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.