public class OccamsRazorInference extends AbstractProteinInference
IntermediateGroup
s as protein,
which together fulfill the Occam's Razor constraints. I.e. the minimal set of
groups is reported, which contain all peptides and each protein is contained,
at least as subset of peptides.
There are 3 constraints for a Group, to be reported:
1) it has no parent-Groups (but implicit accessions, there cannot be a Group
without parents and without accessions)
2) Group fulfills 1) and has any direct peptides -> report it
3) Group fulfills 1) but not 2): get the peptide children groups (i.e. the
Groups, which have the peptides). If the pepChildGroups are not fully
explained by any other Group fulfilling 1), report the Group. (If it is
explained by any other, set it as a subGroup of it).
Modifier and Type | Field and Description |
---|---|
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 |
---|
OccamsRazorInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads) |
Modifier and Type | Method and Description |
---|---|
void |
addToReports(List<InferenceProteinGroup> proteinGroups)
Adds the proteinGroups to the list of reported
ProteinGroup s. |
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.
|
Set<IntermediateGroup> |
getNextCluster()
Returns the next cluster in the intermediate structure null, if no more
clusters are available.
|
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 OccamsRazorInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads)
public List<InferenceProteinGroup> calculateInference(boolean considerModifications)
AbstractProteinInference
calculateInference
in class AbstractProteinInference
public Set<IntermediateGroup> getNextCluster()
public void addToReports(List<InferenceProteinGroup> proteinGroups)
ProteinGroup
s.newProteins
- 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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