def swap_tree(tree):
# make safe tree
if not '"' in tree:
tree = nwk.safe_newick_string(tree)
# swap two nodes of the tree
nodes = list(nwk.nodes_in_tree(tree))[1:]
random.shuffle(nodes)
# choose two nodes to be swapped
nodeA = nodes.pop(0)
# get another node that can be interchanged
while nodes:
nodeB = nodes.pop(0)
if nodeB in nodeA or nodeA in nodeB:
pass
else:
break
tree = tree.replace(nodeA+',', '#dummyA#,')
tree = tree.replace(nodeA+')', '#dummyA#)')
tree = tree.replace(nodeB+',', '#dummyB#,')
tree = tree.replace(nodeB+')', '#dummyB#)')
tree = tree.replace('#dummyA#', nodeB)
tree = tree.replace('#dummyB#', nodeA)
return nwk.sort_tree(tree).replace('"','')
def swap_tree(tree):
# make safe tree
if not '"' in tree:
tree = nwk.safe_newick_string(tree)
# swap two nodes of the tree
nodes = list(nwk.nodes_in_tree(tree))[1:]
random.shuffle(nodes)
# choose two nodes to be swapped
nodeA = nodes.pop(0)
# get another node that can be interchanged
while nodes:
nodeB = nodes.pop(0)
if nodeB in nodeA or nodeA in nodeB:
pass
else:
break
tree = tree.replace(nodeA + ',', '#dummyA#,')
tree = tree.replace(nodeA + ')', '#dummyA#)')
tree = tree.replace(nodeB + ',', '#dummyB#,')
tree = tree.replace(nodeB + ')', '#dummyB#)')
tree = tree.replace('#dummyA#', nodeB)
tree = tree.replace('#dummyB#', nodeA)
return nwk.sort_tree(tree).replace('"', '')
def all_rooted_binary_trees(*taxa):
"""
Compute all rooted trees.
Notes
-----
This procedure yields all rooted binary trees for a given set of taxa, as
described in :bib:`Felsenstein1978`. It implements a depth-first search.
"""
if len(taxa) <= 2:
yield '(' + ','.join(taxa) + ');'
# make queue with taxa included and taxa to be visited
queue = [('(' + ','.join(taxa[:2]) + ')', list(taxa[2:]))]
out = []
while queue:
# add next taxon
tree, rest = queue.pop()
if rest:
next_taxon = rest.pop()
nodes = list(nwk.nodes_in_tree(tree))
random.shuffle(nodes)
for node in nodes:
new_tree = tree.replace(node,
'(' + next_taxon + ',' + node + ')')
r = [x for x in rest]
random.shuffle(r)
queue += [(new_tree, r)]
if not rest:
yield new_tree
def all_rooted_binary_trees(*taxa):
"""
Compute all rooted trees.
Notes
-----
This procedure yields all rooted binary trees for a given set of taxa, as
described in :bib:`Felsenstein1978`. It implements a depth-first search.
"""
if len(taxa) <= 2:
yield '('+','.join(taxa)+');'
# make queue with taxa included and taxa to be visited
queue = [('('+','.join(taxa[:2])+')', list(taxa[2:]))]
out = []
while queue:
# add next taxon
tree, rest = queue.pop()
if rest:
next_taxon = rest.pop()
nodes = list(nwk.nodes_in_tree(tree))
random.shuffle(nodes)
for node in nodes:
new_tree = tree.replace(node, '('+next_taxon+','+node+')')
r = [x for x in rest]
random.shuffle(r)
queue += [(new_tree, r)]
if not rest:
yield new_tree
