def __init__(self, newickstr, periods=None, root_age=None):
"""
newickstr: newick tree with branch lengths
periods: list of durations ordered from present to past
root_age: age of root node for branch length scaling
"""
self.root = newick.parse(newickstr)
phylo.polarize(self.root)
self.periods = periods
# initialize nodes (label interiors, etc)
# and collect leaves and postorder sequence
self.postorder_nodes = []
self.leaves = []
for i, node in enumerate(self.root.descendants(phylo.POSTORDER)):
node.tree = self
node.number = i
node.segments = []
if (not node.istip) and (not node.label):
node.label = str(node.number)
node.age = None
if node.istip:
#node.age = 0.0
self.leaves.append(node)
self.postorder_nodes.append(node)
self.root_age = root_age
if root_age:
self.calibrate(root_age)
self.label2node = dict([(n.label, n) for n in self.postorder_nodes ])
self.assign_node_ages()
## for node in self.postorder_nodes:
## if node.parent and (node.parent.age is None):
## node.parent.age = node.age + node.length
# initialize branch segments
for node in self.postorder_nodes:
if node.parent:
periods = self.periods
anc = node.parent.age
des = node.age
assert anc > des, "%s = %g, %s = %g\n%s" \
% (node.parent.label, anc, node.label, des,
self.root.render_ascii(scaled=1, minwidth=80))
t = des
for i, p in enumerate(periods):
s = sum(periods[:i+1])
if t < s:
duration = min((s - t, anc - t))
if duration > 0:
seg = BranchSegment(duration, i)
node.segments.append(seg)
t += p
if t > anc:
break
def tree2ascii(tree, unitlen=3, minwidth=None, maxwidth=None, scaled=False, show_internal_labels=True, data=None):
phylo.polarize(tree)
depth_length_preorder_traversal(tree)
leaves = tree.leaves()
nleaves = len(leaves)
node2label = dict([(n, n.label) for n in tree.descendants()])
if data:
for k, v in node2label.items():
if v in data:
if k.istip:
node2label[k] = "[%s] %s" % (data[v], v)
else:
node2label[k] = "%s [%s]" % (data[v], v)
maxdepth = max([lf.depth for lf in leaves])
max_labelwidth = max([len(node2label[lf]) for lf in leaves]) + 1
root_offset = 0
if tree.label and show_internal_labels:
root_offset = len(node2label[tree])
width = maxdepth * unitlen + max_labelwidth + 2 + root_offset
# print width
height = 2 * nleaves - 1
if minwidth and (width < minwidth):
unitlen = (minwidth - max_labelwidth - 2 - root_offset) / maxdepth
width = maxdepth * unitlen + max_labelwidth + 2 + root_offset
buf = AsciiBuffer(width, height)
for i, lf in enumerate(leaves):
lf.c = width - max_labelwidth - 2
lf.r = i * 2
for node in tree.descendants(phylo.POSTORDER):
if not node.istip:
children = node.children()
rmin = children[0].r
rmax = children[-1].r
node.r = int(rmin + (rmax - rmin) / 2.0)
node.c = min([ch.c for ch in children]) - unitlen
if not scaled:
for i in range(maxdepth):
smooth_cpos(tree)
else:
maxlen = max([lf.length_to_root for lf in leaves])
scalef = (leaves[0].c + 1 - root_offset) / maxlen
scale_cpos(tree, scalef, root_offset)
for node in tree.descendants(phylo.POSTORDER):
if node.parent:
for r in range(min([node.r, node.parent.r]), max([node.r, node.parent.r])):
buf.putstr(r, node.parent.c, ":")
sym = getattr(node, "hchar", "-")
vbar = sym * (node.c - node.parent.c)
buf.putstr(node.r, node.parent.c, vbar)
if node.istip:
buf.putstr(node.r, node.c + 1, " " + node2label[node])
else:
if node.label and show_internal_labels:
label = node2label[node]
buf.putstr(node.r, node.c - len(label), label)
buf.putstr(node.r, node.c, "+")
return str(buf)