Interface BranchAccess


  • public interface BranchAccess
    • Nested Class Summary

      Nested Classes 
      Modifier and Type Interface Description
      static class  BranchAccess.Utils  
    • 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.