Package pal.tree

Class Tree.TreeBase

    • Constructor Detail

      • TreeBase

        protected TreeBase​(Node theRoot)
        constructor
        Parameters:
        theRoot - the node to base tree on
      • TreeBase

        protected TreeBase()
        constructor
      • TreeBase

        protected TreeBase​(Tree.TreeBase tree,
                           Node newRoot)
        clone constructor
    • Method Detail

      • setRoot

        public void setRoot​(Node theRoot)
        Called by subclasses that can't give root at time of construction (of this class)
        Specified by:
        setRoot in interface Tree
        Parameters:
        theRoot - the root node of the tree to construct.
      • getUnits

        public final int getUnits()
        Return the units that this tree is expressed in.
        Specified by:
        getUnits in interface Tree
        Specified by:
        getUnits in interface UnitsProvider
        Returns:
        the units relating to this object.
      • setUnits

        public final void setUnits​(int units)
        Sets the units that this tree is expressed in.
      • getExternalNodeCount

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

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

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

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

        public Node findNode​(int num)
        return node with number num (as displayed in ASCII tree)
        Parameters:
        num - number of node
        Returns:
        node
      • createNodeList

        public void createNodeList()
        count and list external and internal nodes and compute heights of each node
        Specified by:
        createNodeList in interface Tree
      • setSetupLengthsAndHeights

        protected void setSetupLengthsAndHeights​(boolean value)
        Set whether or not this class should call methods to adjust either heights or lengths automatically
      • toString

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

        public void setAttribute​(Node node,
                                 java.lang.String name,
                                 java.lang.Object value)
        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 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.
      • reroot

        public void reroot​(int num)
        make node with number num to root node
        Parameters:
        num - number of node
      • reroot

        public void reroot​(Node node)
        make provided node the root node
        Parameters:
        node - the node to make the root.
      • getIdCount

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

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

        public 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
      • report

        public void report​(java.io.PrintWriter out)
        Description copied from interface: Report
        print human readable report (e.g., on parameters and associated model)
        Specified by:
        report in interface Report
        Parameters:
        out - output stream