def parsimony_up2(subtree, nodelist, parent, siblings):
"""parsimony part: up direction -> from root to leafs"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
# parent - nodelist element
# siblings - [nodelist element]
element = find_element_in_nodelist(subtree.name, nodelist)
parent_tag = parent[4][
0] # parent[4] could look like [['0', '1'], ['1']] or [['1']]
both_tags = []
both_tags.append(parent_tag)
for sibling in siblings:
both_tags.append(sibling[4][0])
# get intersection or union
tag_list = get_intersect_or_union(both_tags)
# add new tag
element[4].append(tag_list)
# go on with children
if not subtree.is_terminal():
children = []
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
children.append(child)
for i in range(0, len(subtree.clades)):
clade = subtree.clades[i]
child = find_element_in_nodelist(clade.name, nodelist)
sublist = deepcopy(children)
del sublist[i]
parsimony_up2(clade, nodelist, element, sublist)
return
def parsimony_down(subtree, nodelist):
"""parsimony part: down direction -> from leafs to root"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
child_tags = []
for clade in subtree.clades:
child = find_element_in_nodelist(clade.name, nodelist)
# if child is not tagged, first tag it:
if child[4] == []:
parsimony_down(clade, nodelist)
child_tags.append(child[4][0])
element = find_element_in_nodelist(subtree.name, nodelist)
# get intersection or union
tag_list = get_intersect_or_union(child_tags)
# add new tag
element[4].append(tag_list)
return
def parsimony_final(subtree, nodelist):
"""parsimony final part: combine multiple tags of node to one final tag"""
# Arguments:
# subtree
# 0 1 2 3 4
# nodelist - [id, depth, originaltag, finaltag, calc[taglist]]
element = find_element_in_nodelist(subtree.name, nodelist)
if subtree.is_terminal() and len(element[4][0]) == 1:
element[3] = element[4][0][0]
else:
# get intersection or union
tag_list = get_intersect_or_union(element[4])
# add final tag
tag_string = ""
for tag in tag_list:
tag_string += str(tag) + "&"
tag_string = tag_string[:len(tag_string)-1]
element[3] = tag_string
# go on with children
if not subtree.is_terminal():
for clade in subtree.clades:
parsimony_final(clade, nodelist)
return