def draw_tick(self, tickpos, ctr, ticklen, track, draw_label):
""" draw_tick(self, tickpos, ctr, ticklen) -> (element, element)
o tickpos Int, position of the tick on the sequence
o ctr Float, Y co-ord of the center of the track
o ticklen How long to draw the tick
o track Track, the track the tick is drawn on
o draw_label Boolean, write the tick label?
Returns a drawing element that is the tick on the scale
"""
assert self.start <= tickpos and tickpos <= self.end, \
"Tick at %i, but showing %i to %i" \
% (tickpos, self.start, self.end)
fragment, tickx = self.canvas_location(tickpos) # Tick co-ordinates
assert fragment >=0, \
"Fragment %i, tickpos %i" % (fragment, tickpos)
tctr = ctr + self.fragment_lines[fragment][
0] # Center line of the track
tickx += self.x0 # Tick X co-ord
ticktop = tctr + ticklen # Y co-ord of tick top
tick = Line(tickx, tctr, tickx, ticktop, strokeColor=track.scale_color)
if draw_label: # Put tick position on as label
if track.scale_format == 'SInt':
if tickpos >= 1000000:
tickstring = str(tickpos / 1000000) + " Mbp"
elif tickpos >= 1000:
tickstring = str(tickpos / 1000) + " Kbp"
else:
tickstring = str(tickpos)
else:
tickstring = str(tickpos)
label = String(
0,
0,
tickstring, # Make label string
fontName=track.scale_font,
fontSize=track.scale_fontsize,
fillColor=track.scale_color)
labelgroup = Group(label)
rotation = angle2trig(track.scale_fontangle)
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], tickx, ticktop)
else:
labelgroup = None
return tick, labelgroup
def draw_greytrack(self, track):
""" draw_greytrack(self) -> ([element, element,...], [element, element,...])
o track Track object
Put in a grey background to the current track in all fragments,
if track specifies that we should
"""
greytrack_bgs = [] # Holds grey track backgrounds
greytrack_labels = [] # Holds grey foreground labels
if not track.greytrack: # No greytrack required, return early
return [], []
# Get track location
btm, ctr, top = self.track_offsets[self.current_track_level]
# Add greytrack to all fragments for this track
for fragment in range(self.fragments):
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
box = draw_box(
(self.x0, tbtm),
(self.xlim, ttop), # Grey track bg
colors.Color(0.98, 0.98, 0.98)) # is just a box
greytrack_bgs.append(box)
if track.greytrack_labels: # If labels are required
labelstep = (
self.pagewidth
) / track.greytrack_labels # how far apart should they be?
label = String(
0,
0,
track.name, # label contents
fontName=track.greytrack_font,
fontSize=track.greytrack_fontsize,
fillColor=track.greytrack_fontcolor)
# Create a new labelgroup at each position the label is required
for x in range(int(self.x0), int(self.xlim), int(labelstep)):
labelgroup = Group(label)
rotation = angle2trig(track.greytrack_font_rotation)
labelgroup.transform = (rotation[0], rotation[1],
rotation[2], rotation[3], x, tbtm)
if not self.xlim - x <= labelstep: # Don't overlap the end of the track
greytrack_labels.append(labelgroup)
return greytrack_bgs, greytrack_labels
def draw_tick(self, tickpos, ctr, ticklen, track, draw_label):
""" draw_tick(self, tickpos, ctr, ticklen) -> (element, element)
o tickpos Int, position of the tick on the sequence
o ctr Float, Y co-ord of the center of the track
o ticklen How long to draw the tick
o track Track, the track the tick is drawn on
o draw_label Boolean, write the tick label?
