def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('ncols',
'sample this many columns',
100,
low=1,
high=1000),
Form.Matrix('matrix_a', 'first nucleotide rate matrix', g_nt_matrix_a),
Form.Float('weight_a',
'first mixture weight',
g_weight_a,
low_inclusive=0),
Form.Matrix('matrix_b', 'second nucleotide rate matrix',
g_nt_matrix_b),
Form.Float('weight_b',
'second mixture weight',
g_weight_b,
low_inclusive=0),
Form.Matrix('matrix_c', 'third nucleotide rate matrix', g_nt_matrix_c),
Form.Float('weight_c',
'third mixture weight',
g_weight_c,
low_inclusive=0)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default tip data lines
default_tip_data_lines = [
'a : A',
'b : A',
'c : C',
'd : T',
'e : T',
'f : T']
# define the default rate matrix lines
R = np.array([
[-1, 1/3.0, 1/3.0, 1/3.0],
[1/3.0, -1, 1/3.0, 1/3.0],
[1/3.0, 1/3.0, -1, 1/3.0],
[1/3.0, 1/3.0, 1/3.0, -1]])
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('column', 'tip data',
'\n'.join(default_tip_data_lines)),
Form.Matrix('matrix', 'rate matrix',
R, MatrixUtil.assert_rate_matrix),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.IntegerInterval(
'first_index', 'last_index',
'eigenfunction index range (1 means Fiedler)',
0, 12, low=0),
Form.CheckGroup('check_options', 'output options', [
Form.CheckItem('reflect_trees',
'reflect trees across the vertical axis'),
Form.CheckItem('show_subfigure_labels',
'show subfigure labels', True),
Form.CheckItem('show_vertex_labels',
'show vertex labels')]),
Form.Float('width', 'width (centimeters)',
12, low_inclusive=1, high_exclusive=1000),
Form.Float('height', 'height (centimeters)',
8, low_inclusive=1, high_exclusive=1000),
Form.Float('inner_margin', 'inner margin (centimeters)',
0.25, low_inclusive=0, high_exclusive=1000),
Form.RadioGroup('radio_options', 'tree layout options', [
Form.RadioItem('equal_daylight_layout',
'equal daylight layout', True),
Form.RadioItem('equal_arc_layout',
'equal arc layout')]),
Form.TikzFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = Newick.brown_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default alignment string
default_alignment_string = Fasta.brown_example_alignment.strip()
# define the default nucleotide distribution weights
default_nt_lines = [
'A : 1',
'C : 1',
'G : 1',
'T : 1']
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
default_alignment_string),
Form.MultiLine('weights', 'nucleotide weights',
'\n'.join(default_nt_lines)),
Form.Float('kappa', 'transition transversion rate ratio',
2, low_inclusive=0)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# format the default tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# make a real distance matrix
D_s = [line.split() for line in g_default_D_lines]
D_default = np.array([[float(x) for x in row] for row in D_s])
# define the form objects
form_objects = [
Form.MultiLine('test_tree', 'harmonic extension tree',
formatted_tree_string),
Form.Matrix('D', 'leaf distance matrix', D_default,
MatrixUtil.assert_symmetric),
Form.MultiLine('names', 'ordered leaf names',
'\n'.join(g_default_leaf_names)),
Form.Float('scale',
'scale the image of the tree by this factor',
200.0,
low_exclusive=0.0),
Form.ImageFormat()
]
return form_objects
def process_tree(tree, tree_name, show_newick, show_art):
"""
@param tree: a FelTree to be split by each method
@param tree_name: a description of the tree
@param show_newick: an output option
@param show_art: an output option
@return: a multi-line output string
"""
out = StringIO()
# be verbose if requested
if show_newick:
print >> out, 'newick representation of %s:' % tree_name
print >> out, Newick.get_narrow_newick_string(tree, 80)
if show_art:
print >> out, 'ascii art representation of %s:' % tree_name
print >> out, get_art(tree)
# cut the tree using each method
ordered_names = list(sorted(node.get_name() for node in tree.gen_tips()))
n = len(ordered_names)
D = tree.get_distance_matrix(ordered_names)
splitters = (Clustering.StoneExactDMS(), Clustering.StoneSpectralSignDMS())
splitter_names = ('the +1 / -1 split criterion', 'the fiedler criterion')
for splitter, splitter_name in zip(splitters, splitter_names):
small_index_selection = splitter.get_selection(D)
