35 #ifndef OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H 36 #define OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H 121 n_samples(0), quant_proteins(0), too_few_peptides(0),
122 quant_peptides(0), total_peptides(0), quant_features(0),
123 total_features(0), blank_features(0), ambig_features(0) {}
151 void quantifyPeptides(std::vector<ProteinIdentification>& proteins,
152 std::vector<PeptideIdentification>& peptides);
166 const PeptideQuant & getPeptideResults();
169 const ProteinQuant & getProteinResults();
189 PeptideHit getAnnotation_(std::vector<PeptideIdentification> & peptides);
203 template <
typename T>
204 void orderBest_(
const std::map<T, SampleAbundances> abundances,
205 std::vector<T> & result)
207 typedef std::pair<Size, double> PairType;
208 std::multimap<PairType, T, std::greater<PairType> > order;
209 for (
typename std::map<T, SampleAbundances>::const_iterator ab_it =
210 abundances.begin(); ab_it != abundances.end(); ++ab_it)
213 for (SampleAbundances::const_iterator samp_it = ab_it->second.begin();
214 samp_it != ab_it->second.end(); ++samp_it)
216 total += samp_it->second;
218 if (total <= 0.0)
continue;
219 PairType key = std::make_pair(ab_it->second.size(), total);
220 order.insert(std::make_pair(key, ab_it->first));
223 for (
typename std::multimap<PairType, T, std::greater<PairType> >::
224 iterator ord_it = order.begin(); ord_it != order.end(); ++ord_it)
226 result.push_back(ord_it->second);
235 void quantifyPeptides_();
240 void normalizePeptides_();
254 String getAccession_(
const std::set<String> & pep_accessions,
255 std::map<String, String> & accession_to_leader);
262 void countPeptides_(std::vector<PeptideIdentification> & peptides);
265 void updateMembers_();
271 #endif // OPENMS_ANALYSIS_QUANTITATION_PEPTIDEANDPROTEINQUANT_H Size too_few_peptides
Definition: PeptideAndProteinQuant.h:111
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
Statistics()
constructor
Definition: PeptideAndProteinQuant.h:120
Size total_peptides
Definition: PeptideAndProteinQuant.h:114
A more convenient string class.
Definition: String.h:57
Size n_samples
number of samples
Definition: PeptideAndProteinQuant.h:108
ProteinData()
constructor
Definition: PeptideAndProteinQuant.h:97
A container for features.
Definition: FeatureMap.h:93
Size total_features
Definition: PeptideAndProteinQuant.h:117
A container for consensus elements.
Definition: ConsensusMap.h:72
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::set< String > accessions
protein accessions for this peptide
Definition: PeptideAndProteinQuant.h:71
PeptideQuant pep_quant_
Peptide quantification data.
Definition: PeptideAndProteinQuant.h:177
~PeptideAndProteinQuant()
Destructor.
Definition: PeptideAndProteinQuant.h:130
std::map< String, ProteinData > ProteinQuant
Mapping: protein accession -> protein data.
Definition: PeptideAndProteinQuant.h:102
std::map< Int, SampleAbundances > abundances
mapping: charge -> sample -> abundance
Definition: PeptideAndProteinQuant.h:65
std::map< AASequence, PeptideData > PeptideQuant
Mapping: peptide sequence (modified) -> peptide data.
Definition: PeptideAndProteinQuant.h:82
PeptideData()
constructor
Definition: PeptideAndProteinQuant.h:77
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: PeptideAndProteinQuant.h:53
Representation of a peptide hit.
Definition: PeptideHit.h:55
Size id_count
number of identifications
Definition: PeptideAndProteinQuant.h:74
Quantitative and associated data for a peptide.
Definition: PeptideAndProteinQuant.h:62
Statistics stats_
Processing statistics for output in the end.
Definition: PeptideAndProteinQuant.h:174
SampleAbundances total_abundances
mapping: sample -> total abundance
Definition: PeptideAndProteinQuant.h:68
SampleAbundances total_abundances
mapping: sample -> total abundance
Definition: PeptideAndProteinQuant.h:91
void orderBest_(const std::map< T, SampleAbundances > abundances, std::vector< T > &result)
Order keys (charges/peptides for peptide/protein quantification) according to how many samples they a...
Definition: PeptideAndProteinQuant.h:204
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:58
Statistics for processing summary.
Definition: PeptideAndProteinQuant.h:105
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
std::map< String, SampleAbundances > abundances
mapping: peptide (unmodified) -> sample -> abundance
Definition: PeptideAndProteinQuant.h:88
Quantitative and associated data for a protein.
Definition: PeptideAndProteinQuant.h:85
Size id_count
total number of identifications (of peptides mapping to this protein)
Definition: PeptideAndProteinQuant.h:94
ProteinQuant prot_quant_
Protein quantification data.
Definition: PeptideAndProteinQuant.h:180
std::map< UInt64, double > SampleAbundances
Mapping: sample ID -> abundance.
Definition: PeptideAndProteinQuant.h:59