public class ReportAllInference extends AbstractProteinInference
IntermediateGroup
s as one protein.
This is similar to distinguish proteins simply by their peptides and report every possible set and subset.
Modifier and Type | Field and Description |
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protected static String |
name
the human readable name of this filter
|
protected static String |
shortName
the machine readable name of the filter
|
allowedThreads, filters, intermediateStructure, peptideScoring, proteinScoring
Constructor and Description |
---|
ReportAllInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads) |
Modifier and Type | Method and Description |
---|---|
List<InferenceProteinGroup> |
calculateInference(boolean considerModifications)
calculateInference is the method of the abstract class which allows the
class to compute the protein groups and create the List of different
groups.
|
String |
getName()
Get the human readable name of the inference method.
|
Long |
getProgressValue()
If polling of inference is performed, return the current state of the
progress (between 0 and 100 progress in percent, <0 inference aborted,
>100 inference is done).
|
String |
getShortName()
Get the unique machine readable short name of the inference method.
|
addFilter, createClustersFilteredPeptidesMap, createFilteredPeptidesMap, createProteinAmbiguityGroupID, getFilters, getPeptideKey, getPSMKey, groupHasDirectReportPeptides, groupHasReportPeptides, removeFilter
protected static final String name
protected static final String shortName
public ReportAllInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads)
public List<InferenceProteinGroup> calculateInference(boolean considerModifications)
AbstractProteinInference
calculateInference
in class AbstractProteinInference
public String getName()
AbstractProteinInference
getName
in class AbstractProteinInference
public String getShortName()
AbstractProteinInference
getShortName
in class AbstractProteinInference
public Long getProgressValue()
AbstractProteinInference
getProgressValue
in class AbstractProteinInference
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