big_index_selection = set(range(n)) - small_index_selection
names_a = list(sorted(ordered_names[i] for i in small_index_selection))
names_b = list(sorted(ordered_names[i] for i in big_index_selection))
print >> out, 'split inferred by %s:' % splitter_name
print >> out, '{{%s}, {%s}}' % (', '.join(names_a), ', '.join(names_b))
# return the string
return out.getvalue()
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.IntegerInterval('first_index',
'last_index',
'eigenfunction index range (1 means Fiedler)',
0,
12,
low=0),
Form.CheckGroup('check_options', 'output options', [
Form.CheckItem('reflect_trees', 'reflect trees', True),
Form.CheckItem('draw_background', 'draw background', True),
Form.CheckItem('draw_labels', 'draw labels', True)
]),
Form.Integer('width', 'physical width', 880, low=10, high=1000),
Form.Integer('height', 'physical height', 680, low=10, high=1000),
Form.Integer('inner_margin', 'inner margin', 10, low=0, high=1000),
Form.Integer('outer_margin', 'outer margin', 0, low=0, high=1000),
Form.ImageFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree',
formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
g_sample_alignment_string.strip()),
Form.Matrix('matrix_a', 'first nucleotide rate matrix',
g_nt_matrix_a),
Form.Float('weight_a', 'first mixture weight',
1, low_inclusive=0),
Form.Matrix('matrix_b', 'second nucleotide rate matrix',
g_nt_matrix_b),
Form.Float('weight_b', 'second mixture weight',
2, low_inclusive=0),
Form.Matrix('matrix_c', 'third nucleotide rate matrix',
g_nt_matrix_c),
Form.Float('weight_c', 'third mixture weight',
3, low_inclusive=0)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.IntegerInterval(
'first_index', 'last_index',
'eigenfunction index range (1 means Fiedler)',
0, 12, low=0),
Form.CheckGroup('check_options', 'output options', [
Form.CheckItem('reflect_trees', 'reflect trees', True),
Form.CheckItem('draw_background', 'draw background', True),
Form.CheckItem('draw_labels', 'draw labels', True)]),
Form.Integer('width', 'physical width', 880, low=10, high=1000),
Form.Integer('height', 'physical height', 680, low=10, high=1000),
Form.Integer('inner_margin', 'inner margin', 10, low=0, high=1000),
Form.Integer('outer_margin', 'outer margin', 0, low=0, high=1000),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# reformat the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree',
formatted_tree_string),
Form.Float('scaling_factor',
'figure scaling factor', 3.0, low_exclusive=0),
Form.RadioGroup('label_mode', 'label mode', [
Form.RadioItem('label_mode_suppressed',
'suppress all vertex labels', True),
Form.RadioItem('label_mode_leaf_only',
'draw leaf names'),
Form.RadioItem('label_mode_show',
'draw arbitrary short names at all vertices')]),
Form.RadioGroup('sanitization_options',
'taxon label sanitization options', [
Form.RadioItem('no_sanitization',
'allow TikZ to interpret the taxon labels', True),
Form.RadioItem('sanitization',
'attempt an ad-hoc sanitization of taxon labels')]),
Form.RadioGroup('tree_layout', 'tree layout options', [
Form.RadioItem('equal_arc', 'equal arc layout', True),
Form.RadioItem('equal_daylight', 'equal daylight layout')]),
Form.LatexFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = Newick.brown_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default alignment string
default_alignment_string = Fasta.brown_example_alignment.strip()
# define the default nucleotide distribution weights
default_nt_lines = ['A : 1', 'C : 1', 'G : 1', 'T : 1']
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
default_alignment_string),
Form.MultiLine('weights', 'nucleotide weights',
'\n'.join(default_nt_lines)),
Form.Float('kappa',
'transition transversion rate ratio',
2,
low_inclusive=0)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('ncols', 'sample this many nucleotide columns',
100, low=1, high=1000),
Form.MultiLine('frequency_a', 'first component frequencies',
get_frequency_string(0)),
Form.Float('kappa_a', 'first component kappa',
get_kappa(0), low_inclusive=0),
Form.Float('weight_a', 'first component weight',
get_weight(0), low_inclusive=0),
Form.MultiLine('frequency_b', 'second component frequencies',
get_frequency_string(1)),
