def build(self):
(x0, y0) = self._source.position('se')
(x5, y5) = self._dest.position('ne')
pd = SVG.pathdata()
pd.move(x0, y0)
(x1, y1) = (x0 + UNIT, y0 + UNIT)
(x2, y2) = (x0 + UNIT, y0 + 2 * UNIT)
(x3, y3) = (x5 + UNIT, y5 - 2 * UNIT)
(x4, y4) = (x5 + UNIT, y5 - UNIT)
if x2 < x4:
pd.qbezier(x1, y1, x2, y2)
pd.line(x3, y3)
pd.qbezier(x4, y4, x5, y5)
else:
pd.qbezier(x0 + UNIT, (y5 + y0) / 2, x5, y5)
self._extent = (abs(x5 - x0), abs(y5 - y0))
self._widget = SVG.path(pd, 'none', self._color,
self._parent.strokewidth())
self._widget.attributes['stroke-dasharray'] = '5, 5'
def build(self):
(x0,y0) = self._source.position('se')
(x5,y5) = self._dest.position('ne')
pd = SVG.pathdata()
pd.move(x0,y0)
(x1,y1) = (x0+UNIT,y0+UNIT)
(x2,y2) = (x0+UNIT,y0+2*UNIT)
(x3,y3) = (x5+UNIT,y5-2*UNIT)
(x4,y4) = (x5+UNIT,y5-UNIT)
if x2 < x4:
pd.qbezier(x1,y1,x2,y2)
pd.line(x3,y3)
pd.qbezier(x4,y4,x5,y5)
else:
pd.qbezier(x0+UNIT,(y5+y0)/2,x5,y5)
self._extent = (abs(x5-x0),abs(y5-y0))
self._widget = SVG.path(pd, 'none', self._color,
self._parent.strokewidth())
self._widget.attributes['stroke-dasharray']='5, 5'
def addDuplication( self, entries, map_gene2pos, height,
url = None,
with_separator=True,
link_to_previous = False,
quality2symbol = {},
quality2mask = {}):
"""add a dot in row/col."""
mi, ma = None, 0
pos = bisect.bisect( self.mColourThresholds, height )
master_colour = self.mColours[pos]
chrs = {}
points = []
if not link_to_previous:
self.mPreviousPoints = {}
########################################################
########################################################
########################################################
## convert gene list to a set of points
########################################################
for species, transcript, gene, quality in entries:
chr, strand, first_res, last_res = map_gene2pos[gene]
chrs[chr] = 1
pos1 = self.getPosition( chr, strand, first_res )
pos2 = self.getPosition( chr, strand, last_res )
a = min( pos1, pos2 )
b = max( pos1, pos2 )
if mi == None:
mi = a
else:
mi = min(a, mi)
ma = max(b, ma)
points.append( (pos1, pos2, gene, quality, chr) )
########################################################
########################################################
########################################################
## decide whether we need to increment the radius
########################################################
cis = len(chrs) == 1
old_radius = self.mRadius
is_overlap = False
if cis:
if not self.mLastChr:
self.mLastChr = chr
if chr != self.mLastChr:
self.mRadius = self.mRadiusFallBack
self.mLastMax = ma
self.mPreviousMax = ma
self.mLastChr = chr
else:
if self.mPreviousMax + self.mMinDistance > mi:
## overlap due to close proximitiy
self.mRadius += self.mRadiusIncrement
if with_separator: self.addSeparator()
## true overlap
if self.mPreviousMax > mi:
is_overlap = True
elif self.mLastMax + self.mMinDistance > mi:
pass
else:
self.mRadius = self.mRadiusFallBack
self.mLastMax = max(self.mLastMax, ma)
else:
if self.mLastMax > mi:
self.mRadius += self.mRadiusIncrement
if with_separator: self.addSeparator()
self.mPreviousMin = mi
self.mPreviousMax = ma
self.mPreviousCis = cis
self.mRadiusMax = max(self.mRadius, self.mRadiusMax)
########################################################
########################################################
########################################################
## draw points
########################################################
link_colour = master_colour
link_rad_width = self.mLinkRadStrokeWidth
link_arc_width = self.mLinkArcStrokeWidth
new_points = {}
for pos1, pos2, gene, quality, chr in points:
angle = self.getAngle( (pos1 + pos2) / 2 )
x,y = self.getPosOnArc( angle, self.mRadius )
try:
symbol = quality2symbol[quality]
except KeyError:
symbol = "rect"
if quality in quality2mask:
colour = self.mLinkColourSymbolMasked
link_colour = self.mLinkColourMasked
link_rad_width = self.mLinkStrokeWidthMasked
link_arc_width = self.mLinkStrokeWidthMasked
else:
colour = master_colour
if gene in self.mPreviousPoints:
continue
new_points[gene] = (x, y, angle, quality, chr)
if symbol == "circle":
ee = SVGdraw.circle( x, y, self.mLinkSymbolSize,
