public abstract class AbstractProteinInference extends Object
AbstractProteinInference
calculates for the PIA groups,
which are to be reported and in which way.Modifier and Type | Field and Description |
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protected int |
allowedThreads
the number of allowed threads (smaller 1 = all available)
|
protected List<AbstractFilter> |
filters
list of the settings.
|
protected IntermediateStructure |
intermediateStructure
the PIA intermediate structure
|
protected PeptideScoring |
peptideScoring
the currently set peptide scoring
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protected ProteinScoring |
proteinScoring
the currently set protein scoring
|
Constructor and Description |
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AbstractProteinInference(IntermediateStructure intermediateStructure,
PeptideScoring peptideScoring,
ProteinScoring proteinScoring,
List<AbstractFilter> filters,
Integer nrThreads)
The constructor works using a DataAccessController.
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Modifier and Type | Method and Description |
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boolean |
addFilter(AbstractFilter newFilter)
adds a new filter to the inference filters.
|
abstract 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.
|
Map<Integer,Set<IntermediatePeptide>> |
createClustersFilteredPeptidesMap(Set<IntermediateGroup> cluster,
boolean considerModifications)
This method creates a Map from the groups' IDs to the associated
IntermediatePeptide s of the given cluster, which satisfy the
currently set filters. |
Map<Integer,Set<IntermediatePeptide>> |
createFilteredPeptidesMap(boolean considerModifications)
This method creates a Map from the groups' IDs to the associated
IntermediatePeptide s, which satisfy the currently set filters. |
String |
createProteinAmbiguityGroupID(IntermediateGroup group)
Ceates a unique ID for a ProteinAmbiguityGroup from the group ID
|
List<AbstractFilter> |
getFilters()
Returns a
List of all filter settings for this inference filter. |
abstract String |
getName()
Get the human readable name of the inference method.
|
static Comparable |
getPeptideKey(IntermediatePeptide peptide,
boolean considerModifications)
Return a peptide key, depending on whether the modifications are taken
into account or not.
|
abstract 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).
|
static Comparable |
getPSMKey(IntermediatePeptideSpectrumMatch psm,
boolean considerModifications)
Returns a psm key, depending on whether the modifications are taken
into account or not.
|
abstract String |
getShortName()
Get the unique machine readable short name of the inference method.
|
boolean |
groupHasDirectReportPeptides(IntermediateGroup group,
Map<Integer,Set<IntermediatePeptide>> groupIdToReportPeptides)
Tests for the given group, if it has any direct
IntermediatePeptide s,
in the given Map. |
boolean |
groupHasReportPeptides(IntermediateGroup group,
Map<Integer,Set<IntermediatePeptide>> groupIdToReportPeptides)
Tests for the given group, if it has any
IntermediatePeptide s,
whether direct or in the peptideChildren, in the given Map. |
AbstractFilter |
removeFilter(int index)
Removes the filter at the given index
|
protected List<AbstractFilter> filters
protected PeptideScoring peptideScoring
protected ProteinScoring proteinScoring
protected int allowedThreads
protected IntermediateStructure intermediateStructure
public AbstractProteinInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads)
controller
- filters
- any filters, which should be appliedfilterPSMsOnImport
- if true, the PSMs hich fo not pass teh filtering are not imported into the intermediate structurenrThreads
- public abstract List<InferenceProteinGroup> calculateInference(boolean considerModifications)
considerModifications
- psmSetSettings
- public Map<Integer,Set<IntermediatePeptide>> createFilteredPeptidesMap(boolean considerModifications)
IntermediatePeptide
s, which satisfy the currently set filters.considerModifications
- public Map<Integer,Set<IntermediatePeptide>> createClustersFilteredPeptidesMap(Set<IntermediateGroup> cluster, boolean considerModifications)
IntermediatePeptide
s of the given cluster, which satisfy the
currently set filters.considerModifications
- public boolean groupHasDirectReportPeptides(IntermediateGroup group, Map<Integer,Set<IntermediatePeptide>> groupIdToReportPeptides)
IntermediatePeptide
s,
in the given Map. This Map should by created by
createFilteredPeptidesMap(boolean)
prior
to calling this function.public boolean groupHasReportPeptides(IntermediateGroup group, Map<Integer,Set<IntermediatePeptide>> groupIdToReportPeptides)
IntermediatePeptide
s,
whether direct or in the peptideChildren, in the given Map. This Map
should be created by createFilteredPeptidesMap(boolean)
prior to calling this function.public static final Comparable getPeptideKey(IntermediatePeptide peptide, boolean considerModifications)
peptide
- considerModifications
- public static final Comparable getPSMKey(IntermediatePeptideSpectrumMatch psm, boolean considerModifications)
peptide
- considerModifications
- public String createProteinAmbiguityGroupID(IntermediateGroup group)
group
- public abstract Long getProgressValue()
public abstract String getName()
public abstract String getShortName()
public boolean addFilter(AbstractFilter newFilter)
newFilter
- public List<AbstractFilter> getFilters()
List
of all filter settings for this inference filter.public AbstractFilter removeFilter(int index)
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