def makePathDefs(self) -> Defs:
"""
Creates Defs object for reusable `Insertion` and `Skip` elements.
"""
_BW, _BH = self._base_width, self._base_height
_hBW, _hBH = _BW/2, _BH/2
_67BW, _67BH = _BW/1.5, _BH/1.5
p = Path()
p.appendMoveToPath(_hBW, _hBH)
p.appendQuadraticCurveToPath(-_67BW, -_BH, 0, -_BH)
p.appendQuadraticCurveToPath(_67BW, 0, 0, _BH)
p.set_stroke_linecap("round")
g_insertion = G()
g_insertion.setAttribute('id', "insertion")
g_insertion.addElement(p)
d = 0.5 # small delta to compensate for round endcap
line1 = Line(d, d, _BW-d, _BH-d, style="stroke:#cc0000; stroke-width:2")
line2 = Line(_BW-d, d, d, _BH-d, style="stroke:#cc0000; stroke-width:2")
line1.set_stroke_linecap("round")
line2.set_stroke_linecap("round")
g_skip = G()
g_skip.setAttribute('id', "skip")
g_skip.addElement(line1)
g_skip.addElement(line2)
path_defs = Defs()
path_defs.addElement(g_insertion)
path_defs.addElement(g_skip)
return path_defs
def drawFrontFacePair(topCorners, bottomCorners, color):
pointList = []
pointList2 = []
output = G()
YZStyle1 = StyleBuilder()
#YZStyle1.setStroke('black')
#YZStyle1.setStrokeWidth(1.5)
YZStyle1.setFilling(color)
YZStyle1.setFillOpacity(0.75)
YZStyle2 = StyleBuilder()
YZStyle2.setStroke('black')
YZStyle2.setStrokeWidth(0.5)
YZStyle2.setFillOpacity(0.75)
YZStyle2.setFilling('#ffffff')
pointList.append(strPathStart(topCorners[1]))
pointList.append(strPathPoint(topCorners[2]))
pointList.append(strPathPoint(bottomCorners[2]))
pointList.append(strPathPoint(bottomCorners[1]))
svgCode1 = pGram(pointList)
pointList2.append(strPathStart(topCorners[0]))
pointList2.append(strPathPoint(topCorners[3]))
pointList2.append(strPathPoint(bottomCorners[3]))
pointList2.append(strPathPoint(bottomCorners[0]))
svgCode2 = pGram(pointList2)
frontFace = Path(svgCode1)
frontFace.set_style(YZStyle1.getStyle())
backFace = Path(svgCode2)
backFace.set_style(YZStyle2.getStyle())
output.addElement(backFace)
output.addElement(frontFace)
return output
def drawSideFacePair(topCorners, bottomCorners, color):
pointList = []
pointList2 = []
output = G()
XYStyle1 = StyleBuilder()
#XYStyle1.setStroke('black')
#XYStyle1.setStrokeWidth(1.5)
XYStyle1.setFilling(color)
#XYStyle1.setFillOpacity(0.8)
XYStyle2 = StyleBuilder()
XYStyle2.setStroke(color)
XYStyle2.setStrokeWidth(0.5)
XYStyle2.setFilling(color)
pointList.append(strPathStart(topCorners[2]))
pointList.append(strPathPoint(topCorners[3]))
pointList.append(strPathPoint(bottomCorners[3]))
pointList.append(strPathPoint(bottomCorners[2]))
svgCode1 = pGram(pointList)
pointList2.append(strPathStart(topCorners[0]))
pointList2.append(strPathPoint(topCorners[1]))
pointList2.append(strPathPoint(bottomCorners[1]))
pointList2.append(strPathPoint(bottomCorners[0]))
svgCode2 = pGram(pointList2)
rightFace = Path(svgCode1)
rightFace.set_style(XYStyle1.getStyle())
leftFace = Path(svgCode2)
leftFace.set_style(XYStyle2.getStyle())
output.addElement(leftFace)
output.addElement(rightFace)
return output
def _calc_clip_path(self, rect):
rx, ry, width, height = rect
if rx < 0:
width += rx
rx = 0
pathId = "path%d_%d_%d" % (rx, ry, width)
p = Path(pathData="M %d %d H %d V %d H %d" %
(rx, ry + height, rx + width, ry, rx))
return pathId, p
def draw_branch(svg, id, xs, ys, xe, ye):
svgPath = ["M%f,%f" % (xs, ys)]
svgPath += ["C%f,%f %f,%f %f,%f" % (xs, ye, xe, ys, xe, ye)]
ob = SvgPath(pathData=" ".join(svgPath), id=id)
ob.set_stroke_width(dc.branchThickness)
ob.set_stroke(dc.branchColor)
ob.set_fill("none")
svg.addElement(ob)
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
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