Modifier and Type | Method and Description |
---|---|
IntermediatePeptide |
IntermediateStructureCreator.addPeptide(IntermediatePeptide peptide)
adds the given peptide to the peptides map
|
IntermediatePeptide |
IntermediatePeptideSpectrumMatch.getPeptide()
Getter for the peptide.
|
IntermediatePeptide |
IntermediateStructureCreator.getPeptide(Comparable pepId)
getter for the peptide from the map with the given ID
|
Modifier and Type | Method and Description |
---|---|
Set<IntermediatePeptide> |
IntermediateGroup.getAllPeptides()
getter for all peptides, including all children's peptides.
|
Set<IntermediatePeptide> |
IntermediateGroup.getPeptides()
Getter for the peptides.
|
Modifier and Type | Method and Description |
---|---|
IntermediatePeptide |
IntermediateStructureCreator.addPeptide(IntermediatePeptide peptide)
adds the given peptide to the peptides map
|
void |
IntermediateGroup.addPeptide(IntermediatePeptide peptide)
Adds a single peptide to the group.
|
void |
IntermediateStructureCreatorWorkerThread.insertIntoMap(IntermediatePeptide peptide,
Set<IntermediateProtein> proteins,
Map<Integer,IntermediateGroup> subGroups)
Inserts the given peptide with its accessions into the intermediate
format, which is then build up by the groups in subGroups.
|
void |
IntermediatePeptideSpectrumMatch.setPeptide(IntermediatePeptide peptide)
Setter for the peptide (called while parsing the PIA XML file).
|
Modifier and Type | Method and Description |
---|---|
void |
IntermediateGroup.setPeptides(Collection<IntermediatePeptide> peptides)
Setter for the peptides.
|
Modifier and Type | Method and Description |
---|---|
IntermediatePeptide |
InferenceProteinGroup.addPeptide(IntermediatePeptide peptide)
Adds one IntermediatePeptide to the map of peptides
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,Set<IntermediatePeptide>> |
AbstractProteinInference.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>> |
AbstractProteinInference.createFilteredPeptidesMap(boolean considerModifications)
This method creates a Map from the groups' IDs to the associated
IntermediatePeptide s, which satisfy the currently set filters. |
Set<IntermediatePeptide> |
InferenceProteinGroup.getPeptides()
Returns the set of IntermediatePeptides
|
Set<IntermediatePeptide> |
InferenceProteinGroup.getPeptidesWithScoringType(ScoringItemType type)
Returns the peptides with the given
ScoringItemType |
Modifier and Type | Method and Description |
---|---|
IntermediatePeptide |
InferenceProteinGroup.addPeptide(IntermediatePeptide peptide)
Adds one IntermediatePeptide to the map of peptides
|
static Comparable |
AbstractProteinInference.getPeptideKey(IntermediatePeptide peptide,
boolean considerModifications)
Return a peptide key, depending on whether the modifications are taken
into account or not.
|
ScoringItemType |
InferenceProteinGroup.getPeptidesScoringType(IntermediatePeptide peptide)
Returns the
ScoringItemType of the peptide |
void |
InferenceProteinGroup.setPeptidesScoringType(IntermediatePeptide peptide,
ScoringItemType type)
Sets the scoring type of the stated peptide to the given
ScoringItemType . |
Modifier and Type | Method and Description |
---|---|
boolean |
InferenceProteinGroup.addPeptides(Collection<IntermediatePeptide> peptides)
Adds a collection of IntermediatePeptides to the map of peptides
|
boolean |
AbstractProteinInference.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 |
AbstractProteinInference.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. |
Modifier and Type | Method and Description |
---|---|
Double |
PeptideScoringUseBestPSM.calculatePeptideScore(IntermediatePeptide intermediatePeptide) |
abstract Double |
PeptideScoring.calculatePeptideScore(IntermediatePeptide intermediatePeptide)
Calculates the peptide score for the intermediate peptide.
|
int |
IntermediatePeptideComparator.compare(IntermediatePeptide o1,
IntermediatePeptide o2) |
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