class RulerTrack (Track):
"""Track for displaying a base-pair ruler along the genome"""
def __init__(self, top=2.0, bottom=0.0,
minicolor=color(.8,.8,.8), maincolor = color(0,0,0),
align=None,
text_align="middle",
text_color=color(0, 0, 0),
show=True,
fixed_height=True,
**options):
Track.__init__(self, **options)
self.top = top
self.bottom = bottom
self.minicolor = minicolor
self.maincolor = maincolor
self.text_align = text_align
self.text_color = text_color
self.show = show
self.shown = show
self.fixed_height = fixed_height
if align != None:
self.coords = alignlib.CoordConverter(align)
else:
self.coords = None
self.multiscale = Multiscale(marginx=.5, marginy=.5,
scalex=10, scaley=10)
def draw(self):
self.multiscale.init(self.get_window())
self.start = self.view.start-1
self.end = self.view.end
self.height = self.top
self.multiscale.reset()
self.gid = group()
return group(self.gid)
def update(self):
self.win = self.get_window()
if not self.show:
if self.shown:
self.gid = self.win.replace_group(self.gid, group())
self.shown = False
else:
self.shown = True
if not self.multiscale.same_view():
if self.coords == None:
g = self.draw_ruler(self.pos,
self.start,
self.end)
else:
g = self.draw_align_ruler(self.pos, self.start, self.end)
self.gid = self.win.replace_group(self.gid, g)
def set_visible(self, visible):
self.show = visible
def draw_ruler(self, pos, start, end):
worldx1, worldy1, worldx2, worldy2 = self.win.get_visible()
screenwidth, screenheight = self.win.get_size()
worldwidth = worldx2 - worldx1
worldx1 -= worldwidth / 2.0
worldx2 += worldwidth / 2.0
# find appropriate unit if one is not given
unit = visual.getRulerAutoSize(screenwidth, worldwidth)
order = int(math.log10(unit))
unit2, unitstr = visual.getUnitSuffix(unit)
x, y = pos
vis = []
# make mini hashes
if unit >= 10:
vis.append(self.minicolor)
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(lines(x + i - start, y+self.bottom,
x + i - start, y+self.top))
i += unit // 10
# make main hashes
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(self.maincolor)
vis.append(lines(x + i - start, y, x + i - start, y + self.top))
vis.append(self.text_color)
vis.append(text(str(int(i//unit2)) + unitstr,
x + i - start, y, x + i -start - unit, y + self.top,
self.text_align, "right"))
i += unit
# base line
vis.append(lines(self.maincolor, x, y, x + end - start, y))
return group(* vis)
def draw_align_ruler(self, pos, start, end):
worldx1, worldy1, worldx2, worldy2 = self.win.get_visible()
screenwidth, screenheight = self.win.get_size()
worldwidth = worldx2 - worldx1
worldx1 -= worldwidth / 2.0
worldx2 += worldwidth / 2.0
# find appropriate unit if one is not given
unit = visual.getRulerAutoSize(screenwidth, worldwidth)
order = int(math.log10(unit))
unit2, unitstr = visual.getUnitSuffix(unit)
x, y = pos
vis = []
# make mini hashes
vis.append(self.minicolor)
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(lines(x + i - start, y + self.bottom,
x + i - start, y + self.height))
i += max(unit // 10, 1)
# make main hashes
# find starting local coord
seqi = unit * ((start + self.coords.align2local(max(0, worldx1 - x),
clamp=True)) // unit) \
- start-1
# find starting align coord
i = self.coords.local2align(seqi)
endseqi = min(self.coords.align2local(end, clamp=True),
self.coords.align2local(worldx2-x, clamp=True))
# draw all hashes in view
while seqi <= endseqi:
vis.append(self.maincolor)
vis.append(lines(x + i+1, y, x + i+1, y + self.height))
vis.append(self.text_color)
vis.append(text(str(int((seqi+start+1)//unit2)) + unitstr,
x + i+1, y, x + i+1 - unit, y + self.height,
self.text_align, "right"))
seqi += unit
i = self.coords.local2align(seqi, clamp=True)
# base line
vis.append(lines(self.maincolor, x, y, x + end - start, y))
return group(* vis)
class RulerTrack(Track):
