"""

@return: the body of a form

"""

# define the tree and alignment strings

tree_string = '(((Human:0.1, Chimpanzee:0.2)to-chimp:0.8, Gorilla:0.3)to-gorilla:0.7, Orangutan:0.4, Gibbon:0.5)all;'

tree = Newick.parse(tree_string, Newick.NewickTree)

formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)

alignment_string = Fasta.brown_example_alignment.strip()

# define the form objects

form_objects = [

Form.MultiLine('tree', 'newick tree', formatted_tree_string),

Form.MultiLine('fasta', 'fasta alignment', alignment_string)]

# get the tree

tree = Newick.parse(fs.tree, Newick.NewickTree)

tree.assert_valid()

# get the alignment

try:

alignment = Fasta.Alignment(fs.fasta.splitlines())

alignment.force_nucleotide()

except Fasta.AlignmentError as e:

raise HandlingError(e)

# define the jukes cantor rate matrix

dictionary_rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix()

ordered_states = list('ACGT')

row_major_rate_matrix = MatrixUtil.dict_to_row_major(

dictionary_rate_matrix, ordered_states, ordered_states)

rate_matrix_object = RateMatrix.RateMatrix(

row_major_rate_matrix, ordered_states)

# simulate the ancestral alignment

try:

alignment = PhyLikelihood.simulate_ancestral_alignment(

tree, alignment, rate_matrix_object)

except PhyLikelihood.SimulationError as e:

raise HandlingError(e)

# get the alignment string using an ordering defined by the tree

arr = []

for node in tree.preorder():

arr.append(alignment.get_fasta_sequence(node.name))

# return the response