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...

Private Attributes
bool	fast_scoring_ = true
bool	localization_ = false
set< char >	can_xl_

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...

Member Typedef Documentation

NucleotideToFeasibleFragmentAdducts

using NucleotideToFeasibleFragmentAdducts = pair<char, vector<FragmentAdductDefinition_> >

protected

Constructor & Destructor Documentation

RNPxlSearch()

RNPxlSearch ( )

inline

Member Function Documentation

initializeSpectrumGenerators()

void initializeSpectrumGenerators ( TheoreticalSpectrumGenerator &  total_loss_spectrum_generator, TheoreticalSpectrumGenerator &  partial_loss_spectrum_generator, TheoreticalSpectrumGenerator &  a_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &  immonium_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &  precursor_ion_sub_score_spectrum_generator  ) const

inlineprotected

References DefaultParamHandler::getParameters(), 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 RNPxlSearch::AnnotatedHit::a_ion_score, TextFile::addLine(), PeakFileOptions::addMSLevel(), RNPxlReport::annotate(), FalseDiscoveryRate::apply(), ModifiedPeptideGenerator::applyFixedModifications(), ModifiedPeptideGenerator::applyVariableModifications(), OpenMS::Constants::c, MSExperiment::clear(), PeakFileOptions::clearMSLevels(), RNPxlSearch::AnnotatedHit::cross_linked_nucleotide, PeptideIndexing::DATABASE_EMPTY, EnzymaticDigestion::digestUnmodified(), ProgressLogger::endProgress(), RNPxlSearch::AnnotatedHit::err, PeptideIndexing::EXECUTION_OK, AASequence::fromString(), MSSpectrum::getIntegerDataArrays(), AASequence::getMonoWeight(), MzMLFile::getOptions(), DefaultParamHandler::getParameters(), SpectrumSettings::getPrecursors(), TheoreticalSpectrumGenerator::getSpectrum(), MSSpectrum::getStringDataArrays(), FASTAFile::FASTAEntry::identifier, RNPxlSearch::AnnotatedHit::immonium_score, RNPxlModificationsGenerator::initModificationMassesRNA(), RNPxlSearch::AnnotatedHit::isotope_error, MzMLFile::load(), FASTAFile::load(), LOG_DEBUG, LOG_INFO, LOG_WARN, RNPxlSearch::AnnotatedHit::marker_ions_score, RNPxlSearch::AnnotatedHit::MIC, RNPxlModificationMassesResult::mod_combinations, RNPxlModificationMassesResult::mod_masses, RNPxlSearch::AnnotatedHit::Morph, RNPxlSearch::AnnotatedHit::partial_loss_score, PeptideIndexing::PEPTIDE_IDS_EMPTY, RNPxlSearch::AnnotatedHit::peptide_mod_index, RNPxlSearch::AnnotatedHit::pl_err, RNPxlSearch::AnnotatedHit::pl_MIC, RNPxlSearch::AnnotatedHit::pl_Morph, RNPxlSearch::AnnotatedHit::precursor_score, String::reverse(), RNPxlSearch::AnnotatedHit::rna_mod_index, PeptideIndexing::run(), RNPxlSearch::AnnotatedHit::score, FASTAFile::FASTAEntry::sequence, RNPxlSearch::AnnotatedHit::sequence, ProteaseDigestion::setEnzyme(), ProgressLogger::setLogType(), EnzymaticDigestion::setMissedCleavages(), DefaultParamHandler::setParameters(), ProgressLogger::setProgress(), Param::setValue(), MSExperiment::size(), MSSpectrum::sortByPosition(), MSExperiment::sortSpectra(), ProgressLogger::startProgress(), TextFile::store(), IdXMLFile::store(), RNPxlSearch::AnnotatedHit::total_MIC, and PeptideIndexing::UNEXPECTED_RESULT.

mapPrecursorMassesToScans()

void mapPrecursorMassesToScans ( const Int  min_precursor_charge, const Int  max_precursor_charge, const IntList &  precursor_isotopes, const double  small_peptide_mass_filter_threshold, const Size  peptide_min_size, const PeakMap &  spectra, multimap< double, pair< Size, int >> &  multimap_mass_2_scan_index  ) const

inlineprotected

References MSExperiment::begin(), OpenMS::Constants::C13C12_MASSDIFF_U, MSExperiment::end(), and OpenMS::Constants::PROTON_MASS_U.

postProcessHits_()

void postProcessHits_ ( const PeakMap &  exp, vector< vector< AnnotatedHit > > &  annotated_hits, vector< ProteinIdentification > &  protein_ids, vector< PeptideIdentification > &  peptide_ids, Size  top_hits, const RNPxlModificationMassesResult &  mm, const vector< ResidueModification > &  fixed_modifications, const vector< ResidueModification > &  variable_modifications, Size  max_variable_mods_per_peptide  )

inlineprotected

Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information.