"""Track for displaying a base-pair ruler along the genome"""
def __init__(self,
top=2.0,
bottom=0.0,
minicolor=color(.8, .8, .8),
maincolor=color(0, 0, 0),
align=None,
text_align="middle",
text_color=color(0, 0, 0),
show=True,
fixed_height=True,
**options):
Track.__init__(self, **options)
self.top = top
self.bottom = bottom
self.minicolor = minicolor
self.maincolor = maincolor
self.text_align = text_align
self.text_color = text_color
self.show = show
self.shown = show
self.fixed_height = fixed_height
if align != None:
self.coords = alignlib.CoordConverter(align)
else:
self.coords = None
self.multiscale = Multiscale(marginx=.5,
marginy=.5,
scalex=10,
scaley=10)
def draw(self):
self.multiscale.init(self.get_window())
self.start = self.view.start - 1
self.end = self.view.end
self.height = self.top
self.multiscale.reset()
self.gid = group()
return group(self.gid)
def update(self):
self.win = self.get_window()
if not self.show:
if self.shown:
self.gid = self.win.replace_group(self.gid, group())
self.shown = False
else:
self.shown = True
if not self.multiscale.same_view():
if self.coords == None:
g = self.draw_ruler(self.pos, self.start, self.end)
else:
g = self.draw_align_ruler(self.pos, self.start, self.end)
self.gid = self.win.replace_group(self.gid, g)
def set_visible(self, visible):
self.show = visible
def draw_ruler(self, pos, start, end):
worldx1, worldy1, worldx2, worldy2 = self.win.get_visible()
screenwidth, screenheight = self.win.get_size()
worldwidth = worldx2 - worldx1
worldx1 -= worldwidth / 2.0
worldx2 += worldwidth / 2.0
# find appropriate unit if one is not given
unit = visual.getRulerAutoSize(screenwidth, worldwidth)
order = int(math.log10(unit))
unit2, unitstr = visual.getUnitSuffix(unit)
x, y = pos
vis = []
# make mini hashes
if unit >= 10:
vis.append(self.minicolor)
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(
lines(x + i - start, y + self.bottom, x + i - start,
y + self.top))
i += unit // 10
# make main hashes
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(self.maincolor)
vis.append(lines(x + i - start, y, x + i - start,
y + self.top))
vis.append(self.text_color)
vis.append(
text(
str(int(i // unit2)) + unitstr, x + i - start, y,
x + i - start - unit, y + self.top, self.text_align,
"right"))
i += unit
# base line
vis.append(lines(self.maincolor, x, y, x + end - start, y))
return group(*vis)
def draw_align_ruler(self, pos, start, end):
worldx1, worldy1, worldx2, worldy2 = self.win.get_visible()
screenwidth, screenheight = self.win.get_size()
worldwidth = worldx2 - worldx1
worldx1 -= worldwidth / 2.0
worldx2 += worldwidth / 2.0
# find appropriate unit if one is not given
unit = visual.getRulerAutoSize(screenwidth, worldwidth)
order = int(math.log10(unit))
unit2, unitstr = visual.getUnitSuffix(unit)
x, y = pos
vis = []
# make mini hashes
vis.append(self.minicolor)
i = unit * (max(start, worldx1 - x + start) // unit)
while x + i - start <= worldx2 and i < end:
if i >= start:
vis.append(
lines(x + i - start, y + self.bottom, x + i - start,
y + self.height))
i += max(unit // 10, 1)
# make main hashes
# find starting local coord
seqi = unit * ((start + self.coords.align2local(max(0, worldx1 - x),
clamp=True)) // unit) \
- start-1
# find starting align coord
i = self.coords.local2align(seqi)
endseqi = min(self.coords.align2local(end, clamp=True),
self.coords.align2local(worldx2 - x, clamp=True))
# draw all hashes in view
while seqi <= endseqi:
vis.append(self.maincolor)
vis.append(lines(x + i + 1, y, x + i + 1, y + self.height))
vis.append(self.text_color)
vis.append(
text(
str(int((seqi + start + 1) // unit2)) + unitstr, x + i + 1,
y, x + i + 1 - unit, y + self.height, self.text_align,
"right"))
seqi += unit
i = self.coords.local2align(seqi, clamp=True)
# base line
vis.append(lines(self.maincolor, x, y, x + end - start, y))
return group(*vis)
