const char * tool_name

void processDriftTimeStack(const std::vector< MSSpectrum > &stack, std::vector< MSSpectrum > &result)

NASequence sequence

PeakMap MapType

map< double, double > MapRateToScoreType

void collapseIMSpectrum(const MSExperiment &exp, std::vector< MSSpectrum > &result)

Size scan_index

pair< double, vector< double > > IsotopePattern

PrecursorInfo(Size scan_index, Int charge, Size isotope, const String &adduct)

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)

@ IM_MULTIPLE_SPECTRA

IMType determineIMType(const MSExperiment &exp)

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)

IdentificationData::IdentifiedOligoRef oligo_ref

Int charge

IMType

TOPPGNPSExport()

#define SEP

Size max_size_

void registerOptionsAndFlags_() override

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

const Ribonucleotide * ConstRibonucleotidePtr

You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > DCMAKE_PREFIX_PATH

@ IM_NONE

void print_usage(Logger::LogStream &stream=OpenMS_Log_info)

String extractCachedMetaFilename(const String &in)

double precursor_error_ppm

void print_usage()

void calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)

ExitCodes main_(int, const char **) override

HasInvalidLength(Size min_size, Size max_size)

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

String adduct

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

You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > this flag can be used to disable those parts of the documentation and the tests that need an X Server(Default:On)</td ></tr >< tr >< td valign

vector< String > fragment_ion_codes_

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

You can set more CMake variables adding< code > DVARIABLE

map< String, String > ambiguous_mods_

int main(int argc, const char **argv)

vector< IsotopePattern > IsotopePatterns

const char * tool_name

Size min_size_

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

vector< PeptideHit::PeakAnnotation > annotations

int main(int argc, const char **argv)

int main(int argc, const char **argv)

int main(int argc, const char **argv)

int main(int argc, const char **argv)

EmpiricalFormula parseAdduct_(const String &adduct)

const PrecursorInfo * precursor_ref

void print_usage(Logger::LogStream &stream=OpenMS_Log_info)

bool operator()(const NASequence &s)

const char * tool_name

ExitCodes main_(int, const char **) override

Size isotope

int main(int argc, const char **argv)

void resolveAmbiguousMods_(HitsByScore &hits)

@ IM_STACKED

void expandIMSpectrum(const MSSpectrum &tmps, std::vector< MSSpectrum > &result)

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

void registerOptionsAndFlags_()

bool resolve_ambiguous_mods_

NucleicAcidSearchEngine()