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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_
 

Public Member Functions

 RNPxlSearch ()
 

Protected Types

typedef map< String, set< FragmentAdductDefinition_ > > PrecursorToFragmentAdductMapType
 

Protected Member Functions

void registerOptionsAndFlags_ ()
 
vector< ResidueModification > getModifications_ (StringList modNames)
 Query ResidueModifications (given as strings) from ModificationsDB. More...
 
void preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge=false)
 
vector< FragmentAdductDefinition_getFeasibleFragmentAdducts_ (const String &exp_pc_adduct, const String &exp_pc_formula, const PrecursorToFragmentAdductMapType &precursor_to_fragment_adducts)
 
map< String, vector< FragmentAdductDefinition_ > > getAllFeasibleFragmentAdducts_ (const RNPxlModificationMassesResult &precursor_adducts, const PrecursorToFragmentAdductMapType &precursor_to_fragment_adducts)
 
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, TheoreticalSpectrumGenerator spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const map< String, vector< FragmentAdductDefinition_ > > &all_feasible_fragment_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 normalizeAdductName_ (String &name)
 
map< String, set< FragmentAdductDefinition_ > > getPrecursorToFragmentAdducts_ (StringList fragment_adducts)
 
ExitCodes main_ (int, const char **)
 

Member Typedef Documentation

◆ PrecursorToFragmentAdductMapType

typedef map<String, set<FragmentAdductDefinition_> > PrecursorToFragmentAdductMapType
protected

Constructor & Destructor Documentation

◆ RNPxlSearch()

RNPxlSearch ( )
inline

Member Function Documentation

◆ getAllFeasibleFragmentAdducts_()

map<String, vector<FragmentAdductDefinition_> > getAllFeasibleFragmentAdducts_ ( const RNPxlModificationMassesResult &  precursor_adducts,
const PrecursorToFragmentAdductMapType precursor_to_fragment_adducts 
)
inlineprotected

◆ getFeasibleFragmentAdducts_()

vector<FragmentAdductDefinition_> getFeasibleFragmentAdducts_ ( const String &  exp_pc_adduct,
const String &  exp_pc_formula,
const PrecursorToFragmentAdductMapType precursor_to_fragment_adducts 
)
inlineprotected

◆ getModifications_()

vector<ResidueModification> getModifications_ ( StringList  modNames)
inlineprotected

Query ResidueModifications (given as strings) from ModificationsDB.

◆ getPrecursorToFragmentAdducts_()

map<String, set<FragmentAdductDefinition_> > getPrecursorToFragmentAdducts_ ( StringList  fragment_adducts)
inlineprotected

◆ main_()

ExitCodes main_ ( int  ,
const char **   
)
inlineprotected

◆ normalizeAdductName_()

void normalizeAdductName_ ( String &  name)
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,
TheoreticalSpectrumGenerator  spectrum_generator,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const map< String, vector< FragmentAdductDefinition_ > > &  all_feasible_fragment_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_ ( )
inlineprotected

OpenMS / TOPP release 2.1.0 Documentation generated on Sat Apr 8 2017 21:05:40 using doxygen 1.8.13