pal.treesearch
public interface BranchAccess
Modifier and Type | Interface and Description |
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static class |
BranchAccess.Utils |
Modifier and Type | Method and Description |
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UnrootedMLSearcher |
attach(Node subTree,
Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
attach(Node subTree,
Alignment fullAlignment,
SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
attach(java.lang.String newSequence,
Alignment fullAlignment)
Create a new Tree Searcher with a new sub tree attached
|
UnrootedMLSearcher |
attach(java.lang.String newSequence,
Alignment fullAlignment,
SubstitutionModel model)
Create a new Tree Searcher with a new sub tree attached
|
java.lang.Object |
getAnnotation() |
java.lang.String[] |
getLeftLeafNames()
Obtain the leaf names to the "left" of this branch (left/right is an arbitary name to either end of branch - the only guarantee is that left is not right)
|
java.lang.String[] |
getRightLeafNames()
Obtain the leaf names to the "right" of this branch (left/right is an arbitary name to either end of branch - the only guarantee is that left is not right)
|
int[] |
getSplitInformation(java.lang.String[] leafNames)
Constructe an array detailing the split information
|
boolean |
isLeafBranch(java.lang.String leafLabel)
Test if this branch leads directly to a leaf of a particular label
|
void |
setAnnotation(java.lang.Object annotation)
Set the annotation for this branch (will be used when instructing TreeInterfaces
|
void setAnnotation(java.lang.Object annotation)
annotation
- The annotation object (dependent on the TreeInterface instructed)java.lang.Object getAnnotation()
boolean isLeafBranch(java.lang.String leafLabel)
leafLabel
- the label of the leafUnrootedMLSearcher attach(Node subTree, Alignment fullAlignment)
subTree
- the sub tree to attach at this branchfullAlignment
- the full alignment including the sequences already part of the base treeUnrootedMLSearcher attach(java.lang.String newSequence, Alignment fullAlignment)
newSequence
- the new leaf to attach at this branchfullAlignment
- the full alignment including the sequences already part of the base treeUnrootedMLSearcher attach(Node subTree, Alignment fullAlignment, SubstitutionModel model)
subTree
- the sub tree to attach at this branchfullAlignment
- the full alignment including the sequences already part of the base treemodel
- the new substitution model to useUnrootedMLSearcher attach(java.lang.String newSequence, Alignment fullAlignment, SubstitutionModel model)
newSequence
- the new sequence to attach at this branchfullAlignment
- the full alignment including the sequences already part of the base treemodel
- the new substitution model to usejava.lang.String[] getLeftLeafNames()
java.lang.String[] getRightLeafNames()
int[] getSplitInformation(java.lang.String[] leafNames)
leafNames
- the names of the leaves