Form.Float('kappa_b', 'second component kappa',
get_kappa(1), low_inclusive=0),
Form.Float('weight_b', 'second component weight',
get_weight(1), low_inclusive=0),
Form.RadioGroup('fmt', 'output format options', [
Form.RadioItem('fasta', 'fasta'),
Form.RadioItem('nex', 'nexus', True)])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default newick tree
tree_string = '((((a:.05, b:.05)L1:.15, c:.2)L2:.8, x:1)L3:.5, (((m:.05, n:.05)R1:.15, p:.2)R2:.8, y:1)R3:.5)root;'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default rate matrix and its ordered states
R = np.array([[-.3, .1, .1, .1], [.1, -.3, .1, .1], [.1, .1, -.3, .1],
[.1, .1, .1, -.3]])
ordered_states = list('ACGT')
# define the default leaf state assigments
leaf_assignment_lines = [
'a : A', 'b : A', 'c : A', 'x : A', 'm : C', 'n : C', 'p : C', 'y : C'
]
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree with branch lengths',
formatted_tree_string),
Form.Matrix('rate_matrix', 'rate matrix', R,
MatrixUtil.assert_rate_matrix),
Form.MultiLine('states', 'ordered states', '\n'.join(ordered_states)),
Form.MultiLine('assignments', 'leaf states',
'\n'.join(leaf_assignment_lines))
]
return form_objects
def process_tree(tree, tree_name, show_newick, show_art):
"""
@param tree: a FelTree to be split by each method
@param tree_name: a description of the tree
@param show_newick: an output option
@param show_art: an output option
@return: a multi-line output string
"""
out = StringIO()
# be verbose if requested
if show_newick:
print >> out, "newick representation of %s:" % tree_name
print >> out, Newick.get_narrow_newick_string(tree, 80)
if show_art:
print >> out, "ascii art representation of %s:" % tree_name
print >> out, get_art(tree)
# cut the tree using each method
ordered_names = list(sorted(node.get_name() for node in tree.gen_tips()))
n = len(ordered_names)
D = tree.get_distance_matrix(ordered_names)
splitters = (Clustering.StoneExactDMS(), Clustering.StoneSpectralSignDMS())
splitter_names = ("the +1 / -1 split criterion", "the fiedler criterion")
for splitter, splitter_name in zip(splitters, splitter_names):
small_index_selection = splitter.get_selection(D)
big_index_selection = set(range(n)) - small_index_selection
names_a = list(sorted(ordered_names[i] for i in small_index_selection))
names_b = list(sorted(ordered_names[i] for i in big_index_selection))
print >> out, "split inferred by %s:" % splitter_name
print >> out, "{{%s}, {%s}}" % (", ".join(names_a), ", ".join(names_b))
# return the string
return out.getvalue()
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('model', 'DNA frequency mixture model',
get_sample_xml_string().strip()),
Form.Integer('ncols',
'sample this many nucleotide columns',
200,
low=1,
high=1000),
Form.Integer('seed', 'random number seed', 314159, low=0),
Form.RadioGroup('format', 'output format', [
Form.RadioItem('fastaformat', 'fasta alignment'),
Form.RadioItem('nexusformat', 'nexus alignment', True)
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.IntegerInterval('first_index',
'last_index',
'eigenfunction index range (1 means Fiedler)',
0,
4,
low=0),
Form.CheckGroup('check_options', 'output options', [
Form.CheckItem('draw_background', 'draw background', True),
Form.CheckItem('draw_vertices', 'draw vertices'),
Form.CheckItem('draw_labels', 'draw labels', True)
]),
Form.ImageFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '((((a:5)a:5, (b:5)b:5)A:1.5)A:1.5, (((c:5)c:5, (d:5)d:5)B:1.5)B:1.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
def get_form():
"""
@return: the body of a form
"""
# define the newick string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# return the form objects
return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
def get_form():
"""
@return: the body of a form
"""
# format the default tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [Form.MultiLine('tree', 'tree', formatted_tree_string)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '((((a:5)a:5, (b:5)b:5)A:1.5)A:1.5, (((c:5)c:5, (d:5)d:5)B:1.5)B:1.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
return [Form.MultiLine('tree', 'newick tree', formatted_tree_string)]
def get_form():
"""
@return: the body of a form
