def tree_from_order(order):
nodes = script_tree.getNodes(tree)
for n in nodes:
if not script_tree.isRoot(tree, n):
if script_tree.isLeaf(tree, n):
index = len(order)
else:
index = order.index(script_tree.getBootstrap(tree, n))
index_parent = order.index(script_tree.getBootstrap(tree, script_tree.getParent(tree, n)))
script_tree.setLength(tree, n, index - index_parent)
return script_tree.writeTree(tree, root, False)
def tree_from_order(order):
nodes = script_tree.getNodes(tree)
for n in nodes:
if not script_tree.isRoot(tree,n):
if script_tree.isLeaf(tree,n):
index = len(order)
else:
index = order.index(script_tree.getBootstrap(tree,n))
index_parent = order.index(script_tree.getBootstrap(tree,script_tree.getParent(tree,n)))
script_tree.setLength(tree,n,index-index_parent)
return script_tree.writeTree(tree,root,False)
def donnor_search(t, n):
current_node = n
result = -1
while result == -1 and not script_tree.isRoot(t, current_node):
current_node = script_tree.getParent(t, current_node)
annot = script_tree.getBootstrap(t, current_node)
event = annot[1:].split(".")[0]
if event[:2] != "T@" and event[:2] != "D@":
result = event
if annot.find("@T") >= 0:
current_node = script_tree.getRoot(t)
result = -1
return result
def donnor_search(t,n):
current_node = n
result = -1
while result == -1 and not script_tree.isRoot(t,current_node):
current_node = script_tree.getParent(t,current_node)
annot = script_tree.getBootstrap(t,current_node)
event = annot[1:].split(".")[0]
if event[:2] != "T@" and event[:2] != "D@":
result = event
if annot.find("@T") >= 0:
current_node = script_tree.getRoot(t)
result = -1
return result
def parent(x):
#print x
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree,n):
name = script_tree.getName(species_tree,n)
else:
name = script_tree.getBootstrap(species_tree,n)
if name == x:
if script_tree.isRoot(species_tree,n):
result = -1
else:
result = script_tree.getBootstrap(species_tree,script_tree.getParent(species_tree,n))
return result
def parent(x):
#print x
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree, n):
name = script_tree.getName(species_tree, n)
else:
name = script_tree.getBootstrap(species_tree, n)
if name == x:
if script_tree.isRoot(species_tree, n):
result = -1
else:
result = script_tree.getBootstrap(
species_tree, script_tree.getParent(species_tree, n))
return result
line.strip(), " ...ignored"
# sortie = open("distribution_by_family","w")
# keys = by_family.keys()
# keys.sort()
# for f in keys:
# sortie.write(f+" "+str(by_family[f])+"\n")
total_transfers = sum(edge.values())
to_desc = 0
uninformative = 0
# initialise from branches
for n in nodes:
if (not script_tree.isLeaf(tree, n)):
if (not script_tree.isRoot(tree, n)):
parent = script_tree.getBootstrap(tree, script_tree.getParent(tree, n))
child = script_tree.getBootstrap(tree, n)
if edge.has_key(parent + "," + child):
to_desc = to_desc + edge[parent + "," + child]
uninformative = uninformative + edge[parent + "," + child]
else:
graph[parent].append(child)
edge[parent + "," + child] = MAX_NUMBER
else:
parent = script_tree.getBootstrap(tree, script_tree.getParent(tree, n))
child = script_tree.getName(tree, n)
if not child in graph[parent]:
graph[parent].append(child)
edge_keys = edge.keys()
# initialise from nodes
for n in nodes:
if (not script_tree.isLeaf(tree,n)):
node = script_tree.getBootstrap(tree,n)
graph[node] = []
degre_entrant[node] = []
internal_nodes.append(node)
else:
node = script_tree.getName(tree,n)
graph[node] = []
# initialise from branches
for n in nodes:
if (not script_tree.isLeaf(tree,n)):
if (not script_tree.isRoot(tree,n)):
parent = script_tree.getBootstrap(tree,script_tree.getParent(tree,n))
child = script_tree.getBootstrap(tree,n)
graph[parent].append(child)
edge[parent+","+child] = MAX_NUMBER
else:
parent = script_tree.getBootstrap(tree,script_tree.getParent(tree,n))
child = script_tree.getName(tree,n)
graph[parent].append(child)
# parse transfers
total_transfers = 0
uninformative = 0
by_family = {}
for line in constraints:
#print line