def makePathGridlinesGroup(self) -> G:
size = self.cn_doc.max_vhelix_length
_BW = self._base_width
_BH = self._base_height
g = G()
g.setAttribute('id', "GridLines")
for i in range(len(self.cn_doc.vh_order)):
id_num = self.cn_doc.vh_order[i]
x = self.PATH_X_PADDING + self._path_radius_scaled*3
y = self.PATH_Y_PADDING + self._path_vh_margin*i
h_lines = " ".join("M %s,%s h %s" % (x, y-_BH+j*_BH, _BW*size) for j in range(3))
v_lines = " ".join("M %s,%s v %s" % (x+j*_BW, y-_BH, _BH*2) for j in range(int(size)+1))
p = Path(h_lines + " " + v_lines)
grid_style = 'fill:none; stroke:#666666; stroke-width:0.25'
p.set_style(grid_style)
p.setAttribute('id', "grid_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(p)
return g
def makePathOligosGroup(self) -> G:
id_coords = self.mapIdnumsToYcoords()
oligo_list = self.cn_doc.getOligoList()
_BW = self._base_width
_BH = self._base_height
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3 + _BW/2
g = G()
g.setAttribute('id', "Oligos")
i = 0
for color, is_circular, strands in oligo_list:
prev_id, prev5, prev3, prevX, prevY = None, None, None, 0, 0
path_lines = []
if is_circular:
strands.append(strands[0])
for id_num, idx5, idx3, isfwd, _ in strands:
x = _pX + idx5*_BW
if idx5 < idx3: # top strand
y = id_coords[id_num] - _BH/2
else:
y = id_coords[id_num] + _BH/2
dx = (idx3-idx5)*_BW
if prev_id is not None and id_num != prev_id:
# c dx1 dy1, dx2 dy2, dx dy
if isfwd:
x1 = x + abs(y-prevY)*0.03
else:
x1 = x - abs(y-prevY)*0.03
y1 = (y+prevY)/2
path_lines.append("Q %s %s, %s %s" % (x1, y1, x, y))
path_lines.append("h %s" % dx)
else:
path_lines.append("M %s, %s h %s" % (x, y, dx))
prev_id, prev5, prev3, prevX, prevY = id_num, idx5, idx3, x, y
p = Path(" ".join(path_lines))
oligo_style = 'fill:none; stroke:%s; stroke-width:2' % color
p.set_style(oligo_style)
p.setAttribute('id', "oligo_%s" % i)
p.setAttribute("stroke-linejoin", "round")
i += 1
g.addElement(p)
return g