Modifier and Type | Method and Description |
---|---|
void |
DataImportController.addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters)
Adds the filtered PSMs to the
IntermediateStructureCreator . |
void |
DataImportController.addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters,
String cacheScoreAccession)
Adds the filtered PSMs to the
IntermediateStructureCreator . |
void |
IntermediatePeptide.filterPSMs(List<AbstractFilter> filters)
Filters the PSMs using the given filters.
|
Modifier and Type | Method and Description |
---|---|
String |
PrideImportController.addProteinsSpectrumIdentificationsToStructCreator(Comparable proteinId,
List<AbstractFilter> filters,
String cacheScoreAccession)
Adds the spectrum identifications of a single protein to the structure
creator.
|
void |
PrideImportController.addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters) |
void |
PrideImportController.addSpectrumIdentificationsToStructCreator(List<AbstractFilter> filters,
String cacheScoreAccession) |
Modifier and Type | Method and Description |
---|---|
Integer |
PIAModeller.addFileAndImportSpectra(String pathname,
List<AbstractFilter> filters)
Adds a file to the input files and adds the filtered PSMs to the
structure creator.
|
Integer |
PIAModeller.addFileAndImportSpectra(String pathname,
List<AbstractFilter> filters,
String cacheScoreAccession)
Adds a file to the input files and adds the filtered PSMs to the
structure creator.
|
void |
PIAModeller.importDataFromFile(Integer fileID,
List<AbstractFilter> filters)
Imports the filtered PSMs and adds them to the structure creator.
|
void |
PIAModeller.importDataFromFile(Integer fileID,
List<AbstractFilter> filters,
String cacheScoreAccession)
Imports the filtered PSMs and adds them to the structure creator.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
FilterUtilities.satisfiesFilterList(Object item,
List<AbstractFilter> filters)
Checks whether all the filters in the given List are satisfied for the
given object.
|
Modifier and Type | Class and Description |
---|---|
class |
PeptideNrPSMsFilter
Filters for the number of PSMs on peptide level.
|
Modifier and Type | Class and Description |
---|---|
class |
ProteinAccessionFilter
Filters for accessions on PSM level.
|
class |
ProteinNrPSMsFilter
Filters for the number of PSMs on protein level.
|
Modifier and Type | Class and Description |
---|---|
class |
PSMAccessionsFilter
Filters for accessions on PSM level.
|
class |
PSMDecoyFilter
Filter for decoys on PSM level.
|
class |
PSMQValueFilter
Filters for accessions on PSM level.
|
class |
PSMScoreFilter
Filters for a score on PSM level.
|
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 List<AbstractFilter> |
AbstractProteinInference.filters
list of the settings.
|
Modifier and Type | Method and Description |
---|---|
AbstractFilter |
AbstractProteinInference.removeFilter(int index)
Removes the filter at the given index
|
Modifier and Type | Method and Description |
---|---|
List<AbstractFilter> |
AbstractProteinInference.getFilters()
Returns a
List of all filter settings for this inference filter. |
Modifier and Type | Method and Description |
---|---|
boolean |
AbstractProteinInference.addFilter(AbstractFilter newFilter)
adds a new filter to the inference filters.
|
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) |
OccamsRazorWorkerThread(int ID,
OccamsRazorInference parent,
List<AbstractFilter> filters,
boolean considerModifications) |
ReportAllInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads) |
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