fill = "rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width = self.mLinkStrokeWidthSymbol )
elif symbol == "rect":
ee = SVGdraw.rect( x-self.mLinkSymbolSize/2, y-self.mLinkSymbolSize/2,
self.mLinkSymbolSize, self.mLinkSymbolSize,
fill = "rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width = self.mLinkStrokeWidthSymbol )
if url:
e = SVGdraw.link( url % gene )
e.addElement( ee )
else:
e = ee
self.addWheelElement( e )
########################################################
########################################################
########################################################
## write all arcs in between old points and new points
## cis: circular arc
## trans: radial arc
########################################################
angles = []
for x1,y1,angle1,quality1,chr1 in new_points.values():
## reduce clutter by not writing arc to the same angle
for x2,y2,angle2,quality2,chr2 in self.mPreviousPoints.values():
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append( angle2 )
d = SVGdraw.pathdata( x1, y1 )
if chr1 == chr2:
d.relellarc( self.mRadius, self.mRadius, 0, 0, 1, x2-x1, y2-y1 )
link_width = link_rad_width
else:
d.relellarc( self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2-x1, y2-y1 )
link_width = link_arc_width
e = SVGdraw.path( d,
fill = "none",
stroke = "rgb(%i,%i,%i)" % link_colour,
stroke_width = link_width )
self.addWheelElement(e, self.mPlaneLinks)
## plot lines between new points
new_genes = new_points.keys()
for g1 in range(len(new_genes)-1):
x1,y1,angle1,quality1,chr1 = new_points[new_genes[g1]]
for g2 in range(g1+1, len(new_genes)):
x2,y2,angle2,quality2,chr2 = new_points[new_genes[g2]]
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append( angle2 )
d = SVGdraw.pathdata( x1, y1 )
if chr1 == chr2:
d.relellarc( self.mRadius, self.mRadius, 0, 0, 1, x2-x1, y2-y1 )
link_width = link_rad_width
else:
d.relellarc( self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2-x1, y2-y1 )
link_width = link_arc_width
e = SVGdraw.path( d,
fill = "none",
stroke = "rgb(%i,%i,%i)" % link_colour,
stroke_width = link_width )
self.addWheelElement(e, self.mPlaneLinks)
## add new points to old points
for k, v in new_points.items():
self.mPreviousPoints[k] = v
def build(self):
if self._source.branch() == self._dest.branch():
self._widget = None
self._parent.env.log.warn("Invalid operation")
return
# get the position of the changeset to tie
(xs,ys) = self._source.position()
(xe,ye) = self._dest.position()
# swap start and end points so that xs < xe
if xs > xe:
head = True
(self._source, self._dest) = (self._dest, self._source)
(xs,ys) = self._source.position()
(xe,ye) = self._dest.position()
else:
head = False
xbranches = self._parent.xsvgbranches(self._source, self._dest)
# find which points on the changeset widget are used for connections
if xs < xe:
ss = 'e'
se = 'w'
else:
ss = 'w'
se = 'e'
ps = self._source.position(ss)
pe = self._dest.position(se)
# compute the straight line from start to end widgets
a = (ye-ys)/(xe-xs)
b = ys-(a*xs)
bz = []
# compute the points through which the 'operation' curve should go
(xct,yct) = (ps[0],ps[1])
points = [(xct,yct)]
for br in xbranches:
x = br.vaxis()
y = (a*x)+b
ycu = ycd = None
schangesets = br.svgchangesets()
schangesets.sort()
# add an invisible changeset in place of the branch header to avoid
# special case for the first changeset
hpos = br.header().position()
hchg = SvgBaseChangeset(br, 0, (hpos[0], hpos[1]+3*UNIT/2))
schangesets.append(hchg)
schangesets.reverse()
pc = None
for c in schangesets:
# find the changesets which are right above and under the
# selected point, and store their vertical position
yc = c.position()[1]
if yc < y:
ycu = yc
if yc >= y:
ycd = yc
if not ycu:
if pc:
ycu = pc.position()[1]
elif c != schangesets[-1]:
ycu = schangesets[-1].position()[1]
break
pc = c
if not ycu or not ycd:
pass
# in this case, we need to create a virtual point (TODO)
else:
xt = x
yt = (ycu+ycd)/2
if a != 0:
a2 = -1/a
b2 = yt - a2*xt
xl = (b2-b)/(a-a2)
yl = a2*xl + b2
nx = xt-xl
ny = yt-yl
dist = sqrt(nx*nx+ny*ny)
radius = (3*c.extent()[1])/2
add_point = dist < radius
else:
add_point = True
# do not insert a point if the ideal curve is far enough from
# an existing changeset
if add_point:
