def __init__(self, weight=1.0, rooted = True, name='') : self.t = Tree(weight=weight, rooted = rooted, name=name)
class TreeBuilder(object) :
""" A basic helper for building BioPython trees.
Use:
- tb = TreeBuilder()
- Create some terminals via leaf = tb.createLeaf(name)
- use mergeNodes to successively merge nodes.
- Call tb.finalize(root-node) to get the tree
"""
def __init__(self, weight=1.0, rooted = True, name='') :
self.t = Tree(weight=weight, rooted = rooted, name=name)
def createLeaf(self, name) :
""" Create a new leaf.
:param name: taxon name
:returns: node"""
nd = NodeData()
nd.taxon = name
leaf = Nodes.Node(nd)
self.t.add(leaf, None)
return leaf
def newNode(self) :
nd = NodeData()
node = Nodes.Node(nd)
self.t.add(node, None)
return node
def mergeNodes(self, subtrees) :
""" Join subtrees in subtrees into one sub-tree.
Each element in subtrees is a (node,branch) pair, where branch is the length
of the branch connecting the node to its parent.
:param subtrees: sequence of [node,branch]
:returns: node"""
nd = NodeData()
node = Nodes.Node(nd)
self.t.add(node, None)
for n1,h1 in subtrees:
n1.set_prev(node.id)
n1.data.branchlength = h1
node.add_succ([x.id for x,h in subtrees])
return node
def finalize(self, rootNode) :
""" Convert a node to a proper tree with root rootNode.
:param rootNode: node
:returns: biopython tree
"""
t = self.t
rr = t.node(t.root)
if rootNode.succ :
rr.set_succ(rootNode.succ)
for p in rootNode.succ :
t.node(p).set_prev(t.root)
if hasattr(rootNode.data,attributesVarName) :
rr.data.attributes = rootNode.data.attributes
t.kill(rootNode.id)
else :
rr.set_succ([rootNode.id])
rootNode.set_prev(t.root)
return t
