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