Package | Description |
---|---|
uk.ac.ebi.pride.utilities.pia.intermediate | |
uk.ac.ebi.pride.utilities.pia.modeller.protein.inference |
Modifier and Type | Method and Description |
---|---|
IntermediateGroup |
IntermediateProtein.getGroup()
returns the group of this protein
|
IntermediateGroup |
IntermediatePeptide.getGroup()
returns the group of this peptide
|
Modifier and Type | Method and Description |
---|---|
Set<IntermediateGroup> |
IntermediateGroup.getAllChildren()
Getter for all children groups of this group, including children's
children and so on.
|
Set<IntermediateGroup> |
IntermediateGroup.getAllPeptideChildren()
Getter for all children groups of this group that have at least one
peptide, recursive, i.e.
|
Set<IntermediateGroup> |
IntermediateGroup.getChildren()
Getter for the children set
|
Set<IntermediateGroup> |
IntermediateStructure.getCluster(Integer clusterNr)
Returns the cluster given by the clusterNr
|
Map<Integer,Set<IntermediateGroup>> |
IntermediateStructure.getClusters()
Returns the clusters
|
Set<IntermediateGroup> |
IntermediateGroup.getParents()
Getter for the parents.
|
Modifier and Type | Method and Description |
---|---|
void |
IntermediateGroup.addChild(IntermediateGroup child)
Adds a child to the set of children.
|
void |
IntermediateGroup.addParent(IntermediateGroup parent)
Adds a new group to the set of parents.
|
void |
IntermediateProtein.setGroup(IntermediateGroup group)
sets the group of this protein
|
void |
IntermediatePeptide.setGroup(IntermediateGroup group)
sets the group of this peptide
|
Modifier and Type | Method and Description |
---|---|
protected void |
IntermediateStructureCreator.addCluster(Collection<IntermediateGroup> cluster)
Adds the given cluster information into the intermediate structure.
|
void |
IntermediateStructure.addCluster(Collection<IntermediateGroup> cluster)
Adds the given cluster to the clusters in the structure.
|
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.
|
Modifier and Type | Method and Description |
---|---|
Set<IntermediateGroup> |
OccamsRazorInference.getNextCluster()
Returns the next cluster in the intermediate structure null, if no more
clusters are available.
|
Modifier and Type | Method and Description |
---|---|
String |
AbstractProteinInference.createProteinAmbiguityGroupID(IntermediateGroup group)
Ceates a unique ID for a ProteinAmbiguityGroup from the group ID
|
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 |
---|---|
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. |
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