treetime/treeanc.py
def _prepare_nodes(self):
        """
        Set auxilliary parameters to every node of the tree.
        """
        self.tree.root.up = None
        self.tree.root.bad_branch=self.tree.root.bad_branch if hasattr(self.tree.root, 'bad_branch') else False
        internal_node_count = 0
        for clade in self.tree.get_nonterminals(order='preorder'): # parents first
            internal_node_count+=1
            if clade.name is None:
                clade.name = "NODE_" + format(self._internal_node_count, '07d')
                self._internal_node_count += 1
            for c in clade.clades:
                if c.is_terminal():
                    c.bad_branch = c.bad_branch if hasattr(c, 'bad_branch') else False
                c.up = clade

        for clade in self.tree.get_nonterminals(order='postorder'): # parents first
            clade.bad_branch = all([c.bad_branch for c in clade])

        self._calc_dist2root()
        self._internal_node_count = max(internal_node_count, self._internal_node_count)
def _prepare_nodes(self):
        """
        Set auxilliary parameters to every node of the tree.
        """
        self.tree.root.up = None
        self.tree.root.bad_branch=self.tree.root.bad_branch if hasattr(self.tree.root, 'bad_branch') else False
        internal_node_count = 0
        for clade in self.tree.get_nonterminals(order='preorder'): # parents first
            internal_node_count+=1
            if clade.name is None:
                clade.name = "NODE_" + format(self._internal_node_count, '07d')
                self._internal_node_count += 1
            for c in clade.clades:
                if c.is_terminal():
                    c.bad_branch = c.bad_branch if hasattr(c, 'bad_branch') else False
                c.up = clade

        for clade in self.tree.get_nonterminals(order='postorder'): # parents first
            clade.bad_branch = all([c.bad_branch for c in clade])

        self._calc_dist2root()
        self._internal_node_count = max(internal_node_count, self._internal_node_count)
Set auxilliary parameters to every node of the tree.