OpenMS  2.6.0
AccurateMassSearch.cpp File Reference
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/MzTab.h>
#include <OpenMS/FORMAT/MzTabFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>
Include dependency graph for AccurateMassSearch.cpp:
tool_name
const char * tool_name
Definition: TOPPView.cpp:78
OpenMS::processDriftTimeStack
void processDriftTimeStack(const std::vector< MSSpectrum > &stack, std::vector< MSSpectrum > &result)
Process a stack of drift time spectra.
Definition: FileConverter.cpp:178
NucleicAcidSearchEngine::AnnotatedHit::sequence
NASequence sequence
Definition: NucleicAcidSearchEngine.cpp:274
NucleicAcidSearchEngine::PrecursorInfo
Definition: NucleicAcidSearchEngine.cpp:256
MapType
PeakMap MapType
Definition: PeakPickerIterative.cpp:84
MapRateToScoreType
map< double, double > MapRateToScoreType
Definition: MetaProSIP.cpp:84
OpenMS::collapseIMSpectrum
void collapseIMSpectrum(const MSExperiment &exp, std::vector< MSSpectrum > &result)
Collapses multiple IM spectra from the same frame into a single MSSpectrum.
Definition: FileConverter.cpp:283
NucleicAcidSearchEngine::PrecursorInfo::scan_index
Size scan_index
Definition: NucleicAcidSearchEngine.cpp:257
IsotopePattern
pair< double, vector< double > > IsotopePattern
Definition: MetaProSIP.cpp:85
NucleicAcidSearchEngine::PrecursorInfo::PrecursorInfo
PrecursorInfo(Size scan_index, Int charge, Size isotope, const String &adduct)
Definition: NucleicAcidSearchEngine.cpp:262
NucleicAcidSearchEngine::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)
Definition: NucleicAcidSearchEngine.cpp:531
OpenMS::IM_MULTIPLE_SPECTRA
@ IM_MULTIPLE_SPECTRA
ion mobility is recorded as multiple spectra per frame
Definition: FileConverter.cpp:157
OpenMS::determineIMType
IMType determineIMType(const MSExperiment &exp)
Definition: FileConverter.cpp:160
NucleicAcidSearchEngine::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)
Definition: NucleicAcidSearchEngine.cpp:375
NucleicAcidSearchEngine::AnnotatedHit::oligo_ref
IdentificationData::IdentifiedOligoRef oligo_ref
Definition: NucleicAcidSearchEngine.cpp:273
NucleicAcidSearchEngine::PrecursorInfo::charge
Int charge
Definition: NucleicAcidSearchEngine.cpp:258
OpenMS::IMType
IMType
Definition: FileConverter.cpp:154
TOPPGNPSExport::TOPPGNPSExport
TOPPGNPSExport()
Definition: GNPSExport.cpp:82
SEP
#define SEP
Definition: DigestorMotif.cpp:49
NucleicAcidSearchEngine::HasInvalidLength::max_size_
Size max_size_
Definition: NucleicAcidSearchEngine.cpp:328
TOPPGNPSExport::registerOptionsAndFlags_
void registerOptionsAndFlags_() override
Definition: GNPSExport.cpp:93
NucleicAcidSearchEngine::getModifications_
set< ConstRibonucleotidePtr > getModifications_(const set< String > &mod_names)
Definition: NucleicAcidSearchEngine.cpp:283
NucleicAcidSearchEngine::ConstRibonucleotidePtr
const Ribonucleotide * ConstRibonucleotidePtr
Definition: NucleicAcidSearchEngine.cpp:143
DCMAKE_PREFIX_PATH
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
Definition: common-cmake-parameters.doxygen:19
OpenMS::IM_NONE
@ IM_NONE
no ion mobility
Definition: FileConverter.cpp:155
print_usage
void print_usage(Logger::LogStream &stream=OpenMS_Log_info)
Definition: SwathWizard.cpp:99
extractCachedMetaFilename
String extractCachedMetaFilename(const String &in)
Definition: FileConverter.cpp:136
NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm
double precursor_error_ppm
Definition: NucleicAcidSearchEngine.cpp:275
FeatureLinkerBase.cpp
TOPPGNPSExport
Definition: GNPSExport.cpp:80
print_usage
void print_usage()
Definition: TOPPView.cpp:84
NucleicAcidSearchEngine::calculateAndFilterFDR_
void calculateAndFilterFDR_(IdentificationData &id_data, bool only_top_hits)
Definition: NucleicAcidSearchEngine.cpp:841
TOPPGNPSExport::main_
ExitCodes main_(int, const char **) override
Definition: GNPSExport.cpp:115
OpenMS
Definition: INIFileEditorWindow.cpp:53
NucleicAcidSearchEngine::HasInvalidLength::HasInvalidLength
HasInvalidLength(Size min_size, Size max_size)
Definition: NucleicAcidSearchEngine.cpp:330
TOPPBase
NucleicAcidSearchEngine::postProcessHits_