References ModifiedPeptideGenerator::applyFixedModifications(), ModifiedPeptideGenerator::applyVariableModifications(), PeptideIdentification::assignRanks(), ProteinIdentification::SearchParameters::charges, ListUtils::concatenate(), ProteinIdentification::SearchParameters::db, ProteinIdentification::SearchParameters::digestion_enzyme, ProteinIdentification::SearchParameters::fixed_modifications, ProteinIdentification::SearchParameters::fragment_mass_tolerance, ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm, AASequence::fromString(), DigestionEnzymeDB< DigestionEnzymeType, InstanceType >::getEnzyme(), DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >::getInstance(), EmpiricalFormula::getMonoWeight(), PeptideHit::getScore(), VersionInfo::getVersion(), ProteinIdentification::SearchParameters::missed_cleavages, RNPxlModificationMassesResult::mod_combinations, DateTime::now(), OPENMS_POSTCONDITION, ProteinIdentification::SearchParameters::precursor_mass_tolerance, ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm, PeptideHit::setCharge(), PeptideIdentification::setHigherScoreBetter(), PeptideIdentification::setHits(), MetaInfoInterface::setMetaValue(), PeptideIdentification::setMZ(), PeptideHit::setPeakAnnotations(), PeptideIdentification::setRT(), PeptideHit::setScore(), PeptideIdentification::setScoreType(), PeptideHit::setSequence(), and ProteinIdentification::SearchParameters::variable_modifications.

postScoreHits_()

void postScoreHits_ ( const PeakMap &  exp, vector< vector< AnnotatedHit > > &  annotated_hits, Size  top_hits, const RNPxlModificationMassesResult &  mm, const vector< ResidueModification > &  fixed_modifications, const vector< ResidueModification > &  variable_modifications, Size  max_variable_mods_per_peptide, const TheoreticalSpectrumGenerator &  partial_loss_spectrum_generator, double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts &  all_feasible_adducts  )

inlineprotected

References RNPxlFragmentAnnotationHelper::addShiftedPeakFragmentAnnotation_(), PeptideHit::PeakAnnotation::annotation, ModifiedPeptideGenerator::applyFixedModifications(), ModifiedPeptideGenerator::applyVariableModifications(), OpenMS::Constants::c, PeptideHit::PeakAnnotation::charge, RNPxlSearch::AnnotatedHit::cross_linked_nucleotide, RNPxlFragmentAnnotationHelper::fragmentAnnotationDetailsToPHFA(), AASequence::fromString(), MSSpectrum::getIntegerDataArrays(), Peak1D::getIntensity(), EmpiricalFormula::getMonoWeight(), Peak1D::getMZ(), DefaultParamHandler::getParameters(), SpectrumSettings::getPrecursors(), AASequence::getPrefix(), TheoreticalSpectrumGenerator::getSpectrum(), SpectrumAlignment::getSpectrumAlignment(), MSSpectrum::getStringDataArrays(), AASequence::getSuffix(), String::hasPrefix(), PeptideHit::PeakAnnotation::intensity, OpenMS::Constants::k, LOG_DEBUG, RNPxlModificationMassesResult::mod_combinations, PeptideHit::PeakAnnotation::mz, String::number(), OPENMS_POSTCONDITION, DefaultParamHandler::setParameters(), Param::setValue(), RNPxlFragmentAnnotationHelper::shiftedIonsToString(), MSExperiment::size(), AASequence::size(), MSSpectrum::sortByPosition(), String::split(), String::substitute(), String::toInt(), AASequence::toString(), and AASequence::toUnmodifiedString().

preprocessSpectra_()

void preprocessSpectra_ ( PeakMap &  exp, double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, bool  single_charge_spectra, bool  annotate_charge = false  )

inlineprotected

References Deisotoper::deisotopeAndSingleCharge(), ThresholdMower::filterPeakMap(), Normalizer::filterPeakMap(), NLargest::filterPeakSpectrum(), WindowMower::filterPeakSpectrum(), DefaultParamHandler::getParameters(), DefaultParamHandler::setParameters(), Param::setValue(), MSExperiment::size(), 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(), ModificationsDB::getAllSearchModifications(), DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >::getInstance(), and ModificationsDB::getInstance().

scorePartialLossFragments_()

void scorePartialLossFragments_ ( const PeakSpectrum &  exp_spectrum, double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  partial_loss_spectrum_z1, const PeakSpectrum &  partial_loss_spectrum_z2, const PeakSpectrum &  marker_ions_sub_score_spectrum_z1, float &  partial_loss_sub_score, float &  marker_ions_sub_score, float &  plss_MIC, float &  plss_err, float &  plss_Morph  ) const

inlineprotected

References MorpheusScore::compute(), HyperScore::compute(), SpectrumSettings::getPrecursors(), and LOG_DEBUG.

scoreTotalLossFragments_()

void scoreTotalLossFragments_ ( const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  total_loss_spectrum, double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  a_ion_sub_score_spectrum, const PeakSpectrum &  precursor_sub_score_spectrum, const PeakSpectrum &  immonium_sub_score_spectrum, float &  total_loss_score, float &  tlss_MIC, float &  tlss_err, float &  tlss_Morph, float &  immonium_sub_score, float &  precursor_sub_score, float &  a_ion_sub_score  ) const

inlineprotected

References MorpheusScore::compute(), and HyperScore::compute().

Member Data Documentation

ANNOTATIONS_MARKER_ION_PREFIX

constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"

staticprotected

can_xl_

set<char> can_xl_

private

fast_scoring_

bool fast_scoring_ = true

private

localization_

bool localization_ = false

private