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

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< ConstRibonucleotidePtrgetModifications_ (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()

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_()

◆ parseAdduct_()

AdductInfo parseAdduct_ ( const String &  adduct)
inlineprotected

Referenced by main_().

◆ postProcessHits_()

◆ 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

◆ fragment_ion_codes_

vector<String> fragment_ion_codes_
protected

Referenced by main_(), and registerOptionsAndFlags_().

◆ resolve_ambiguous_mods_

bool resolve_ambiguous_mods_
protected