Returns a drawing element that is the tick on the scale
"""
assert self.start <= tickpos and tickpos <= self.end, \
"Tick at %i, but showing %i to %i" \
% (tickpos, self.start, self.end)
fragment, tickx = self.canvas_location(tickpos) # Tick co-ordinates
assert fragment >=0, \
"Fragment %i, tickpos %i" % (fragment, tickpos)
tctr = ctr + self.fragment_lines[fragment][0] # Center line of the track
tickx += self.x0 # Tick X co-ord
ticktop = tctr + ticklen # Y co-ord of tick top
tick = Line(tickx, tctr, tickx, ticktop, strokeColor=track.scale_color)
if draw_label: # Put tick position on as label
if track.scale_format == 'SInt':
if tickpos >= 1000000:
tickstring = str(tickpos/1000000) + " Mbp"
elif tickpos >= 1000:
tickstring = str(tickpos/1000) + " Kbp"
else:
tickstring = str(tickpos)
else:
tickstring = str(tickpos)
label = String(0, 0, tickstring, # Make label string
fontName=track.scale_font,
fontSize=track.scale_fontsize,
fillColor=track.scale_color)
labelgroup = Group(label)
rotation = angle2trig(track.scale_fontangle)
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], tickx, ticktop)
else:
labelgroup = None
return tick, labelgroup
def draw_greytrack(self, track):
""" draw_greytrack(self) -> ([element, element,...], [element, element,...])
o track Track object
Put in a grey background to the current track in all fragments,
if track specifies that we should
"""
greytrack_bgs = [] # Holds grey track backgrounds
greytrack_labels = [] # Holds grey foreground labels
if not track.greytrack: # No greytrack required, return early
return [], []
# Get track location
btm, ctr, top = self.track_offsets[self.current_track_level]
# Add greytrack to all fragments for this track
for fragment in range(self.fragments):
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
box = draw_box((self.x0, tbtm), (self.xlim, ttop), # Grey track bg
colors.Color(0.98,0.98, 0.98)) # is just a box
greytrack_bgs.append(box)
if track.greytrack_labels: # If labels are required
labelstep = (self.pagewidth)/track.greytrack_labels # how far apart should they be?
label = String(0, 0, track.name, # label contents
fontName=track.greytrack_font,
fontSize=track.greytrack_fontsize,
fillColor=track.greytrack_fontcolor)
# Create a new labelgroup at each position the label is required
for x in range(int(self.x0), int(self.xlim), int(labelstep)):
labelgroup = Group(label)
rotation = angle2trig(track.greytrack_font_rotation)
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], x, tbtm)
if not self.xlim-x <= labelstep: # Don't overlap the end of the track
greytrack_labels.append(labelgroup)
return greytrack_bgs, greytrack_labels
def get_feature_sigil(self, feature, x0, x1, fragment, **kwargs):
""" get_feature_sigil(self, feature, x0, x1, fragment) -> (element, element, element)
o feature Feature object
o x0 Start X co-ordinate on diagram
o x1 End X co-ordinate on diagram
o fragment The fragment on which the feature appears
Returns a drawable indicator of the feature, and any required label
for it
"""
# Establish co-ordinates for drawing
x0, x1 = self.x0 + x0, self.x0 + x1
btm, ctr, top = self.track_offsets[self.current_track_level]
try:
btm += self.fragment_lines[fragment][0]
ctr += self.fragment_lines[fragment][0]
top += self.fragment_lines[fragment][0]
except: # Only called if the method screws up big time
print "We've got a screw-up"
print self.start, self.end
print self.fragment_bases
print x0, x1
for locstart, locend in feature.locations:
print self.canvas_location(locstart)
print self.canvas_location(locend)
print 'FEATURE\n', feature
1 / 0
# Distribution dictionary for various ways of drawing the feature
# Each method takes the corners of a containing box and a color
# as argument
draw_methods = {
'BOX': draw_box,
'ARROW': draw_arrow,
}
method = draw_methods[feature.sigil]
kwargs['head_length_ratio'] = feature.arrowhead_length
kwargs['shaft_height_ratio'] = feature.arrowshaft_height
strand = feature.strand
# Get sigil for the feature, location dependent on the feature strand
if strand == 0:
sigil = method((x0, btm), (x1, top), color=feature.color, **kwargs)
if strand == 1:
sigil = method((x0, ctr), (x1, top),
color=feature.color,
orientation='right',
**kwargs)
if strand == -1:
sigil = method((x1, btm), (x0, ctr),
color=feature.color,
orientation='left',
**kwargs)
if feature.label: # Feature requires a label
label = String(0,
0,
feature.name,
fontName=feature.label_font,
fontSize=feature.label_size,
fillColor=feature.label_color)
labelgroup = Group(label)
# Feature is on top, or covers both strands (location affects
# the height and rotation of the label)
if feature.strand in (0, 1):
rotation = angle2trig(feature.label_angle)
if feature.label_position in ('start', "5'", 'left'):
pos = x0
elif feature.label_position in ('middle', 'center', 'centre'):
pos = (x1 + x0) / 2.
