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OpenMS
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Classes | |
struct | AnnotatedHit |
class | HasInvalidLength |
struct | PrecursorInfo |
Public Member Functions | |
NucleicAcidSearchEngine () | |
Protected Types | |
typedef multimap< double, AnnotatedHit, greater< double > > | HitsByScore |
Protected Member Functions | |
void | registerOptionsAndFlags_ () override |
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 |
Protected Attributes | |
vector< String > | fragment_ion_codes_ |
map< String, String > | ambiguous_mods_ |
bool | resolve_ambiguous_mods_ |
Private Types | |
using | ConstRibonucleotidePtr = const Ribonucleotide* |
struct NucleicAcidSearchEngine::AnnotatedHit |
Class Members | ||
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vector< PeakAnnotation > | annotations | |
IdentifiedOligoRef | oligo_ref | |
double | precursor_error_ppm | |
const PrecursorInfo * | precursor_ref | |
NASequence | sequence |
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private |
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protected |
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inline |
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inlineprotected |
Referenced by main_().
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inlineprotected |
Referenced by main_().
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inlineprotected |
Referenced by preprocessSpectra_().
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inlineprotected |
Referenced by main_().
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inlineprotected |
References ambiguous_mods_, and resolve_ambiguous_mods_.
Referenced by main_().
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inlineoverrideprotected |
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inlineprotected |
Referenced by main_().
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inlineprotected |
References resolve_ambiguous_mods_, resolveAmbiguousMods_(), and NucleicAcidSearchEngine::AnnotatedHit::sequence.
Referenced by main_().
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inlineprotected |
References deisotopeAndSingleChargeMSSpectrum_().
Referenced by main_().
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inlineoverrideprotected |
References fragment_ion_codes_.
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inlineprotected |
References ambiguous_mods_.
Referenced by postProcessHits_().
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Referenced by getModifications_(), and resolveAmbiguousMods_().
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Referenced by main_(), and registerOptionsAndFlags_().
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Referenced by getModifications_(), main_(), and postProcessHits_().