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 """ # 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