def read_tree_string(s, return_end_point=False, starting_point=0):
tree = arbre.Tree()
tree.id = 1
tree.root = tree
node = tree
k = starting_point
while k < len(s):
c = s[k]
if c == "(":
node.left = arbre.Tree()
node.left.parent = node
node.left.root = node.root
node.left.id = node.id * 2
node = node.left
elif c == ",":
node = node.parent
if node.right == None:
node.right = arbre.Tree()
node.right.parent = node
node.right.root = node.root
node.right.id = node.id * 2 + 1
node = node.right
else:
if node.right2 == None:
node.right2 = arbre.Tree()
node.right2.parent = node
node.right2.root = node.root
node.right2.id = node.id * 2 + 1.5 #noeud qui apparait quand l'arbre n'est pas raciné
node = node.right2
else:
print("Wasn't expecting multifurcating tree")
elif c == ")":
node = node.parent
elif c == ";":
if return_end_point:
#print(s[k],k,len(s))
#print("sk", s[k:])
return tree, k + 2
else:
return tree
else:
name = ""
while not c in ["(", ")", ",", ":", ";"]:
name += c
k += 1
c = s[k]
if c == ":":
while not c in ["(", ")", ",", ";"]:
k += 1
c = s[k]
if len(name) > 0:
node.name = name
k -= 1
k += 1
def generate_tree(freq_by_branch, orig_prob, plus_S=0):
#origination
orig_branch=(rd.choices([u for u in orig_prob], weights=[orig_prob[u] for u in orig_prob]))[0]
r=dict()
tree=arbre.Tree()
r[tree]=[orig_branch]
to_see=[tree]
while len(to_see)>0:
u=to_see.pop()
#e is the last host of u
e=r[u][-1]
weights_to_use=[]
for E in freq_by_branch[e]:
E2=E
if type(E)==tuple:
E2,h=E
if E2=="SL" or E2=="S" or E2=="E":
weights_to_use.append(freq_by_branch[e][E]+plus_S)
else:
weights_to_use.append(freq_by_branch[e][E])
#E=rd.choices([E for E in freq_by_branch[e]], weights=[freq_by_branch[e][E] for E in freq_by_branch[e]])[0]
E=rd.choices([E for E in freq_by_branch[e]], weights=weights_to_use)[0]
if type(E)==tuple:
E,h=E
if E=="S":
u.undated_birth()
r[u.right]=[e.right]
r[u.left]=[e.left]
to_see.append(u.left)
to_see.append(u.right)
if E=="D":
u.undated_birth()
r[u.right]=[e]
r[u.left]=[e]
to_see.append(u.left)
to_see.append(u.right)
if E=="SL":
r[u].append(h)
to_see.append(u)
if E=="T":
u.undated_birth()
r[u.left]=[e]
r[u.right]=[h]
to_see.append(u.left)
to_see.append(u.right)
if E=="TL":
r[u].append(h)
to_see.append(u)
#if E=="E"#on s'arrête, rien à faire
for u in tree.leaves():
u.match=r[u][-1]
return tree
def read_tree_string_sagephy(s, more_output=False):
nodes_info = dict()
tree = arbre.Tree()
tree.id = 1
tree.root = tree
node = tree
k = 0
while k < len(s):
c = s[k]
if c == "(":
node.left = arbre.Tree()
node.left.parent = node
node.left.root = node.root
node.left.id = node.id * 2
node = node.left
elif c == ",":
node = node.parent
if node.right == None:
node.right = arbre.Tree()
node.right.parent = node
node.right.root = node.root
node.right.id = node.id * 2 + 1
node = node.right
else:
if node.right2 == None:
node.right2 = arbre.Tree()
node.right2.parent = node
node.right2.root = node.root
node.right2.id = node.id * 2 + 1.5 #noeud qui apparait quand l'arbre n'est pas raciné
node = node.right2
else:
print("Wasn't expecting multifurcating tree")
elif c == ")":
node = node.parent
elif c == ";":
if more_output:
return tree, nodes_info
else:
return tree
else:
name = ""
while not c in ["(", ")", ",", ":", ";", "[", "]"]:
name += c
k += 1
c = s[k]
if c == ":":
while not c in ["(", ")", ",", ";", "[", "]"]:
k += 1
c = s[k]
if c == "[":
