def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = '\n'.join(get_tikz_lines(fs))
tikzpicture = tikz.get_picture(tikz_body, 'auto')
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = "\n".join(get_tikz_lines(fs))
tikzpicture = tikz.get_picture(tikz_body, "auto")
return tikz.get_response(tikzpicture, fs.tikzformat, tikz.get_w_color_package_set(), tikz.get_w_color_preamble())
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = '\n'.join(get_tikz_lines(fs))
tikzpicture = tikz.get_picture(tikz_body, 'auto')
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = get_tikz_body(fs)
tikzpicture = tikz.get_picture(tikz_body, "auto")
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = get_tikzpicture_body(fs.ncurves, fs.nsegs, fs.morph)
tikzpicture = tikz.get_picture(tikz_body, 'auto')
return tikz.get_response(
tikzpicture, fs.tikzformat,
tikz.get_w_color_package_set(), tikz.get_w_color_preamble())
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = get_tikz_body(fs)
tikzpicture = tikz.get_picture(tikz_body, 'auto')
tikzlibraries = ['decorations.pathreplacing']
return tikz.get_response(
tikzpicture, fs.tikzformat, tikzlibraries=tikzlibraries)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = get_tikz_body(fs)
tikzpicture = tikz.get_picture(tikz_body, 'auto')
tikzlibraries = ['decorations.pathreplacing']
return tikz.get_response(tikzpicture,
fs.tikzformat,
tikzlibraries=tikzlibraries)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body_lines = TreeProjection.get_tikz_lines(fs.tree,
fs.eigenvector_index,
fs.yaw, fs.pitch)
tikz_body = '\n'.join(tikz_body_lines)
options = {'x': '1em', 'y': '1em', 'inner sep': '0pt'}
tikzpicture = tikz.get_picture(tikz_body, **options)
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = "\n".join(get_tikz_lines())
tikzpicture = tikz.get_picture(tikz_body, "auto")
packages = ["color"]
preamble_lines = []
preamble_lines.append(tikz.get_w_color_preamble())
preamble_lines.extend(get_tikz_style_definitions())
preamble = "\n".join(preamble_lines)
return tikz.get_response(tikzpicture, fs.tikzformat, packages, preamble)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body = '\n'.join(get_tikz_lines())
tikzpicture = tikz.get_picture(tikz_body, 'auto')
packages = ['color']
preamble_lines = []
preamble_lines.append(tikz.get_w_color_preamble())
preamble_lines.extend(get_tikz_style_definitions())
preamble = '\n'.join(preamble_lines)
return tikz.get_response(tikzpicture, fs.tikzformat, packages, preamble)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
tikz_body_lines = TreeProjection.get_tikz_lines(
fs.tree, fs.eigenvector_index, fs.yaw, fs.pitch)
tikz_body = '\n'.join(tikz_body_lines)
options = {
'x' : '1em',
'y' : '1em',
'inner sep': '0pt'}
tikzpicture = tikz.get_picture(tikz_body, **options)
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
T, B, N = FtreeIO.newick_to_TBN(fs.tree_string)
# sanitize taxon labels if requested
if fs.sanitization:
for v in N:
N[v] = latexutil.sanitize(N[v])
# scale branch lengths so the diameter is 1
diameter = np.max(Ftree.TB_to_D(T, B, Ftree.T_to_leaves(T)))
# scale the branch lengths
for u_edge in T:
B[u_edge] /= diameter
info = FigureInfo(T, B, N, fs.label_mode)
# get the texts
tikz_bodies = [
info.get_tikz_tree(fs.tree_layout),
info.get_tikz_MDS_full(),
info.get_tikz_MDS_partial(),
info.get_tikz_MDS_harmonic(),
]
tikz_pictures = []
for b in tikz_bodies:
tikzpicture = tikz.get_picture(b, 'auto', scale=fs.scaling_factor)
tikz_pictures.append(tikzpicture)
figure_body = '\n'.join([
'\\subfloat[]{',
tikz_pictures[0],
'}',
'\\subfloat[]{',
tikz_pictures[1],
'} \\\\',
'\\subfloat[]{',
tikz_pictures[2],
'}',
'\\subfloat[]{',
tikz_pictures[3],
'}',
])
packages = ['tikz', 'subfig']
preamble = ''
figure_caption = None
figure_label = None
return latexutil.get_centered_figure_response(
figure_body, fs.latexformat, figure_caption, figure_label,
packages, preamble)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
# decide which hardcoded tree to use
if fs.six_leaves:
layout = SixLeafLayout()
elif fs.seven_leaves:
layout = SevenLeafLayout()
# decide which subtrees to show
show_full_tree = False
show_pruned_trees = False
if fs.full_tree_only:
show_full_tree = True
if fs.pruned_trees_only:
show_pruned_trees = True
if fs.all_trees:
show_full_tree = True
show_pruned_trees = True
# get the texts
tikz_body = layout.get_tikz_contents(show_full_tree, show_pruned_trees)
tikzpicture = tikz.get_picture(tikz_body, 'auto', scale=fs.scaling_factor)
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_response_content(fs):
"""
@param fs: a FieldStorage object containing the cgi arguments
@return: the response
"""
# decide which hardcoded tree to use
if fs.six_leaves:
layout = SixLeafLayout()
elif fs.seven_leaves:
layout = SevenLeafLayout()
# decide which subtrees to show
show_full_tree = False
show_pruned_trees = False
if fs.full_tree_only:
show_full_tree = True
if fs.pruned_trees_only:
show_pruned_trees = True
if fs.all_trees:
show_full_tree = True
show_pruned_trees = True
# get the texts
tikz_body = layout.get_tikz_contents(show_full_tree, show_pruned_trees)
tikzpicture = tikz.get_picture(tikz_body, 'auto', scale=fs.scaling_factor)
return tikz.get_response(tikzpicture, fs.tikzformat)
def get_tikz_text(newick, scaling_factor):
options = {'inner sep': '0pt', 'scale': scaling_factor}
tikz_body = '\n'.join(get_tikz_lines(newick))
return tikz.get_picture(tikz_body, **options)
def get_tikz_text(tikz_body):
return tikz.get_picture(tikz_body, scale='0.8')
def get_tikz_text(newick, scaling_factor):
options = {"inner sep": "0pt", "scale": scaling_factor}
tikz_body = "\n".join(get_tikz_lines(newick))
return tikz.get_picture(tikz_body, **options)
def get_tikz_text(tikz_body):
return tikz.get_picture(tikz_body, scale='0.8')
