Modifier and Type | Method and Description |
---|---|
void |
ProteinModeller.infereProteins(PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
Class<? extends AbstractProteinInference> proteinInferenceClass,
List<AbstractFilter> filters,
boolean considerModifications)
Runs the protein inference with the given settings and stores the protein
groups in a list, which can be returned by
ProteinModeller.getInferredProteins() |
Modifier and Type | Field and Description |
---|---|
protected PeptideScoring |
AbstractProteinInference.peptideScoring
the currently set peptide scoring
|
Constructor and Description |
---|
AbstractProteinInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads)
The constructor works using a DataAccessController.
|
OccamsRazorInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads) |
ReportAllInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads) |
Modifier and Type | Class and Description |
---|---|
class |
PeptideScoringUseBestPSM
This class uses the PSM with the best score for scoring of a peptide.
|
Constructor and Description |
---|
IntermediatePeptideComparator(PeptideScoring peptideScoring)
Creates the comparator and gets the value for higherScoreBetter from the
given
PeptideScoring . |
Modifier and Type | Field and Description |
---|---|
protected PeptideScoring |
ProteinScoring.peptideScoring
the peptide scoring used
|
Constructor and Description |
---|
ProteinScoring(boolean countSpectrumOnce,
PeptideScoring peptideScoring) |
ProteinScoringAdditive(boolean countSpectrumOnce,
PeptideScoring peptideScoring) |
ProteinScoringMultiplicative(boolean countSpectrumOnce,
PeptideScoring peptideScoring) |
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