"""
# format the default tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'tree', formatted_tree_string)]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# reformat the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree',
formatted_tree_string)]
return form_objects
def get_form():
"""
@return: a list of form objects
"""
# reformat the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree', formatted_tree_string)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# format the default tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'tree', formatted_tree_string),
Form.SingleLine('vertex',
'distinguished vertex of articulation', 'r')]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = stone_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.SingleLine('node', 'the name of the node to remove', 'a')]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Float('sf', 'scaling factor', 0.333333, low_exclusive=0)]
return form_objects
def get_form():
"""
@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)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Float('sf', 'scaling factor', 0.333333, low_exclusive=0)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree and alignment strings
tree_string = Newick.brown_example_tree
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)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('segments',
'minimum segment count', 200, low=1, high=10000)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string and the ordered labels
tree = Newick.parse(g_default_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
labels = list('xyabcmnp')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('order', 'sequence order', '\n'.join(labels)),
Form.Integer('length', 'sequence length', 60, low=2)]
return form_objects
def get_form():
"""
@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)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string and the ordered labels
tree = Newick.parse(g_default_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
labels = list('xyabcmnp')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('order', 'sequence order', '\n'.join(labels)),
Form.Integer('length', 'sequence length', 60, low=2)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip()),
Form.Integer('ncols', 'sample this many columns',
100, low=1, high=10000)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
g_sample_alignment_string.strip()),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip())]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Float('width', 'width (centimeters)',
12, low_inclusive=1, high_exclusive=1000),
Form.Float('height', 'height (centimeters)',
8, low_inclusive=1, high_exclusive=1000),
Form.TikzFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# get the form objects
form_objects = [
Form.MultiLine('tree', 'tree', formatted_tree_string),
Form.Integer('eigenvector_index',
'eigenvector index (1 is Fiedler)',
g_default_eigenvector_index, low=1),
Form.Float('yaw', 'yaw', g_default_yaw),
Form.Float('pitch', 'pitch', g_default_pitch),
Form.TikzFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree',
formatted_tree_string),
Form.MultiLine('model', 'Direct Protein mixture model',
DirectProtein.get_sample_xml_string().strip()),
Form.Integer('ncols', 'sample this many codon columns',
100, low=1, high=1000)]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('layout', 'tree layout options', [
Form.RadioItem('daylight', 'equal daylight layout', True),
Form.RadioItem('arc', 'equal arc layout'),
Form.RadioItem('curved', 'curved branch layout')]),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the newick string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('alignment', 'nucleotide alignment',
g_sample_alignment_string.strip()),
Form.MultiLine('model', 'Direct RNA mixture model',
DirectRna.get_sample_xml_string().strip())
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = LeafWeights.stone_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('method', 'weight calculation method', [
Form.RadioItem('stone', 'use the method of Stone and Sidow', True),
Form.RadioItem('thompson', 'use the Thompson et al.')
