def spacer_ticker(canvas, feature, cLen, Y0, nudge, offset, side):
"""Draw separator indicators."""
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
# calculate loop offset coordinates
loop_offZs = offset_coord(Zs, cLen, offset)
loop_offZe = offset_coord(Ze, cLen, offset)
# calculate nudge offset coordinates
offZs = nudge_coord(loop_offZs, nudge)
offZe = nudge_coord(loop_offZe, nudge)
xs, xe = offZs*u, offZe*u
# set Y axis coordinates
y0 = Y0-dop*3.5
if side == 'low':
yT1 = y0-h*4
else:
yT1 = y0+h*4
# draw
canvas.setLineWidth(2)
ttl = canvas.beginPath()
ttl.moveTo(xs,y0)
ttl.lineTo(xs,yT1)
ttl.lineTo(xe,yT1)
ttl.lineTo(xe,y0)
canvas.drawPath(ttl, stroke=1, fill=0)
ttl.close()
def ref_ticker(canvas, feature, cLen, Y0, nudge, offset):
"""Draw contig separators."""
# get contig name
name = feature.qualifiers.get('id')[0]
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
# calculate loop offset coordinates
loop_offZs = offset_coord(Zs, cLen, offset)
loop_offZe = offset_coord(Ze, cLen, offset)
# calculate nudge offset coordinates
offZs = nudge_coord(loop_offZs, nudge)
offZe = nudge_coord(loop_offZe, nudge)
xs, xe = offZs*u, offZe*u
xmid = (xe+xs)/2
# set Y axis coordinates
y0 = Y0+dop*3
# draw
canvas.setLineWidth(2)
ttl = canvas.beginPath()
ttl.moveTo(xs,y0+w)
ttl.lineTo(xs,y0+w+h*2)
ttl.lineTo(xe,y0+w+h*2)
ttl.lineTo(xe,y0+w)
canvas.drawPath(ttl, stroke=1, fill=0)
canvas.setFont(bFont, NfSize)
canvas.drawCentredString(xmid, y0+h*5, name)
canvas.setFont(rFont, NfSize)
ttl.close()
def orf_coords(feature, Y_map, cLen, nudge, offset):
"""Calculate CDS coordinates in drawing space."""
# evaluate what strand the ORF is on (determines direction of arrow)
cstrand = feature.strand
if cstrand is None:
cstrand = 1
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
featL = Ze - Zs
# calculate loop offset coordinates
loop_offZs = offset_coord(Zs, cLen, offset)
loop_offZe = offset_coord(Ze, cLen, offset)
# calculate nudge offset coordinates
offZs = nudge_coord(loop_offZs, nudge)
offZe = nudge_coord(loop_offZe, nudge)
# calculate X axis coordinates (expr of cstrand has changed)
if cstrand == -1 : # reverse orientation
xs,xe = offZe*u,offZs*u # start and end
xn = xe+minL*u # neck of arrow
else : # forward orientation
xs,xe = offZs*u,offZe*u # start and end
xn = xe-minL*u # neck of arrow
midLZ = ((offZs+offZe)/2)*u # middle of ORF for optional label
# evaluate splits
split_flag = False
if (xs < xe and cstrand == -1) or (xs > xe and cstrand == 1):
midLZ = 0
split_flag = True
# set Y axis coordinates
y0 = Y_map
yt,yb,ynt,ynb = y0+w,y0-w,y0+h,y0-h
coords = xs, xe, xn, y0, yt, yb, ynt, ynb
return featL, midLZ, coords, split_flag
def contig_ticker(canvas, feature, cLen, Y0, offset, offset_mode):
"""Draw contig separators."""
# get contig name
name = feature.qualifiers.get('id')[0]
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
# calculate offset coordinates
if offset_mode == 'loop':
offZs = offset_coord(Zs, cLen, offset)
offZe = offset_coord(Ze, cLen, offset)
elif offset_mode == 'nudge':
offZs = nudge_coord(Zs, offset)
offZe = nudge_coord(Ze, offset)
else:
offZs = Zs
offZe = Ze
xs, xe = offZs*u, offZe*u
# set Y axis coordinates
y0 = Y0-dop*3.5
# draw
canvas.setLineWidth(2)
ttl = canvas.beginPath()
ttl.moveTo(xs,y0)
ttl.lineTo(xs,y0-h*4)
ttl.lineTo(xs+dop,y0-h*4)
canvas.drawPath(ttl, stroke=1, fill=0)
canvas.setFont(bFont, NfSize)
canvas.drawString(xs+dop*2, y0-h*4.5, name)
canvas.setFont(rFont, SfSize)
canvas.drawString(xs+dop*2,y0-h*8,"".join(["[",str(Zs),"-",str(Ze),"]"]))
canvas.setFont(rFont, NfSize)
ttl.close()
def baseliner(cLen, canvas, Y_map, nudge): # loop offset has no effect
"""Draw sequence baseline."""
canvas.setLineWidth(3)
y0 = Y_map
Zs = 0 # all sequences are initially aligned on the left
Ze = cLen
# calculate nudge offsets
offZs = nudge_coord(Zs, nudge)
offZe = nudge_coord(Ze, nudge)
# set zeroes
x0 = offZs*u
x1 = offZe*u
pBL = canvas.beginPath()
pBL.moveTo(x0,y0)
pBL.lineTo(x1,y0)
canvas.drawPath(pBL, stroke=1, fill=0)
pBL.close()
def contig_ticker(canvas, feature, cLen, Y0, nudge, offset, side):
"""Draw contig separators."""