words, k = read_from_to(s, k + 1, ["]"])
l_word = words.split(sep=" ")
l_word2 = []
for u in l_word:
l_word2.append(u.split(sep="="))
if not node in nodes_info:
#voir ce qu'on fait avec les infos dans l'autre cas
nodes_info[node] = l_word2
if len(name) > 0:
node.name = name
k -= 1
k += 1
def generate_tree_SPR2(host,freq_by_branch, orig_prob, plus_S=0):
tree=host.copy()
freq_by_branch_with_name=dict()
for e in freq_by_branch:
freq_by_branch_with_name[e.name]=dict()
for E in freq_by_branch[e]:
freq_by_branch_with_name[e.name][E]=freq_by_branch[e][E]
freq_by_branch=freq_by_branch_with_name
r=dict()
name_to_tree_host=dict()
for u in host.liste():
name_to_tree_host[u.name]=u
print(u.name)
name_to_tree=dict()
for u in tree.liste():
print(u.name)
name_to_tree[u.name]=u
l_name=[e_name for e_name in freq_by_branch]
rd.shuffle(l_name)
for e_name in l_name:
if e_name in [u.name for u in tree.liste()]:
e=name_to_tree[e_name]
weights_to_use=[]
for E in freq_by_branch[e_name]:
E2=E
if type(E)==tuple:
E2,h=E
if E2=="SL" or E2=="S" or E2=="E":
weights_to_use.append(freq_by_branch[e_name][E]+plus_S)
else:
weights_to_use.append(freq_by_branch[e_name][E])
E=rd.choices([E for E in freq_by_branch[e_name]], weights=weights_to_use)[0]
if type(E)==tuple:
E,h=E
if E=="T" or E=="TL":
print("once")
print(e.name, e.isLeaf())
if e.isLeaf():
e.left=arbre.Tree()
e.left.name=e.name
e.left.parent=e
e.right=h
else:
tmpl=e.left
print(type(e.left))
tmpr=e.right
e.left=arbre.Tree()
e.left.left=tmpl
e.left.right=tmpl
tmpl.parent=e.left
tmpr.parent=e.left
e.right=h
print(h.parent.name)
print(h.name)
print(h.parent.left.name, h.parent.right.name)
if h.parent.left==h:
sibling=h.parent.right
else:
sibling=h.parent.left
if sibling.isLeaf():
sibling.parent.name=sibling
sibling.parent.left=None
sibling.parent.right=None
else:
sibling.parent.left=sibling.left
sibling.parent.right=sibling.right
sibling.parent.left.parent=sibling.parent
sibling.parent.right.parent=sibling.parent
h.parent=e
for u in tree.leaves():
u.match=name_to_tree_host[u.name]
return tree
def generate_tree_SPR(freq_by_branch, orig_prob):
#origination
orig_branch=(rd.choices([u for u in orig_prob], weights=[orig_prob[u] for u in orig_prob]))[0]
r=dict()
tree=arbre.Tree()
tree.time=0.1
r[tree]=[orig_branch]
to_see=[tree]
upper_seen=dict()
upper_seen[orig_branch]=True
while len(to_see)>0:
u=to_see.pop(rd.randrange(len(to_see)))
#u=to_see.pop()
#e is the last host of u
e=r[u][-1]
E=rd.choices([E for E in freq_by_branch[e]], weights=[freq_by_branch[e][E] for E in freq_by_branch[e]])[0]
if type(E)==tuple:
E,h=E
if E=="S":
if e.right in upper_seen:
if not e.left in upper_seen:
E=="SL"
h=e.left
if e.left in upper_seen:
if not e.right in upper_seen:
E=="SL"
h=e.right
if not(e.left in upper_seen or e.right in upper_seen):
u.birth(0.5)
u.left.time=0.5
u.right.time=0.5
r[u.right]=[e.right]
r[u.left]=[e.left]
to_see.append(u.left)
to_see.append(u.right)
upper_seen[e.right]=True
upper_seen[e.left]=True
if E=="T":
if not h in upper_seen:
u.birth(0.5)
u.left.time=0.5
u.right.time=0.5
r[u.left]=[e]
r[u.right]=[h]
to_see.append(u.left)
to_see.append(u.right)
upper_seen[h]=True
if E=="SL":
if not h in upper_seen:
r[u].append(h)
to_see.append(u)
if E=="TL":
if not h in upper_seen:
r[u].append(h)
to_see.append(u)
upper_seen[h]=True
if E=="E":
u.time=1
for u in tree.leaves():
u.match=r[u][-1]
tree.prune_tree()
return tree