# update the vertical position for the bezier control
# point with the point that stands between both closest
# changesets
(xt,yt) = self._parent.fixup_point((xt,yt))
points.append((xt,yt))
if head:
points.append(pe)
else:
points.append((pe[0]-UNIT,pe[1]))
# now compute the qbezier curve
pd = SVG.pathdata()
pd.move(points[0][0],points[0][1])
if head:
pd.line(points[0][0]+UNIT,points[0][1])
for i in range(len(points)-1):
(xl,yl) = points[i]
(xr,yr) = points[i+1]
(xi,yi) = ((xl+xr)/2,(yl+yr)/2)
pd.qbezier(xl+2*UNIT,yl,xi,yi)
pd.qbezier(xr-2*UNIT,yr,xr,yr)
if not head:
pd.line(pe[0],pe[1])
self._widget = SVG.path(pd, 'none', self._color,
self._parent.strokewidth())
self._widget.attributes['marker-%s' % (head and 'start' or 'end') ] = \
self._parent.svgarrow(self._color, head)
if self._classes:
self._widget.attributes['class'] = ' '.join(self._classes)
def build(self):
SvgBaseChangeset.build(self)
(fgc, bgc) = (self._strokecolor, self._fillcolor)
txc = self._textcolor
if 'firstchangeset' in self._classes:
(fgc, bgc) = (bgc, fgc)
if 'lastchangeset' in self._classes:
bgc = SvgColor('black')
txc = SvgColor('white')
widgets = []
if self._shape == 'circle':
widgets.append(SVG.circle(self._position[0], self._position[1],
self._radius, bgc, fgc,
self._parent.strokewidth()))
if self._enhance:
(x,y) = self._position
(d,hr) = (self._radius*SQRT3/2, self._radius/2)
widgets.append(SVG.line(x-d,y-hr,x+d,y-hr,
fgc, self._parent.strokewidth()))
widgets.append(SVG.line(x-d,y+hr,x+d,y+hr,
fgc, self._parent.strokewidth()))
elif self._shape == 'square':
r = UNIT/6
size = self._radius-r
widgets.append(SVG.rect(self._position[0]-size,
self._position[1]-size,
2*size, 2*size, bgc, fgc,
self._parent.strokewidth()))
outline.attributes['rx'] = r
outline.attributes['ry'] = r
elif self._shape == 'hexa':
(x,y) = self._position
(r,hr) = (self._radius, self._radius/2)
pd = SVG.pathdata()
pd.move(x,y-r)
pd.line(x+r,y-hr)
pd.line(x+r,y+hr)
pd.line(x,y+r)
pd.line(x-r,y+hr)
pd.line(x-r,y-hr)
pd.line(x,y-r)
widgets.append(SVG.path(pd, bgc, fgc,
self._parent.strokewidth()))
else:
raise AssertionError, \
"unsupported changeset shape (%d)" % self._revision
title = SVG.text(self._position[0],
self._position[1] + UNIT/6,
str(self._revision),
self._parent.fontsize(), self._parent.fontname())
title.attributes['style'] = 'fill:%s; text-anchor: middle' % txc.rgb()
widgets.append(title)
g = SVG.group('grp%d' % self._revision, elements=widgets)
link = "%s/changeset/%d" % (self._parent.urlbase(), self._revision)
self._link = SVG.link(link, elements=[g])
if self._revision:
self._link.attributes['style'] = \
'color: %s; background-color: %s' % \
(self._strokecolor, self._fillcolor)
self._link.attributes['id'] = 'rev%d' % self._revision
self._link.attributes['class'] = ' '.join(self._classes)
def getElements(self, x, y, map_node2height ):
t = self.mTree.get_terminals()
elements = []
## print locations
if self.mPrintLocation:
for i in range(len(t)):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
elements.append( SVGdraw.text( x, y1,
str(self.mMapId2Location[taxon1]),
self.mFontSize,
self.mFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "left" ))
## print connectors
for i in range(len(t)-1):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
for j in range(i+1, len(t)):
node_id2 = t[j]
taxon2 = self.mTree.node(node_id2).data.taxon
if self.mExtractSpecies:
species1 = self.mExtractSpecies(taxon1)
species2 = self.mExtractSpecies(taxon2)
if species1 != species2: continue
if species1 not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species1] = COLOURS[len(self.mMapSpecies2Colour) % len(COLOURS) ]
colour = self.mMapSpecies2Colour[species1]
else:
colour = self.mDefaultColour
l1 = self.mMapId2Location[taxon1]
l2 = self.mMapId2Location[taxon2]
if l1.contig != l2.contig:
continue
if self.mMaxSeparation:
s = min( abs(l1.mFrom - l2.mTo), abs(l1.mTo - l2.mFrom))
if s >= self.mMaxSeparation: continue
y2 = map_node2height[node_id2] + y
distance = y2 - y1
d = SVGdraw.pathdata( x, y1 )
d.line( x + self.mTickWidth, y1 )
d.ellarc( distance, distance, 0, 0, 1, x + self.mTickWidth, y2 )
d.line( x, y2 )
e = SVGdraw.path( d,
fill = "none",
stroke = "rgb(%i,%i,%i)" % colour,
stroke_width = 1 )
elements.append( e )
return elements