def get_form():
"""
@return: the body of a form
"""
# define the default tree lines
default_tree_lines = [
'(((a:0.05, b:0.05):0.15, c:0.2):0.8, x:1.0, (((m:0.05, n:0.05):0.15, p:0.2):0.8, y:1.0):1.0);',
'(a:1.062, c:0.190, (d:1.080, b:2.30):2.112);',
'((d:0.083, b:0.614):0.150, e:0.581, (c:1.290, a:0.359):1.070);',
'((b:1.749, d:0.523):0.107, e:1.703, (a:0.746, c:0.070):4.025);'
]
# define the list of form objects
form_objects = [
Form.MultiLine('trees', 'newick trees (one tree per line)',
'\n'.join(default_tree_lines)),
Form.Float('epsilon', 'non-negligible eigenvalue', '1e-9'),
Form.CheckGroup('options', 'show these tree sets', [
CheckItem('show_all', 'all reconstructed trees', True),
CheckItem('show_incomplete',
'incompletely resolved reconstructed trees', True),
CheckItem('show_conflicting', 'conflicting reconstructed trees',
True),
CheckItem('show_negligible',
'trees with potentially informative but small loadings',
True)
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree = NewickIO.parse(g_default_string, FelTree.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.RadioGroup('matrix', 'nodes used for the distance matrix', [
RadioItem('standard', 'tips only', True),
RadioItem('augmented', 'all nodes'),
RadioItem('named', 'all named nodes')
]),
Form.CheckGroup('output_options', 'output options', [
CheckItem('show_split', 'exact criterion partition', True),
CheckItem('show_value', 'exact criterion value', True),
CheckItem('show_value_minus_trace',
'exact criterion value minus trace', True),
CheckItem('show_fiedler_split', 'show the spectral sign partition',
True),
CheckItem('show_fiedler_eigenvector',
'show the eigenvector of interest', True),
CheckItem('show_labels', 'ordered labels', True),
CheckItem('show_distance_matrix', 'distance matrix', True),
CheckItem('show_M_matrix', 'M matrix', True)
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree = get_default_original_tree()
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree', 'original tree with branch lengths',
formatted_tree_string),
Form.Integer('iterations', 'reconstruct this many trees', 10, low=1),
Form.Integer('length', 'use sequences that are this long', 100, low=2),
Form.RadioGroup('criterion', 'bipartition function', [
RadioItem('exact', 'exact criterion'),
RadioItem('sign', 'spectral sign approximation', True),
RadioItem('threshold', 'spectral threshold approximation'),
RadioItem('nj', 'neighbor joining criterion'),
RadioItem('random', 'random bipartition')
]),
Form.RadioGroup('recourse', 'recourse for degenerate partitions', [
RadioItem('njrecourse', 'neighbor joining', True),
RadioItem('halvingrecourse', 'leaf stem length halving')
]),
Form.CheckGroup(
'output_options', 'extra output option',
[CheckItem('showtrees', 'show reconstructed tree topologies')])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
# define the default tree string and ordered tip labels
tree_string = '(a:1, (b:2, d:5):1, c:4);'
tree = NewickIO.parse(tree_string, FelTree.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
labels = list(sorted(tip.name for tip in tree.gen_tips()))
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('inlabels', 'ordered labels', '\n'.join(labels)),
Form.Float('strength', 'perturbation strength', 0.1, low_inclusive=0),
Form.CheckGroup('options', 'output options', [
CheckItem('perturbed', 'a perturbed distance matrix', True),
CheckItem('distance', 'the original distance matrix'),
CheckItem('outlabels', 'ordered labels')
])
]
return form_objects
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.RadioGroup('leaf_options', 'number of leaves', [
RadioItem('six_leaves', '6', True),
RadioItem('seven_leaves', '7')]),
Form.CheckGroup('requirements', 'requirements', [
CheckItem('invalid_dendrogram',
'the topology of the naive dendrogram must be incorrect',
True),
CheckItem('informative_children',
'splits of the child trees must be informative',
True),
CheckItem('force_difference',
'full graph split must differ from Schur graph split',
False),
CheckItem('informative_full_split',
'full graph split must be informative', False)]),
Form.CheckGroup('sampling_options', 'branch length sampling', [
CheckItem('allow_integers',
'allow single digit integer branch lengths', True),
CheckItem('allow_reciprocals',
'allow reciprocal single digit integer branch lengths',
False)])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
L = np.array([
[1.0, 0.0, 0.0, 0.0, -1.0, 0.0],
[0.0, 1.0, 0.0, 0.0, -1.0, 0.0],
[0.0, 0.0, 1.0, 0.0, 0.0, -1.0],
[0.0, 0.0, 0.0, 1.0, 0.0, -1.0],
[-1.0, -1.0, 0.0, 0.0, 3.0, -1.0],
[0.0, 0.0, -1.0, -1.0, -1.0, 3.0]])
# define the form objects
form_objects = [
Form.Matrix('laplacian', 'combinatorial Laplacian matrix',
L, MatrixUtil.assert_symmetric),
Form.RadioGroup('normalization', 'use this matrix', [
RadioItem('combinatorial', 'combinatorial Laplacian', True),
RadioItem('normalized', 'normalized Laplacian')]),
Form.CheckGroup('options', 'output options', [
CheckItem('show_magnitudes',
'show the distance of each point from the origin'),
CheckItem('show_contrasts',
'show the contrast loading matrix')])]
return form_objects
def get_form():
"""
@return: the body of a form
"""
form_objects = [
RadioGroup('distance_options', 'recursive matrix construction', [
RadioItem('like_pruning',
'go through the Laplacian, like Felsenstein pruning',
True),
RadioItem('like_nj',
'directly use distances, like neighbor joining')
]),
CheckGroup('format_options', 'options', [
CheckItem('supplementary', 'download the supplementary data', True)
])
]
return form_objects