OpenMS  2.4.0
Classes | Public Member Functions | Protected Types | Protected Member Functions | Static Protected Attributes | Private Attributes | List of all members
RNPxlSearch Class Reference
Inheritance diagram for RNPxlSearch:
TOPPBase

Classes

struct  AnnotatedHit
 Slimmer structure as storing all scored candidates in PeptideHit objects takes too much space. More...
 
struct  FragmentAdductDefinition_
 
struct  MS2AdductsOfSinglePrecursorAdduct
 
class  RNPxlFragmentIonGenerator
 
struct  RNPxlParameterParsing
 

Public Member Functions

 RNPxlSearch ()
 

Protected Types

using NucleotideToFeasibleFragmentAdducts = pair< char, vector< FragmentAdductDefinition_ > >
 

Protected Member Functions

void registerOptionsAndFlags_ () override
 
void preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge=false)
 
void postScoreHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide, const TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts &all_feasible_adducts)
 
void postProcessHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide)
 Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information. More...
 
void mapPrecursorMassesToScans (const Int min_precursor_charge, const Int max_precursor_charge, const IntList &precursor_isotopes, const double small_peptide_mass_filter_threshold, const Size peptide_min_size, const PeakMap &spectra, multimap< double, pair< Size, int >> &multimap_mass_2_scan_index) const
 
void initializeSpectrumGenerators (TheoreticalSpectrumGenerator &total_loss_spectrum_generator, TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, TheoreticalSpectrumGenerator &a_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &immonium_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &precursor_ion_sub_score_spectrum_generator) const
 
ExitCodes main_ (int, const char **) override
 
void scoreTotalLossFragments_ (const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &a_ion_sub_score_spectrum, const PeakSpectrum &precursor_sub_score_spectrum, const PeakSpectrum &immonium_sub_score_spectrum, float &total_loss_score, float &tlss_MIC, float &tlss_err, float &tlss_Morph, float &immonium_sub_score, float &precursor_sub_score, float &a_ion_sub_score) const
 
void scorePartialLossFragments_ (const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &partial_loss_spectrum_z1, const PeakSpectrum &partial_loss_spectrum_z2, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, float &plss_err, float &plss_Morph) const
 

Static Protected Attributes

static constexpr const char * ANNOTATIONS_MARKER_ION_PREFIX = "MI:"
 

Private Attributes

bool fast_scoring_ = true
 
bool localization_ = false
 
set< char > can_xl_
 

Member Typedef Documentation

◆ NucleotideToFeasibleFragmentAdducts

using NucleotideToFeasibleFragmentAdducts = pair<char, vector<FragmentAdductDefinition_> >
protected

Constructor & Destructor Documentation

◆ RNPxlSearch()

RNPxlSearch ( )
inline

Member Function Documentation

◆ initializeSpectrumGenerators()

void initializeSpectrumGenerators ( TheoreticalSpectrumGenerator &  total_loss_spectrum_generator,
TheoreticalSpectrumGenerator &  partial_loss_spectrum_generator,
TheoreticalSpectrumGenerator &  a_ion_sub_score_spectrum_generator,
TheoreticalSpectrumGenerator &  immonium_ion_sub_score_spectrum_generator,
TheoreticalSpectrumGenerator &  precursor_ion_sub_score_spectrum_generator 
) const
inlineprotected

◆ main_()

ExitCodes main_ ( int  ,
const char **   
)
inlineoverrideprotected

◆ mapPrecursorMassesToScans()

void mapPrecursorMassesToScans ( const Int  min_precursor_charge,
const Int  max_precursor_charge,
const IntList &  precursor_isotopes,
const double  small_peptide_mass_filter_threshold,
const Size  peptide_min_size,
const PeakMap &  spectra,
multimap< double, pair< Size, int >> &  multimap_mass_2_scan_index 
) const
inlineprotected

◆ postProcessHits_()

void postProcessHits_ ( const PeakMap &  exp,
vector< vector< AnnotatedHit > > &  annotated_hits,
vector< ProteinIdentification > &  protein_ids,
vector< PeptideIdentification > &  peptide_ids,
Size  top_hits,
const RNPxlModificationMassesResult &  mm,
const vector< ResidueModification > &  fixed_modifications,
const vector< ResidueModification > &  variable_modifications,
Size  max_variable_mods_per_peptide 
)
inlineprotected

Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information.

◆ postScoreHits_()

void postScoreHits_ ( const PeakMap &  exp,
vector< vector< AnnotatedHit > > &  annotated_hits,
Size  top_hits,
const RNPxlModificationMassesResult &  mm,
const vector< ResidueModification > &  fixed_modifications,
const vector< ResidueModification > &  variable_modifications,
Size  max_variable_mods_per_peptide,
const TheoreticalSpectrumGenerator &  partial_loss_spectrum_generator,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const RNPxlParameterParsing::PrecursorsToMS2Adducts all_feasible_adducts 
)
inlineprotected

◆ preprocessSpectra_()

void preprocessSpectra_ ( PeakMap &  exp,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
bool  single_charge_spectra,
bool  annotate_charge = false 
)
inlineprotected

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )
inlineoverrideprotected

◆ scorePartialLossFragments_()

void scorePartialLossFragments_ ( const PeakSpectrum &  exp_spectrum,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const PeakSpectrum &  partial_loss_spectrum_z1,
const PeakSpectrum &  partial_loss_spectrum_z2,
const PeakSpectrum &  marker_ions_sub_score_spectrum_z1,
float &  partial_loss_sub_score,
float &  marker_ions_sub_score,
float &  plss_MIC,
float &  plss_err,
float &  plss_Morph 
) const
inlineprotected

◆ scoreTotalLossFragments_()

void scoreTotalLossFragments_ ( const PeakSpectrum &  exp_spectrum,
const PeakSpectrum &  total_loss_spectrum,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const PeakSpectrum &  a_ion_sub_score_spectrum,
const PeakSpectrum &  precursor_sub_score_spectrum,
const PeakSpectrum &  immonium_sub_score_spectrum,
float &  total_loss_score,
float &  tlss_MIC,
float &  tlss_err,
float &  tlss_Morph,
float &  immonium_sub_score,
float &  precursor_sub_score,
float &  a_ion_sub_score 
) const
inlineprotected

Member Data Documentation

◆ ANNOTATIONS_MARKER_ION_PREFIX

constexpr const char* ANNOTATIONS_MARKER_ION_PREFIX = "MI:"
staticprotected

◆ can_xl_

set<char> can_xl_
private

◆ fast_scoring_

bool fast_scoring_ = true
private

◆ localization_

bool localization_ = false
private