else:
pos = x1
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], pos, top)
else: # Feature on bottom strand
rotation = angle2trig(feature.label_angle + 180)
if feature.label_position in ('start', "5'", 'left'):
pos = x1
elif feature.label_position in ('middle', 'center', 'centre'):
pos = (x1 + x0) / 2.
else:
pos = x0
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], pos, btm)
else:
labelgroup = None
return sigil, labelgroup
def draw_scale(self, track):
""" draw_scale(self, track) -> ([element, element,...], [element, element,...])
o track Track object
Returns a tuple of (list of elements in the scale, list of labels
in the scale)
"""
scale_elements = [] # Holds axes and ticks
scale_labels = [] # Holds labels
if not track.scale: # No scale required, exit early
return [], []
# Get track location
btm, ctr, top = self.track_offsets[self.current_track_level]
trackheight = (top - ctr)
# For each fragment, draw the scale for this track
for fragment in range(self.fragments):
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
# X-axis
if fragment == self.fragments - 1:
frag, x = self.canvas_location(self.end)
scale_elements.append(
Line(self.x0,
tctr,
self.x0 + x,
tctr,
strokeColor=track.scale_color))
else:
scale_elements.append(
Line(self.x0,
tctr,
self.xlim,
tctr,
strokeColor=track.scale_color))
# Y-axis
scale_elements.append(
Line(self.x0,
tbtm,
self.x0,
ttop,
strokeColor=track.scale_color))
if track.scale_ticks: # Ticks are required on the scale
# Draw large ticks
#I want the ticks to be consistently positioned relative to
#the start of the sequence (position 0), not relative to the
#current viewpoint (self.start and self.end)
ticklen = track.scale_largeticks * trackheight
tickiterval = int(track.scale_largetick_interval)
#Note that we could just start the list of ticks using
#range(0,self.end,tickinterval) and the filter out the
#ones before self.start - but this seems wasteful.
#Using tickiterval * (self.start/tickiterval) is a shortcut.
largeticks = [pos for pos \
in range(tickiterval * (self.start/tickiterval),
int(self.end),
tickiterval) \
if pos >= self.start]
for tickpos in largeticks:
tick, label = self.draw_tick(tickpos, ctr, ticklen, track,
track.scale_largetick_labels)
scale_elements.append(tick)
if label is not None: # If there's a label, add it
scale_labels.append(label)
# Draw small ticks
ticklen = track.scale_smallticks * trackheight
tickiterval = int(track.scale_smalltick_interval)
smallticks = [pos for pos \
in range(tickiterval * (self.start/tickiterval),
int(self.end),
tickiterval) \
if pos >= self.start]
for tickpos in smallticks:
tick, label = self.draw_tick(tickpos, ctr, ticklen, track,
track.scale_smalltick_labels)
scale_elements.append(tick)
if label is not None: # If there's a label, add it
scale_labels.append(label)
# Check to see if the track contains a graph - if it does, get the
# minimum and maximum values, and put them on the scale Y-axis
if track.axis_labels:
for set in track.get_sets(): # Check all sets...
if set.__class__ is GraphSet: # ...for a graph set
graph_label_min = []
graph_label_mid = []
graph_label_max = []
for graph in set.get_graphs():
quartiles = graph.quartiles()
minval, maxval = quartiles[0], quartiles[4]
if graph.center is None:
midval = (maxval + minval) / 2.
