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render_rna_flip.py
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import sys
import svg
import re
import random
import math
class RNATreeNode:
def __init__(self):
self.children_ = []
self.is_pair_ = False
self.index_a_ = -1
self.index_b_ = -1
self.x_ = 0
self.y_ = 0
self.go_x_ = 0
self.go_y_ = 0
def get_pairmap_from_secstruct(secstruct):
"""
generates dictionary containing pair mappings
args:
secstruct contains secondary structure string
returns:
dictionary with pair mappings
"""
pair_stack = []
end_stack = []
pairs_array = []
i_range = range(0,len(secstruct))
# initialize all values to -1, meaning no pair
for ii in i_range:
pairs_array.append(-1)
# assign pairs based on secstruct
for ii in i_range:
if(secstruct[ii] == "("):
pair_stack.append(ii)
elif(secstruct[ii] == ")"):
if not pair_stack:
end_stack.append(ii)
else:
index = pair_stack.pop()
pairs_array[index] = ii
pairs_array[ii] = index
if len(pair_stack) == len(end_stack):
n = len(pair_stack)
for ii in range(n):
pairs_array[pair_stack[ii]] = end_stack[-ii]
pairs_array[end_stack[-ii]] = pair_stack[ii]
else:
print "ERROR: pairing incorrect %s" % secstruct
return pairs_array
def add_nodes_recursive(bi_pairs, rootnode, start_index, end_index):
if(start_index > end_index) :
print ("Error occured while drawing RNA %d %d" % (start_index, end_index))
sys.exit(0)
if(bi_pairs[start_index] == end_index) :
newnode = RNATreeNode()
newnode.is_pair_ = True
newnode.index_a_ = start_index
newnode.index_b_ = end_index
add_nodes_recursive(bi_pairs, newnode, start_index+1, end_index-1)
else :
newnode = RNATreeNode()
jj = start_index
while jj <= end_index:
if(bi_pairs[jj] > jj) :
add_nodes_recursive(bi_pairs,newnode, jj, bi_pairs[jj])
jj = bi_pairs[jj] + 1
else :
newsubnode = RNATreeNode()
newsubnode.is_pair_ = False
newsubnode.index_a_ = jj
newnode.children_.append(newsubnode)
jj += 1
rootnode.children_.append(newnode)
def setup_coords_recursive(rootnode, parentnode, start_x, start_y, go_x, go_y, NODE_R, PRIMARY_SPACE, PAIR_SPACE):
cross_x = -go_y
cross_y = go_x
children_width = len(rootnode.children_) * NODE_R * 2
rootnode.go_x_ = go_x
rootnode.go_y_ = go_y
if(len(rootnode.children_) == 1) :
rootnode.x_ = start_x
rootnode.y_ = start_y
if(rootnode.children_[0].is_pair_):
setup_coords_recursive(rootnode.children_[0], rootnode, start_x + go_x * PRIMARY_SPACE, start_y - go_y * PRIMARY_SPACE, go_x, go_y, NODE_R, PRIMARY_SPACE, PAIR_SPACE)
elif(rootnode.children_[0].is_pair_ == False and rootnode.children_[0].index_a_ < 0):
setup_coords_recursive(rootnode.children_[0], rootnode, start_x, start_y, go_x, go_y, NODE_R, PRIMARY_SPACE, PAIR_SPACE)
else:
setup_coords_recursive(rootnode.children_[0], rootnode, start_x + go_x * PRIMARY_SPACE, start_y - go_y * PRIMARY_SPACE, go_x, go_y, NODE_R, PRIMARY_SPACE, PAIR_SPACE)
elif(len(rootnode.children_) > 1) :
npairs = 0
for ii in range(0, len(rootnode.children_)):
if(rootnode.children_[ii].is_pair_) :
npairs+=1
circle_length = (len(rootnode.children_) + 1) * PRIMARY_SPACE + (npairs + 1) * PAIR_SPACE
circle_radius = circle_length / (2 * math.pi)
length_walker = PAIR_SPACE / 2.0
if (parentnode == None) :
rootnode.x_ = go_x * circle_radius
rootnode.y_ = go_y * circle_radius
else :
rootnode.x_ = parentnode.x_ + go_x * circle_radius
rootnode.y_ = parentnode.y_ - go_y * circle_radius
for ii in range(0,len(rootnode.children_)):
length_walker += PRIMARY_SPACE
if(rootnode.children_[ii].is_pair_) :
length_walker += PAIR_SPACE / 2.0
rad_angle = length_walker/circle_length * 2 * math.pi - math.pi / 2.0
child_x = rootnode.x_ + math.cos(rad_angle) * cross_x * circle_radius + math.sin(rad_angle) * go_x * circle_radius
child_y = rootnode.y_ - math.cos(rad_angle) * cross_y * circle_radius - math.sin(rad_angle) * go_y * circle_radius
child_go_x = child_x - rootnode.x_
child_go_y = child_y - rootnode.y_
child_go_len = math.sqrt(child_go_x * child_go_x + child_go_y * child_go_y)
setup_coords_recursive(rootnode.children_[ii], rootnode, child_x, child_y, child_go_x / child_go_len, -child_go_y / child_go_len, NODE_R, PRIMARY_SPACE, PAIR_SPACE)