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('eig_idx1',
'first eigenfunction index (1 means Fiedler)', 1, low=0),
Form.Integer('eig_idx2',
'second eigenfunction index (1 means Fiedler)', 2, low=0),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('segments',
'minimum segment count',
200,
low=1,
high=10000)
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('layout', 'tree layout options', [
Form.RadioItem('daylight', 'equal daylight layout', True),
Form.RadioItem('arc', 'equal arc layout'),
Form.RadioItem('curved', 'curved branch layout')
]),
Form.ImageFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = g_ucsc_tree_string
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# default name selection
default_name_selection = ('human_hg18', 'chimp_panTro1', 'rabbit_oryCun1')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('selection', 'selected tip names',
'\n'.join(default_name_selection)),
Form.RadioGroup('method', 'weighting method', [
RadioItem('stone', 'use the method of Stone and Sidow', True),
RadioItem('thompson', 'use the method of Thompson et al.')])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree = Newick.parse(g_default_tree, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# get the form objects
form_objects = [
Form.MultiLine('tree', 'tree', formatted_tree_string),
Form.Integer('eigenvector_index',
'eigenvector index (1 is Fiedler)',
g_default_eigenvector_index,
low=1),
Form.Float('yaw', 'yaw', g_default_yaw),
Form.Float('pitch', 'pitch', g_default_pitch),
Form.TikzFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.Integer('ncols',
'sample this many nucleotide columns',
100,
low=1,
high=1000),
Form.MultiLine('frequency_a', 'first component frequencies',
get_frequency_string(0)),
Form.Float('kappa_a',
'first component kappa',
get_kappa(0),
low_inclusive=0),
Form.Float('weight_a',
'first component weight',
get_weight(0),
low_inclusive=0),
Form.MultiLine('frequency_b', 'second component frequencies',
get_frequency_string(1)),
Form.Float('kappa_b',
'second component kappa',
get_kappa(1),
low_inclusive=0),
Form.Float('weight_b',
'second component weight',
get_weight(1),
low_inclusive=0),
Form.RadioGroup('fmt', 'output format options', [
Form.RadioItem('fasta', 'fasta'),
Form.RadioItem('nex', 'nexus', True)
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = g_tree_string
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default tip data lines
default_tip_data_lines = [
'a : A', 'b : A', 'c : C', 'd : T', 'e : T', 'f : T'
]
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('column', 'tip data',
'\n'.join(default_tip_data_lines)),
Form.ImageFormat()
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the default color lines
default_color_lines = [
'A : ff0000',
'B : 00ff00',
'C : 0000ff']
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('coloration', 'branch colors',
'\n'.join(default_color_lines)),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.IntegerInterval(
'first_index', 'last_index',
'eigenfunction index range (1 means Fiedler)',
0, 4, low=0),
Form.CheckGroup('check_options', 'output options', [
Form.CheckItem('draw_background', 'draw background', True),
Form.CheckItem('draw_vertices', 'draw vertices'),
Form.CheckItem('draw_labels', 'draw labels', True)]),
Form.ImageFormat()]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('group1', 'output options', [
Form.RadioItem('choice1',
'a simple indented format', True),
Form.RadioItem('choice2',
'ascii art with branch lengths'),
Form.RadioItem('choice3',
'ascii art with topology only and less whitespace'),
Form.RadioItem('choice4',
'ascii art with topology only and more whitespace')])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = g_ucsc_tree_string
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# default name selection
default_name_selection = ('human_hg18', 'chimp_panTro1', 'rabbit_oryCun1')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('selection', 'selected tip names',
'\n'.join(default_name_selection)),
Form.RadioGroup('method', 'weighting method', [
RadioItem('stone', 'use the method of Stone and Sidow', True),
RadioItem('thompson', 'use the method of Thompson et al.')
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = "(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);"
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine("tree", "newick tree", formatted_tree_string),
Form.MultiLine("model", "DNA frequency mixture model", get_sample_xml_string().strip()),
Form.Integer("ncols", "sample this many nucleotide columns", 200, low=1, high=1000),
Form.Integer("seed", "random number seed", 314159, low=0),
Form.RadioGroup(
"format",
"output format",
[Form.RadioItem("fastaformat", "fasta alignment"), Form.RadioItem("nexusformat", "nexus alignment", True)],
),
]
return form_objects
