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NucleicAcidSearchEngine Class Reference
Inheritance diagram for NucleicAcidSearchEngine:
[legend]
Collaboration diagram for NucleicAcidSearchEngine:
[legend]

Classes

struct  PrecursorInfo
struct  AnnotatedHit
class  HasInvalidLength

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*

Class Documentation

◆ NucleicAcidSearchEngine::AnnotatedHit

struct NucleicAcidSearchEngine::AnnotatedHit
Collaboration diagram for NucleicAcidSearchEngine::AnnotatedHit:
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Class Members
vector< PeakAnnotation > annotations
IdentifiedOligoRef oligo_ref
double precursor_error_ppm
const PrecursorInfo * precursor_ref
NASequence sequence

Member Typedef Documentation

◆ ConstRibonucleotidePtr

using ConstRibonucleotidePtr = const Ribonucleotide*
private

◆ HitsByScore

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

Constructor & Destructor Documentation

◆ NucleicAcidSearchEngine()

NucleicAcidSearchEngine ( )
inline

References fragment_ion_codes_.

Member Function Documentation

◆ calculateAndFilterFDR_()

void calculateAndFilterFDR_ ( IdentificationData & id_data,
bool only_top_hits )
inlineprotected

Referenced by main_().

◆ calculatePrecursorMass_()

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

Referenced by main_().

◆ 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 )
inlineprotected

Referenced by preprocessSpectra_().

◆ generateLFQInput_()

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

Referenced by main_().

◆ getModifications_()

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

References ambiguous_mods_, and resolve_ambiguous_mods_.

Referenced by main_().

◆ main_()

ExitCodes main_ ( int ,
const char **  )
inlineoverrideprotected

References NucleicAcidSearchEngine::AnnotatedHit::annotations, calculateAndFilterFDR_(), calculatePrecursorMass_(), fragment_ion_codes_, generateLFQInput_(), getModifications_(), NucleicAcidSearchEngine::AnnotatedHit::oligo_ref, parseAdduct_(), postProcessHits_(), NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm, NucleicAcidSearchEngine::AnnotatedHit::precursor_ref, preprocessSpectra_(), resolve_ambiguous_mods_, and NucleicAcidSearchEngine::AnnotatedHit::sequence.

◆ parseAdduct_()

AdductInfo parseAdduct_ ( const String & adduct)
inlineprotected

Referenced by main_().

◆ postProcessHits_()

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

References NucleicAcidSearchEngine::PrecursorInfo::adduct, NucleicAcidSearchEngine::AnnotatedHit::annotations, NucleicAcidSearchEngine::PrecursorInfo::charge, NucleicAcidSearchEngine::PrecursorInfo::isotope, NucleicAcidSearchEngine::AnnotatedHit::oligo_ref, NucleicAcidSearchEngine::AnnotatedHit::precursor_error_ppm, NucleicAcidSearchEngine::AnnotatedHit::precursor_ref, resolve_ambiguous_mods_, resolveAmbiguousMods_(), and NucleicAcidSearchEngine::AnnotatedHit::sequence.

Referenced by main_().

◆ 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 )
inlineprotected

References deisotopeAndSingleChargeMSSpectrum_().

Referenced by main_().

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )
inlineoverrideprotected

References fragment_ion_codes_.

◆ resolveAmbiguousMods_()

void resolveAmbiguousMods_ ( HitsByScore & hits)
inlineprotected

References ambiguous_mods_.

Referenced by postProcessHits_().

Member Data Documentation

◆ ambiguous_mods_

map<String, String> ambiguous_mods_
protected

Referenced by getModifications_(), and resolveAmbiguousMods_().

◆ fragment_ion_codes_

vector<String> fragment_ion_codes_
protected

Referenced by main_(), NucleicAcidSearchEngine(), and registerOptionsAndFlags_().

◆ resolve_ambiguous_mods_

bool resolve_ambiguous_mods_
protected

Referenced by getModifications_(), main_(), and postProcessHits_().