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):
        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 ) : 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.
Set auxilliary parameters to every node of the tree .