pal.treesearch
Interface BranchAccess

public interface BranchAccess

Nested Class Summary

static class

BranchAccess.Utils

Method Summary

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

Method Detail

setAnnotation

void setAnnotation(java.lang.Object annotation)

Set the annotation for this branch (will be used when instructing TreeInterfaces

Parameters:

annotation - The annotation object (dependent on the TreeInterface instructed)

getAnnotation

java.lang.Object getAnnotation()

isLeafBranch

boolean isLeafBranch(java.lang.String leafLabel)

Test if this branch leads directly to a leaf of a particular label

Parameters:

leafLabel - the label of the leaf

Returns:

true if this branch is a leaf branch and the leaf has the right label

attach

UnrootedMLSearcher attach(Node subTree,
                          Alignment fullAlignment)

Create a new Tree Searcher with a new sub tree attached

Parameters:

subTree - the sub tree to attach at this branch

fullAlignment - the full alignment including the sequences already part of the base tree

Returns:

a new unrooted searcher

attach

UnrootedMLSearcher attach(java.lang.String newSequence,
                          Alignment fullAlignment)

Create a new Tree Searcher with a new sub tree attached

Parameters:

newSequence - the new leaf to attach at this branch

fullAlignment - the full alignment including the sequences already part of the base tree

Returns:

a new unrooted searcher

attach

UnrootedMLSearcher attach(Node subTree,
                          Alignment fullAlignment,
                          SubstitutionModel model)

Create a new Tree Searcher with a new sub tree attached

Parameters:

subTree - the sub tree to attach at this branch

fullAlignment - the full alignment including the sequences already part of the base tree

model - the new substitution model to use

Returns:

a new unrooted searcher

attach

UnrootedMLSearcher attach(java.lang.String newSequence,
                          Alignment fullAlignment,
                          SubstitutionModel model)

Create a new Tree Searcher with a new sub tree attached

Parameters:

newSequence - the new sequence to attach at this branch

fullAlignment - the full alignment including the sequences already part of the base tree

model - the new substitution model to use

Returns:

a new unrooted searcher

getLeftLeafNames

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)

Returns:

the appropriate leaf names

getRightLeafNames

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)

Returns:

the appropriate leaf names

getSplitInformation

int[] getSplitInformation(java.lang.String[] leafNames)

Constructe an array detailing the split information

Parameters:

leafNames - the names of the leaves

Returns:

an array matching the input array length, where each element should have the values -1, 1, or 0 depending on whether the name is in the "left" set, the "right" set, or unknown respectively.