def get_form():
"""
@return: the body of a form
"""
tree = NewickIO.parse(
Contrasts.g_felsenstein_tree_string, FelTree.NewickTree)
ordered_labels = ('a', 'b', 'c', 'd', 'e')
C = Contrasts.get_contrast_matrix(tree, ordered_labels)
# define the form objects
form_objects = [
Form.Matrix('contrast_matrix', 'contrast matrix',
C, Contrasts.assert_contrast_matrix),
Form.MultiLine('labels', 'ordered labels',
'\n'.join(ordered_labels))]
return form_objects
def get_form():
"""
@return: the body of a form
"""
tree = NewickIO.parse(Contrasts.g_felsenstein_tree_string,
FelTree.NewickTree)
ordered_labels = ('a', 'b', 'c', 'd', 'e')
C = Contrasts.get_contrast_matrix(tree, ordered_labels)
# define the form objects
form_objects = [
Form.Matrix('contrast_matrix', 'contrast matrix', C,
Contrasts.assert_contrast_matrix),
Form.MultiLine('labels', 'ordered labels', '\n'.join(ordered_labels))
]
return form_objects
def get_response_content(fs):
# get the tree
tree = NewickIO.parse(fs.tree, FelTree.NewickTree)
# read the ordered labels
ordered_labels = Util.get_stripped_lines(fs.labels.splitlines())
# validate the input
observed_label_set = set(node.get_name() for node in tree.gen_tips())
if set(ordered_labels) != observed_label_set:
msg = 'the labels should match the labels of the leaves of the tree'
raise HandlingError(msg)
# get the matrix of pairwise distances among the tips
C = Contrasts.get_contrast_matrix(tree, ordered_labels)
# set elements with small absolute value to zero
C[abs(C) < fs.epsilon] = 0
# return the reponse
if fs.plain_format:
return MatrixUtil.m_to_string(C) + '\n'
elif fs.matlab_format:
return MatrixUtil.m_to_matlab_string(C) + '\n'
elif fs.r_format:
return MatrixUtil.m_to_R_string(C) + '\n'