def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
tree.add_branch_lengths()
if tree.has_negative_branch_lengths():
msg_a = 'calculating weights for a tree '
msg_b = 'with negative branch lengths is not implemented'
raise HandlingError(msg_a + msg_b)
# get the selected names
selection = Util.get_stripped_lines(fs.selection.splitlines())
selected_name_set = set(selection)
possible_name_set = set(node.get_name() for node in tree.gen_tips())
extra_names = selected_name_set - possible_name_set
if extra_names:
msg_a = 'the following selected names are not valid tips: '
msg_b = str(tuple(extra_names))
raise HandlingError(msg_a + msg_b)
# prune the tree
for name in set(node.name for node in tree.gen_tips()) - set(selection):
try:
node = tree.get_unique_node(name)
except NewickSearchError as e:
raise HandlingError(e)
tree.prune(node)
# get the weights
if fs.stone:
name_weight_pairs = LeafWeights.get_stone_weights(tree)
elif fs.thompson:
name_weight_pairs = LeafWeights.get_thompson_weights(tree)
# report the weights
lines = ['%s: %f' % pair for pair in name_weight_pairs]
return '\n'.join(lines) + '\n'
def get_response_content(fs):
# get the tree
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
tree.add_branch_lengths()
if tree.has_negative_branch_lengths():
msg_a = 'calculating weights for a tree '
msg_b = 'with negative branch lengths is not implemented'
raise HandlingError(msg_a + msg_b)
# get the selected names
selection = Util.get_stripped_lines(fs.selection.splitlines())
selected_name_set = set(selection)
possible_name_set = set(node.get_name() for node in tree.gen_tips())
extra_names = selected_name_set - possible_name_set
if extra_names:
msg_a = 'the following selected names are not valid tips: '
msg_b = str(tuple(extra_names))
raise HandlingError(msg_a + msg_b)
# prune the tree
for name in set(node.name for node in tree.gen_tips()) - set(selection):
try:
node = tree.get_unique_node(name)
except NewickSearchError as e:
raise HandlingError(e)
tree.prune(node)
# get the weights
if fs.stone:
name_weight_pairs = LeafWeights.get_stone_weights(tree)
elif fs.thompson:
name_weight_pairs = LeafWeights.get_thompson_weights(tree)
# report the weights
lines = ['%s: %f' % pair for pair in name_weight_pairs]
return '\n'.join(lines) + '\n'
def get_response_content(fs):
tree = Newick.parse(fs.tree, Newick.NewickTree)
tree.assert_valid()
tree.add_branch_lengths()
if tree.has_negative_branch_lengths():
msg_a = 'calculating weights for a tree '
msg_b = 'with negative branch lengths is not implemented'
raise HandlingError(msg_a + msg_b)
if fs.stone:
name_weight_pairs = LeafWeights.get_stone_weights(tree)
elif fs.thompson:
name_weight_pairs = LeafWeights.get_thompson_weights(tree)
lines = ['%s: %f' % pair for pair in name_weight_pairs]
return '\n'.join(lines) + '\n'