# get contig name
try:
name = feature.qualifiers.get('locus_tag')[0]
except TypeError:
name = 'unnamed feature'
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
# calculate loop offset coordinates
loop_offZs = offset_coord(Zs, cLen, offset)
loop_offZe = offset_coord(Ze, cLen, offset)
# calculate nudge offset coordinates
offZs = nudge_coord(loop_offZs, nudge)
offZe = nudge_coord(loop_offZe, nudge)
xs, xe = offZs*u, offZe*u
# set Y axis coordinates
if side == 'low':
y0 = Y0-dop*3.5
yT1 = y0-h*4
yT2 = y0-h*4.5
yT3 = y0-h*8
else:
y0 = Y0+dop*3.5
yT1 = y0+h*4
yT2 = y0+h*4.5
yT3 = y0+h*8
# draw
canvas.setLineWidth(2)
ttl = canvas.beginPath()
ttl.moveTo(xs,y0)
ttl.lineTo(xs,yT1)
ttl.lineTo(xs+dop,yT1)
canvas.drawPath(ttl, stroke=1, fill=0)
canvas.setFont(bFont, NfSize)
canvas.drawString(xs+dop*2, yT2, name)
canvas.setFont(rFont, SfSize)
canvas.drawString(xs+dop*2,yT3,"".join(["[",str(Zs),"-",str(Ze),"]"]))
canvas.setFont(rFont, NfSize)
ttl.close()
def baseliner(cLen, canvas, Y_map, offset, offset_mode):
"""Draw sequence baseline."""
canvas.setLineWidth(3)
y0 = Y_map
Zs = 0 # all sequences are initially aligned on the left
Ze = cLen
# calculate offsets
if offset_mode == 'nudge':
offZs = nudge_coord(Zs, offset)
offZe = nudge_coord(Ze, offset)
else:
offZs = Ze
offZe = Zs
x0 = offZs * u
x1 = offZe * u
pBL = canvas.beginPath()
pBL.moveTo(x0, y0)
pBL.lineTo(x1, y0)
canvas.drawPath(pBL, stroke=1, fill=0)
pBL.close()
def baseliner(cLen, canvas, Y_map, offset, offset_mode):
"""Draw sequence baseline."""
canvas.setLineWidth(3)
y0 = Y_map
Zs = 0 # all sequences are initially aligned on the left
Ze = cLen
# calculate offsets
if offset_mode == 'nudge':
offZs = nudge_coord(Zs, offset)
offZe = nudge_coord(Ze, offset)
else:
offZs = Ze
offZe = Zs
x0 = offZs*u
x1 = offZe*u
pBL = canvas.beginPath()
pBL.moveTo(x0,y0)
pBL.lineTo(x1,y0)
canvas.drawPath(pBL, stroke=1, fill=0)
pBL.close()
def contig_ticker(canvas, feature, cLen, Y0, offset, offset_mode):
"""Draw contig separators."""
# get contig name
name = feature.qualifiers.get('id')[0]
# take start and end points
location = feature.location
Zs = location.nofuzzy_start
Ze = location.nofuzzy_end
# calculate offset coordinates
if offset_mode == 'loop':
offZs = offset_coord(Zs, cLen, offset)
offZe = offset_coord(Ze, cLen, offset)
elif offset_mode == 'nudge':
offZs = nudge_coord(Zs, offset)
offZe = nudge_coord(Ze, offset)
else:
offZs = Zs
offZe = Ze
xs, xe = offZs * u, offZe * u
# set Y axis coordinates
y0 = Y0 - dop * 3.5
# draw
canvas.setLineWidth(2)
ttl = canvas.beginPath()
ttl.moveTo(xs, y0)
ttl.lineTo(xs, y0 - h * 4)
ttl.lineTo(xs + dop, y0 - h * 4)
canvas.drawPath(ttl, stroke=1, fill=0)
canvas.setFont(bFont, NfSize)
canvas.drawString(xs + dop * 2, y0 - h * 4.5, name)
canvas.setFont(rFont, SfSize)
canvas.drawString(xs + dop * 2, y0 - h * 8,
"".join(["[", str(Zs), "-",
str(Ze), "]"]))
canvas.setFont(rFont, NfSize)
ttl.close()
