custom_dendropy_datamodel1.py

# Problem:
#    You want to use DendroPy's rich parsing infrastructure to read/write trees, 
#    but you have your own classes of Trees/Nodes that you want to use. 

# Solution:
#    Don't just derive from DendroPy's Node/Tree/TreeList class, but at each
#    level, specify the appropriate type and/or factory function for the
#    component types.

# Derive from dendropy.Node, delegating most work there, 
# just adding stuff you want here
class PhyloNode(dendropy.Node):

    def __init__(self, *args, **kwargs):
        dendropy.Node.__init__(self, *args, **kwargs)

    def _get_clades(self):
        return self.child_nodes()
    clades = property(_get_clades)

    def _get_branch_length(self):
        return self.edge.length
    branch_length = property(_get_branch_length)

# Your custom trees must be composed of your custom Nodes.
# Derive from dendropy.Tree to let it do most of the work,
# including parsing/reading/writing, but make sure to 
# override the ``node_factory`` class function to return
# the custom Node-types, in addition to adding extra
# functionality that you want.
class PhyloTree(dendropy.Tree):
    
    @classmethod
    def node_factory(cls, *args, **kwargs):
        return PhyloNode(*args, **kwargs)

    def get_nonterminals(self, order):
        if order == "postorder":
            return list(self.postorder_internal_node_iter())
        else:
            raise ValueError(order)

    def get_terminals(self):
        return list(self.leaf_node_iter())

# Again, override the factories to return your
# classes instead of the native DendroPy ones.
# There are actually two ways to go about 
# this. You can simply set the class-level
# variable ``DEFAULT_TREE_TYPE`` if the 
# constructor signature is the same as the 
# native dendropy.Tree. Otherwise, you can
# override the ``tree_factory`` class 
# function. As a special case, you can 
# actually create custom tree  on a 
# per-instance basis, by setting the 
# dendropy.TreeList.tree_type instance variable.
class PhyloTreeList(dendropy.TreeList):

    DEFAULT_TREE_TYPE = PhyloTree