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TOPPMetaProSIP Class Reference
Inheritance diagram for TOPPMetaProSIP:
TOPPBase

Public Member Functions

 TOPPMetaProSIP ()
 

Protected Member Functions

void registerOptionsAndFlags_ ()
 
void filterIsotopicIntensities (vector< double >::const_iterator &pattern_begin, vector< double >::const_iterator &pattern_end, vector< double >::const_iterator &intensities_begin, vector< double >::const_iterator &intensities_end, double TIC_threshold=0.99)
 > filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation More...
 
void calculateCorrelation (Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, String labeling_element, double mass, double min_correlation_distance_to_averagine)
 Returns highest scoring rate and score pair in the map. More...
 
void getBestRateScorePair (const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score)
 
PeakSpectrum extractPeakSpectrum (Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const MSExperiment<> &peak_map)
 
vector< double > extractIsotopicIntensities (Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const MSExperiment< Peak1D > &peak_map)
 
void writePeakIntensities_ (SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks)
 
MapRateToScoreType normalizeToMax (const MapRateToScoreType &map_rate_to_decomposition_weight)
 
vector< double > findApexRT (const FeatureMap::iterator feature_it, double hit_rt, const MSExperiment< Peak1D > &peak_map, Size n_scans)
 
PeakSpectrum mergeSpectra (const MSExperiment<> &to_merge)
 
PeakSpectrum isotopicIntensitiesToSpectrum (double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities)
 > converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size More...
 
void extractIncorporationsAtCorrelationMaxima (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_decomposition_weight=10.0)
 
void extractIncorporationsAtHeighestDecompositionWeights (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_low_RIA_threshold=-1, double min_decomposition_weight=10.0)
 > Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window. More...
 
double calculateGlobalLR (const vector< double > &isotopic_intensities)
 > calculate the global labeling ration based on all but the first 4 peaks More...
 
ExitCodes main_ (int, const char **)
 

Protected Attributes

Size ADDITIONAL_ISOTOPES
 
std::string FEATURE_STRING
 
std::string UNASSIGNED_ID_STRING
 
std::string UNIDENTIFIED_STRING
 

Constructor & Destructor Documentation

◆ TOPPMetaProSIP()

TOPPMetaProSIP ( )
inline

Member Function Documentation

◆ calculateCorrelation()

void calculateCorrelation ( Size  n_element,
const vector< double > &  isotopic_intensities,
IsotopePatterns  patterns,
MapRateToScoreType map_rate_to_correlation_score,
String  labeling_element,
double  mass,
double  min_correlation_distance_to_averagine 
)
inlineprotected

Returns highest scoring rate and score pair in the map.

◆ calculateGlobalLR()

double calculateGlobalLR ( const vector< double > &  isotopic_intensities)
inlineprotected

> calculate the global labeling ration based on all but the first 4 peaks

◆ extractIncorporationsAtCorrelationMaxima()

void extractIncorporationsAtCorrelationMaxima ( SIPPeptide sip_peptide,
const IsotopePatterns patterns,
double  weight_merge_window = 5.0,
double  min_corr_threshold = 0.5,
double  min_decomposition_weight = 10.0 
)
inlineprotected

◆ extractIncorporationsAtHeighestDecompositionWeights()

void extractIncorporationsAtHeighestDecompositionWeights ( SIPPeptide sip_peptide,
const IsotopePatterns patterns,
double  weight_merge_window = 5.0,
double  min_corr_threshold = 0.5,
double  min_low_RIA_threshold = -1,
double  min_decomposition_weight = 10.0 
)
inlineprotected

◆ extractIsotopicIntensities()

vector<double> extractIsotopicIntensities ( Size  element_count,
double  mass_diff,
double  mz_tolerance_ppm,
double  seed_rt,
double  seed_mz,
double  seed_charge,
const MSExperiment< Peak1D > &  peak_map 
)
inlineprotected

◆ extractPeakSpectrum()

PeakSpectrum extractPeakSpectrum ( Size  element_count,
double  mass_diff,
double  rt,
double  feature_hit_theoretical_mz,
Int  feature_hit_charge,
const MSExperiment<> &  peak_map 
)
inlineprotected

◆ filterIsotopicIntensities()

void filterIsotopicIntensities ( vector< double >::const_iterator &  pattern_begin,
vector< double >::const_iterator &  pattern_end,
vector< double >::const_iterator &  intensities_begin,
vector< double >::const_iterator &  intensities_end,
double  TIC_threshold = 0.99 
)
inlineprotected

> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation

Calculates the correlation between measured isotopic_intensities and the theoretical isotopic patterns for all incorporation rates

◆ findApexRT()

vector<double> findApexRT ( const FeatureMap::iterator  feature_it,
double  hit_rt,
const MSExperiment< Peak1D > &  peak_map,
Size  n_scans 
)
inlineprotected

◆ getBestRateScorePair()

void getBestRateScorePair ( const MapRateToScoreType map_rate_to_score,
double &  best_rate,
double &  best_score 
)
inlineprotected

◆ isotopicIntensitiesToSpectrum()

PeakSpectrum isotopicIntensitiesToSpectrum ( double  mz_start,
double  mass_diff,
Int  charge,
vector< double >  isotopic_intensities 
)
inlineprotected

> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size

◆ main_()

ExitCodes main_ ( int  ,
const char **   
)
inlineprotected

< number of PSMs. If 0 IDMapper has not been called.

References SIPPeptide::accessions, SIPPeptide::accumulated, MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), SIPPeptide::charge, RIntegration::checkRDependencies(), MetaProSIPClustering::clusterSIPPeptides(), SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), MetaProSIPReporting::createQualityReport(), SIPPeptide::decomposition_map, MetaProSIPXICExtraction::extractXICsOfIsotopeTraces(), SIPPeptide::feature_mz, SIPPeptide::feature_rt, SIPPeptide::feature_type, MetaProSIPInterpolation::getHighPoints(), MetaProSIPDecomposition::getNumberOfLabelingElements(), MetaProSIPClustering::getRIAClusterCenter(), SIPPeptide::global_LR, SIPPeptide::incorporations, SIPPeptide::mass_diff, SIPPeptide::mass_theo, SIPPeptide::mz_theo, SIPPeptide::patterns, SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, SIPPeptide::score, SIPPeptide::sequence, and SIPPeptide::unique.

◆ mergeSpectra()

PeakSpectrum mergeSpectra ( const MSExperiment<> &  to_merge)
inlineprotected

◆ normalizeToMax()

MapRateToScoreType normalizeToMax ( const MapRateToScoreType map_rate_to_decomposition_weight)
inlineprotected

◆ registerOptionsAndFlags_()

void registerOptionsAndFlags_ ( )
inlineprotected

◆ writePeakIntensities_()

void writePeakIntensities_ ( SVOutStream &  out_stream,
vector< double >  isotopic_intensities,
bool  write_13Cpeaks 
)
inlineprotected

Member Data Documentation

◆ ADDITIONAL_ISOTOPES

Size ADDITIONAL_ISOTOPES
protected

◆ FEATURE_STRING

std::string FEATURE_STRING
protected

◆ UNASSIGNED_ID_STRING

std::string UNASSIGNED_ID_STRING
protected

◆ UNIDENTIFIED_STRING

std::string UNIDENTIFIED_STRING
protected

OpenMS / TOPP release 2.1.0 Documentation generated on Sun Jun 11 2017 18:22:14 using doxygen 1.8.13