graph_label_min.append("%.3f" % minval)
graph_label_max.append("%.3f" % maxval)
else:
diff = max((graph.center - minval),
(maxval - graph.center))
minval = graph.center - diff
maxval = graph.center + diff
midval = graph.center
graph_label_mid.append("%.3f" % midval)
graph_label_min.append("%.3f" % minval)
graph_label_max.append("%.3f" % maxval)
for fragment in range(
self.fragments): # Add to all fragment axes
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
for val, pos in [(join(graph_label_min, ';'), tbtm),
(join(graph_label_max, ';'), ttop),
(join(graph_label_mid, ';'), tctr)]:
label = String(0,
0,
val,
fontName=track.scale_font,
fontSize=track.scale_fontsize,
fillColor=track.scale_color)
labelgroup = Group(label)
rotation = angle2trig(track.scale_fontangle)
labelgroup.transform = (rotation[0], rotation[1],
rotation[2], rotation[3],
self.x0, pos)
scale_labels.append(labelgroup)
return scale_elements, scale_labels
def get_feature_sigil(self, feature, x0, x1, fragment, **kwargs):
""" get_feature_sigil(self, feature, x0, x1, fragment) -> (element, element, element)
o feature Feature object
o x0 Start X co-ordinate on diagram
o x1 End X co-ordinate on diagram
o fragment The fragment on which the feature appears
Returns a drawable indicator of the feature, and any required label
for it
"""
# Establish co-ordinates for drawing
x0, x1 = self.x0 + x0, self.x0 + x1
btm, ctr, top = self.track_offsets[self.current_track_level]
try:
btm += self.fragment_lines[fragment][0]
ctr += self.fragment_lines[fragment][0]
top += self.fragment_lines[fragment][0]
except: # Only called if the method screws up big time
print "We've got a screw-up"
print self.start, self.end
print self.fragment_bases
print x0, x1
for locstart, locend in feature.locations:
print self.canvas_location(locstart)
print self.canvas_location(locend)
print 'FEATURE\n', feature
1/0
# Distribution dictionary for various ways of drawing the feature
# Each method takes the corners of a containing box and a color
# as argument
draw_methods = {'BOX': draw_box,
'ARROW': draw_arrow,
}
method = draw_methods[feature.sigil]
kwargs['head_length_ratio'] = feature.arrowhead_length
kwargs['shaft_height_ratio'] = feature.arrowshaft_height
strand = feature.strand
# Get sigil for the feature, location dependent on the feature strand
if strand == 0:
sigil = method((x0, btm), (x1, top), color=feature.color,
**kwargs)
if strand == 1:
sigil = method((x0, ctr), (x1, top), color=feature.color,
orientation='right', **kwargs)
if strand == -1:
sigil = method((x1, btm), (x0, ctr), color=feature.color,
orientation='left', **kwargs)
if feature.label: # Feature requires a label
label = String(0, 0, feature.name,
fontName=feature.label_font,
fontSize=feature.label_size,
fillColor=feature.label_color)
labelgroup = Group(label)
# Feature is on top, or covers both strands (location affects
# the height and rotation of the label)
if feature.strand in (0, 1):
rotation = angle2trig(feature.label_angle)
if feature.label_position in ('start', "5'", 'left'):
pos = x0
elif feature.label_position in ('middle', 'center', 'centre'):
pos = (x1 + x0)/2.
else:
pos = x1
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], pos, top)
else: # Feature on bottom strand
rotation = angle2trig(feature.label_angle + 180)
if feature.label_position in ('start', "5'", 'left'):
pos = x1
elif feature.label_position in ('middle', 'center', 'centre'):
pos = (x1 + x0)/2.
else:
pos = x0
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], pos, btm)
else:
labelgroup = None
return sigil, labelgroup
def draw_scale(self, track):
""" draw_scale(self, track) -> ([element, element,...], [element, element,...])