if(rootnode.children_[ii].is_pair_) :
length_walker += PAIR_SPACE / 2.0
else :
rootnode.x_ = start_x
rootnode.y_ = start_y
def get_coords_recursive(rootnode, xarray, yarray, PRIMARY_SPACE, PAIR_SPACE):
if(rootnode.is_pair_) :
cross_x = -rootnode.go_y_
cross_y = rootnode.go_x_
xarray[rootnode.index_a_] = rootnode.x_ + cross_x * PAIR_SPACE/2.0
xarray[rootnode.index_b_] = rootnode.x_ - cross_x * PAIR_SPACE/2.0
yarray[rootnode.index_a_] = rootnode.y_ - cross_y * PAIR_SPACE/2.0
yarray[rootnode.index_b_] = rootnode.y_ + cross_y * PAIR_SPACE/2.0
elif(rootnode.index_a_ >= 0) :
xarray[rootnode.index_a_] = rootnode.x_
yarray[rootnode.index_a_] = rootnode.y_
for ii in range(0, len(rootnode.children_)):
get_coords_recursive(rootnode.children_[ii], xarray, yarray, PRIMARY_SPACE, PAIR_SPACE)
class RNARenderer:
def __init__(self):
self.root_ = None
self.xarray_ = None
self.yarray_ = None
self.size_ = None
def setup_tree(self, secstruct, NODE_R,PRIMARY_SPACE, PAIR_SPACE):
dangling_start = 0
dangling_end = 0
bi_pairs = get_pairmap_from_secstruct(secstruct)
self.NODE_R = NODE_R
self.root_ = None
for ii in range(0,len(bi_pairs)):
if bi_pairs[ii] < 0:
dangling_start+=1
else:
break
for ii in (len(bi_pairs)-1,-1, -1) :
if(bi_pairs[ii] < 0):
dangling_end+=1
else:
break
self.root_ = RNATreeNode()
#for jj in range(0,len(bi_pairs)):
jj = 0
while (jj < len(bi_pairs)):
if (bi_pairs[jj] > jj) :
add_nodes_recursive(bi_pairs,self.root_, jj, bi_pairs[jj])
jj = bi_pairs[jj] + 1
else:
newsubnode = RNATreeNode()
newsubnode.is_pair_ = False
newsubnode.index_a_ = jj
self.root_.children_.append(newsubnode)
jj += 1
xarray = []
yarray = []
for ii in range(0,len(secstruct)):
xarray.append(0.0)
yarray.append(0.0)
self.setup_coords(NODE_R,PRIMARY_SPACE,PAIR_SPACE)
self.get_coords(xarray,yarray,PRIMARY_SPACE,PAIR_SPACE)
min_x = xarray[0] - NODE_R
min_y = yarray[0] - NODE_R
max_x = xarray[0] + NODE_R
max_y = xarray[0] + NODE_R
for x in xarray:
if x - NODE_R < min_x:
min_x = x - NODE_R
if x + NODE_R > max_x:
max_x = x + NODE_R
for y in yarray:
if y - NODE_R < min_y:
min_y = y - NODE_R
if y + NODE_R > max_y:
max_y = y + NODE_R
for ii in range(0,len(xarray)):
xarray[ii] -= min_x
yarray[ii] -= min_y
self.size_ = [max_x - min_x, max_y - min_y]
self.xarray_ = xarray
self.yarray_ = yarray
def get_size(self):
return self.size_
def draw(self,svgobj,offset_x,offset_y,colors, pairs, sequence, render_in_letter, line=False):
if self.xarray_ != None:
if line:
for ii in range(len(self.xarray_)-1):
if colors == None:
svgobj.line(self.xarray_[ii], self.yarray_[ii], self.xarray_[ii+1], self.yarray_[ii+1],
'black')
else:
svgobj.line(self.xarray_[ii], self.yarray_[ii], self.xarray_[ii+1], self.yarray_[ii+1],
colors[ii])
else:
if pairs:
for pair in pairs:
svgobj.line(offset_x + self.xarray_[pair['from']], offset_y + self.yarray_[pair['from']], offset_x + self.xarray_[pair['to']], offset_y + self.yarray_[pair['to']], pair['color'], self.NODE_R)
for ii in range(0,len(self.xarray_)):
if colors == None:
svgobj.circle(self.xarray_[ii] + offset_x,self.yarray_[ii] + offset_y, self.NODE_R, "#000000", "#000000")
else:
svgobj.circle(self.xarray_[ii] + offset_x,self.yarray_[ii] + offset_y, self.NODE_R, colors[ii], colors[ii])
if sequence and render_in_letter:
for ii in range(0,len(self.xarray_)):
text_size = self.NODE_R * 1.5
if colors[ii] == [0,0,0]:
color = "#FFFFFF"
else:
color = "#000000"
text_offset_x = -4.0
text_offset_y = (text_size)/2.0 - 1.0
svgobj.text(self.xarray_[ii] + offset_x + text_offset_x, self.yarray_[ii] + offset_y + text_offset_y, text_size, color, "center", sequence[ii])
def get_coords(self, xarray, yarray, PRIMARY_SPACE, PAIR_SPACE):
if(self.root_ != None) :
get_coords_recursive(self.root_, xarray, yarray, PRIMARY_SPACE, PAIR_SPACE)
else :
for ii in range(0,len(xarray)):
xarray[ii] = 0
yarray[ii] = ii * PRIMARY_SPACE
def setup_coords(self, NODE_R, PRIMARY_SPACE, PAIR_SPACE):
if self.root_ != None:
setup_coords_recursive(self.root_, None, 0, 0, 0, 1, NODE_R, PRIMARY_SPACE, PAIR_SPACE)