void postProcessHits_(const PeakMap &exp, vector< HitsByScore > &annotated_hits, IdentificationData &id_data, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:738
NucleicAcidSearchEngine::PrecursorInfo::adduct
String adduct
Definition: NucleicAcidSearchEngine.cpp:260
NucleicAcidSearchEngine::calculatePrecursorMass_
double calculatePrecursorMass_(double mz, Int charge, Int isotope, double adduct_mass, bool negative_mode)
Definition: NucleicAcidSearchEngine.cpp:656
Server
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
NucleicAcidSearchEngine::fragment_ion_codes_
vector< String > fragment_ion_codes_
Definition: NucleicAcidSearchEngine.cpp:154
NucleicAcidSearchEngine::generateLFQInput_
void generateLFQInput_(IdentificationData &id_data, const String &out_file)
Definition: NucleicAcidSearchEngine.cpp:869
DVARIABLE
You can set more CMake variables adding< code > DVARIABLE
Definition: common-cmake-parameters.doxygen:1
NucleicAcidSearchEngine::ambiguous_mods_
map< String, String > ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:155
main
int main(int argc, const char **argv)
Definition: SwathWizard.cpp:114
IsotopePatterns
vector< IsotopePattern > IsotopePatterns
Definition: MetaProSIP.cpp:86
tool_name
const char * tool_name
Definition: TOPPAS.cpp:94
NucleicAcidSearchEngine::AnnotatedHit
Definition: NucleicAcidSearchEngine.cpp:272
NucleicAcidSearchEngine::HasInvalidLength::min_size_
Size min_size_
Definition: NucleicAcidSearchEngine.cpp:327
NucleicAcidSearchEngine::registerIDMetaData_
void registerIDMetaData_(IdentificationData &id_data, const String &in_mzml, const vector< String > &primary_files, const IdentificationData::DBSearchParam &search_param)
Definition: NucleicAcidSearchEngine.cpp:807
NucleicAcidSearchEngine::AnnotatedHit::annotations
vector< PeptideHit::PeakAnnotation > annotations
Definition: NucleicAcidSearchEngine.cpp:276
main
int main(int argc, const char **argv)
Definition: GNPSExport.cpp:378
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
main
int main(int argc, const char **argv)
Definition: NucleicAcidSearchEngine.cpp:1378
main
int main(int argc, const char **argv)
Definition: TOPPAS.cpp:115
NucleicAcidSearchEngine::parseAdduct_
EmpiricalFormula parseAdduct_(const String &adduct)
Definition: NucleicAcidSearchEngine.cpp:338
NucleicAcidSearchEngine::AnnotatedHit::precursor_ref
const PrecursorInfo * precursor_ref
Definition: NucleicAcidSearchEngine.cpp:277
print_usage
void print_usage(Logger::LogStream &stream=OpenMS_Log_info)
Definition: TOPPAS.cpp:100
NucleicAcidSearchEngine::HasInvalidLength::operator()
bool operator()(const NASequence &s)
Definition: NucleicAcidSearchEngine.cpp:334
tool_name
const char * tool_name
Definition: SwathWizard.cpp:93
NucleicAcidSearchEngine::main_
ExitCodes main_(int, const char **) override
Definition: NucleicAcidSearchEngine.cpp:922
NucleicAcidSearchEngine::PrecursorInfo::isotope
Size isotope
Definition: NucleicAcidSearchEngine.cpp:259
main
int main(int argc, const char **argv)
Definition: TOPPView.cpp:108
NucleicAcidSearchEngine::resolveAmbiguousMods_
void resolveAmbiguousMods_(HitsByScore &hits)
Definition: NucleicAcidSearchEngine.cpp:677
OpenMS::IM_STACKED
@ IM_STACKED
ion mobility frame is stacked in a single spectrum
Definition: FileConverter.cpp:156
OpenMS::expandIMSpectrum
void expandIMSpectrum(const MSSpectrum &tmps, std::vector< MSSpectrum > &result)
Expands a single MSSpectrum (single frame) into individual ion mobility spectrum.
Definition: FileConverter.cpp:226
NucleicAcidSearchEngine::HitsByScore
multimap< double, AnnotatedHit, greater< double > > HitsByScore
Definition: NucleicAcidSearchEngine.cpp:280
NucleicAcidSearchEngine::HasInvalidLength
Definition: NucleicAcidSearchEngine.cpp:326
NucleicAcidSearchEngine::registerOptionsAndFlags_
void registerOptionsAndFlags_()
Definition: NucleicAcidSearchEngine.cpp:159
NucleicAcidSearchEngine::resolve_ambiguous_mods_
bool resolve_ambiguous_mods_
Definition: NucleicAcidSearchEngine.cpp:156
NucleicAcidSearchEngine
Definition: NucleicAcidSearchEngine.cpp:142
NucleicAcidSearchEngine::NucleicAcidSearchEngine
NucleicAcidSearchEngine()
Definition: NucleicAcidSearchEngine.cpp:146