o track Track object
Returns a tuple of (list of elements in the scale, list of labels
in the scale)
"""
scale_elements = [] # Holds axes and ticks
scale_labels = [] # Holds labels
if not track.scale: # No scale required, exit early
return [], []
# Get track location
btm, ctr, top = self.track_offsets[self.current_track_level]
trackheight = (top-ctr)
# For each fragment, draw the scale for this track
for fragment in range(self.fragments):
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
# X-axis
if fragment == self.fragments - 1:
frag, x = self.canvas_location(self.end)
scale_elements.append(Line(self.x0, tctr, self.x0 + x, tctr,
strokeColor=track.scale_color))
else:
scale_elements.append(Line(self.x0, tctr, self.xlim, tctr,
strokeColor=track.scale_color))
# Y-axis
scale_elements.append(Line(self.x0, tbtm, self.x0, ttop,
strokeColor=track.scale_color))
if track.scale_ticks: # Ticks are required on the scale
# Draw large ticks
#I want the ticks to be consistently positioned relative to
#the start of the sequence (position 0), not relative to the
#current viewpoint (self.start and self.end)
ticklen = track.scale_largeticks * trackheight
tickiterval = int(track.scale_largetick_interval)
#Note that we could just start the list of ticks using
#range(0,self.end,tickinterval) and the filter out the
#ones before self.start - but this seems wasteful.
#Using tickiterval * (self.start/tickiterval) is a shortcut.
largeticks = [pos for pos \
in range(tickiterval * (self.start/tickiterval),
int(self.end),
tickiterval) \
if pos >= self.start]
for tickpos in largeticks:
tick, label = self.draw_tick(tickpos, ctr, ticklen,
track,
track.scale_largetick_labels)
scale_elements.append(tick)
if label is not None: # If there's a label, add it
scale_labels.append(label)
# Draw small ticks
ticklen = track.scale_smallticks * trackheight
tickiterval = int(track.scale_smalltick_interval)
smallticks = [pos for pos \
in range(tickiterval * (self.start/tickiterval),
int(self.end),
tickiterval) \
if pos >= self.start]
for tickpos in smallticks:
tick, label = self.draw_tick(tickpos, ctr, ticklen,
track,
track.scale_smalltick_labels)
scale_elements.append(tick)
if label is not None: # If there's a label, add it
scale_labels.append(label)
# Check to see if the track contains a graph - if it does, get the
# minimum and maximum values, and put them on the scale Y-axis
if track.axis_labels:
for set in track.get_sets(): # Check all sets...
if set.__class__ is GraphSet: # ...for a graph set
graph_label_min = []
graph_label_mid = []
graph_label_max = []
for graph in set.get_graphs():
quartiles = graph.quartiles()
minval, maxval = quartiles[0], quartiles[4]
if graph.center is None:
midval = (maxval + minval)/2.
graph_label_min.append("%.3f" % minval)
graph_label_max.append("%.3f" % maxval)
else:
diff = max((graph.center-minval),
(maxval-graph.center))
minval = graph.center-diff
maxval = graph.center+diff
midval = graph.center
graph_label_mid.append("%.3f" % midval)
graph_label_min.append("%.3f" % minval)
graph_label_max.append("%.3f" % maxval)
for fragment in range(self.fragments): # Add to all fragment axes
tbtm = btm + self.fragment_lines[fragment][0]
tctr = ctr + self.fragment_lines[fragment][0]
ttop = top + self.fragment_lines[fragment][0]
for val, pos in [(join(graph_label_min, ';'), tbtm),
(join(graph_label_max, ';'), ttop),
(join(graph_label_mid, ';'), tctr)]:
label = String(0, 0, val,
fontName=track.scale_font,
fontSize=track.scale_fontsize,
fillColor=track.scale_color)
labelgroup = Group(label)
rotation = angle2trig(track.scale_fontangle)
labelgroup.transform = (rotation[0], rotation[1], rotation[2],
rotation[3], self.x0, pos)
scale_labels.append(labelgroup)
return scale_elements, scale_labels