Package pal.tree

Class ParameterizedTree.ParameterizedTreeBase

    • Constructor Detail

      • ParameterizedTreeBase

        public ParameterizedTreeBase()
      • ParameterizedTreeBase

        public ParameterizedTreeBase​(Tree baseTree)
    • Method Detail

      • setBaseTree

        protected void setBaseTree​(Tree baseTree)
      • getBaseTree

        protected Tree getBaseTree()
      • getRoot

        public final Node getRoot()
        Returns the root node of this tree.
        Specified by:
        getRoot in interface Tree
        Returns:
        the root node of this tree.
      • setRoot

        public final void setRoot​(Node root)
        Description copied from interface: Tree
        This method constructs a tree from the given root node.
        Specified by:
        setRoot in interface Tree
        Parameters:
        root - the root node of the tree to construct.
      • getIdentifier

        public final Identifier getIdentifier​(int i)
        Description copied from interface: IdGroup
        Returns the ith identifier.
        Specified by:
        getIdentifier in interface IdGroup
      • setIdentifier

        public final void setIdentifier​(int i,
                                        Identifier id)
        Description copied from interface: IdGroup
        Sets the ith identifier.
        Specified by:
        setIdentifier in interface IdGroup
      • getIdCount

        public final int getIdCount()
        Description copied from interface: IdGroup
        Returns the number of identifiers in this group
        Specified by:
        getIdCount in interface IdGroup
      • whichIdNumber

        public final int whichIdNumber​(java.lang.String s)
        Description copied from interface: IdGroup
        returns the index of the identifier with the given name.
        Specified by:
        whichIdNumber in interface IdGroup
      • getExternalNodeCount

        public final int getExternalNodeCount()
        returns a count of the number of external nodes (tips) in this tree.
        Specified by:
        getExternalNodeCount in interface Tree
        Returns:
        a count of the number of external nodes (tips) in this tree.
      • getInternalNodeCount

        public final int getInternalNodeCount()
        returns a count of the number of internal nodes (and hence clades) in this tree.
        Specified by:
        getInternalNodeCount in interface Tree
        Returns:
        a count of the number of internal nodes (and hence clades) in this tree.
      • getNodeCount

        public final int getNodeCount()
      • getExternalNode

        public final Node getExternalNode​(int i)
        returns the ith external node in the tree.
        Specified by:
        getExternalNode in interface Tree
        Returns:
        the ith external node in the tree.
      • getInternalNode

        public final Node getInternalNode​(int i)
        returns the ith internal node in the tree.
        Specified by:
        getInternalNode in interface Tree
        Returns:
        the ith internal node in the tree.
      • createNodeList

        public final void createNodeList()
        This method is called to ensure that the calls to other methods in this interface are valid.
        Specified by:
        createNodeList in interface Tree
      • getUnits

        public final int getUnits()
        Description copied from interface: Tree
        Gets the units that this tree's branch lengths and node heights are expressed in.
        Specified by:
        getUnits in interface Tree
        Specified by:
        getUnits in interface UnitsProvider
        Returns:
        the units relating to this object.
      • setAttribute

        public final void setAttribute​(Node node,
                                       java.lang.String name,
                                       java.lang.Object value)
        Description copied from interface: Tree
        Sets an named attribute for a given node.
        Specified by:
        setAttribute in interface Tree
        Parameters:
        node - the node whose attribute is being set.
        name - the name of the attribute.
        value - the new value of the attribute.
      • getAttribute

        public final java.lang.Object getAttribute​(Node node,
                                                   java.lang.String name)
        Specified by:
        getAttribute in interface Tree
        Parameters:
        node - the node being interrogated.
        name - the name of the attribute of interest.
        Returns:
        an object representing the named attributed for the numbered node.
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • getCopy

        public Tree getCopy()
        The cheapy copy that just creates a SimpleTree
        Specified by:
        getCopy in interface Tree
        Returns:
        a clone of this tree
      • getOrthogonalHints

        public OrthogonalHints getOrthogonalHints()
        Returns:
        null by default (implying not hint information)