def save_node_data(t, d, node_dict, debug=False):
# join items like (('A','B'),'C') into 'ABC'
left = ''.join(utils.list_elements(t[0]))
right = ''.join(utils.list_elements(t[1]))
new_node = ''.join(utils.list_elements(left+right))
d *= 0.5
node_dict[new_node] = { 'left':left, 'right':right, 'to_tips':d }
if debug:
print 'new node:'
print new_node, node_dict[new_node]
for i,child_node in enumerate([left,right]):
if not child_node in node_dict:
node_dict[child_node] = {'parent':new_node, 'up':d }
else:
up_d = d - node_dict[child_node]['to_tips']
node_dict[child_node].update({ 'parent':new_node, 'up':up_d} )
if debug:
print ['left node:','right_node:'][i]
print child_node, node_dict[child_node]
def average_distance(t, D, debug=False):
if debug:
print "average_distance",
print t
dL = list()
t0 = utils.list_elements(t[0])
t1 = utils.list_elements(t[1])
if debug:
print t0, t1,
for u in t0:
for v in t1:
d = D[(u, v)]
if debug:
print u+v, d,
dL.append(d)
average = sum(dL)*1.0/len(dL)
if debug:
print 'avg =', average
return average
def save_node_data(t,d,node_dict,debug=False):
# join items like (('A','B'),'C') into 'ABC'
left = ''.join(utils.list_elements(t[0]))
right = ''.join(utils.list_elements(t[1]))
new_node = ''.join(utils.list_elements(left+right))
d *= 0.5
node_dict[new_node] = { 'left':left, 'right':right, 'to_tips':d }
if debug:
print 'new node:'
print new_node, node_dict[new_node]
for i,child_node in enumerate([left,right]):
if not child_node in node_dict:
node_dict[child_node] = {'parent':new_node, 'up':d }
else:
up_d = d - node_dict[child_node]['to_tips']
node_dict[child_node].update({ 'parent':new_node, 'up':up_d} )
if debug:
print ['left node:','right_node:'][i]
print child_node, node_dict[child_node]
def average_distance(t,D,debug=False):
if debug:
print 'average_distance',
print t
dL = list()
t0 = utils.list_elements(t[0])
t1 = utils.list_elements(t[1])
if debug:
print t0, t1,
for u in t0:
for v in t1:
d = D[(u,v)]
if debug:
print u+v, d,
dL.append(d)
average = sum(dL)*1.0/len(dL)
if debug:
print 'avg =', average
return average
def collapse(L, node_in, debug=False):
node = ''.join(utils.list_elements(node_in))
if debug:
print 'node', node
print 'L'
node, utils.print_list(L, n=4)
rL = list()
for item in L:
left,right = item
if debug:
print 'left', left, 'right', right
for tip in left:
if tip in node:
left = node
for tip in right:
if tip in node:
right = node
if not left == right:
rL.append((left,right))
rL = sorted(list(set(rL)))
if debug:
print 'rL after set:'
utils.print_list(rL)
return rL
def collapse(L,node_in,debug=False):
node = ''.join(utils.list_elements(node_in))
if debug:
print 'node', node
print 'L'
node, utils.print_list(L, n=4)
rL = list()
for item in L:
left,right = item
if debug:
print 'left', left, 'right', right
for tip in left:
if tip in node:
left = node
for tip in right:
if tip in node:
right = node
if not left == right:
rL.append((left,right))
rL = sorted(list(set(rL)))
if debug:
print 'rL after set:'
utils.print_list(rL)
return rL
ct = colors.color_names
if ct.has_key(color):
color = ct[color]
for k,v in table.iteritems():
if ct.has_key(k):
table[ct[k]] = v;
for k,v in table.iteritems():
if ct.has_key(v):
table[k] = ct[v];
svg_in = svgparser.parse(sys.stdin)
elts = utils.list_elements(svg_in)
if dofill:
for e in elts:
if not 'get_fill' in dir(e): continue;
if not colorall and not e.get_fill():
continue
if table.has_key(e.get_fill()):
e.set_fill(table[e.get_fill()])
else:
e.set_fill(color)
if dolines:
for e in elts:
if not 'get_color' in dir(e): continue;
if (not colorall ) and ( not e.get_color()):
continue
table = dict([[e.strip() for e in re.split(re.compile('\s+'), l)]
for l in fopen.readlines()])
ct = colors.color_names
if ct.has_key(color):
color = ct[color]
for k, v in table.iteritems():
if ct.has_key(k):
table[ct[k]] = v
for k, v in table.iteritems():
if ct.has_key(v):
table[k] = ct[v]
svg_in = svgparser.parse(sys.stdin)
elts = utils.list_elements(svg_in)
if dofill:
for e in elts:
if not 'get_fill' in dir(e): continue
if not colorall and not e.get_fill():
continue
if table.has_key(e.get_fill()):
e.set_fill(table[e.get_fill()])
else:
e.set_fill(color)
if dolines:
for e in elts:
if not 'get_color' in dir(e): continue
if (not colorall) and (not e.get_color()):
continue