def build(self):
(sx, sy) = self._srcchgset.position()
h_offset = self._srcchgset.tag_offset(self._h)
self._position = (sx + (self._srcchgset.extent()[0])/2,
sy - (3*self._h)/2 + h_offset)
x = self._position[0]+(self._w-self._tw)/2
y = self._position[1]
r = UNIT/2
rect = SVG.rect(x,y,self._tw,self._h,
self._srcchgset.strokecolor(),
self._srcchgset.fillcolor(),
self._srcchgset.strokewidth())
rect.attributes['rx'] = r
rect.attributes['ry'] = r
rect.attributes['opacity'] = str(self._opacity/100.0)
text = SVG.text(self._position[0]+self._w/2,
self._position[1]+self._h/2+UNIT/4,
"%s" % self._title.encode('utf-8'),
self._srcchgset.fontsize(),
self._srcchgset.fontname())
txc = SvgColor('white')
text.attributes['style'] = 'fill:%s; text-anchor: middle' % txc.rgb()
name = self._title.encode('utf-8').replace('/','')
g = SVG.group('grp%d' % self._revision, elements=[rect, text])
link = "%s/changeset/%d" % (self._parent.urlbase(), self._revision)
self._link = SVG.link(link, elements=[g])
self._link.attributes['id'] = 'rev%d' % self._revision
self._link.attributes['style'] = \
'color: %s; background-color: %s' % \
(self._srcchgset.fillcolor(), self._srcchgset.strokecolor())
def build(self):
self._position = self._parent.position()
x = self._position[0] + (self._w - self._tw) / 2
y = self._position[1]
r = UNIT / 2
rect = SVG.rect(x, y, self._tw, self._h, self._parent.fillcolor(),
self._parent.strokecolor(), self._parent.strokewidth())
rect.attributes['rx'] = r
rect.attributes['ry'] = r
text = SVG.text(self._position[0] + +self._w / 2,
self._position[1] + self._h / 2 + UNIT / 6,
"/%s" % self._title.encode('utf-8'),
self._parent.fontsize(), self._parent.fontname())
text.attributes['style'] = 'text-anchor: middle'
name = self._title.encode('utf-8').replace('/', '')
g = SVG.group('grp%s' % name, elements=[rect, text])
href = Href(self._parent.urlbase())
self._link = SVG.link(plink(href.browser(self._title)), elements=[g])
def build(self):
self._position = self._parent.position()
x = self._position[0]+(self._w-self._tw)/2
y = self._position[1]
r = UNIT/2
rect = SVG.rect(x,y,self._tw,self._h,
self._parent.fillcolor(),
self._parent.strokecolor(),
self._parent.strokewidth())
rect.attributes['rx'] = r
rect.attributes['ry'] = r
text = SVG.text(self._position[0]++self._w/2,
self._position[1]+self._h/2+UNIT/6,
"/%s" % self._title.encode('utf-8'),
self._parent.fontsize(), self._parent.fontname())
text.attributes['style'] = 'text-anchor: middle'
name = self._title.encode('utf-8').replace('/','')
g = SVG.group('grp%s' % name, elements=[rect, text])
href = Href(self._parent.urlbase())
self._link = SVG.link(plink(href.browser(self._title)), elements=[g])
def getElements( self, node_id, x, y, x_label = None, y_label = None):
e = NodeDecorator.getElements( self, node_id, x, y )
if x_label == None: x_label = x
if y_label == None: y_label = y
t = self.mTree.node(node_id).data.taxon
species = self.mExtractSpecies(t)
if species not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species] = COLOURS[len(self.mMapSpecies2Colour) % len(COLOURS) ]
if species in self.mMapSpecies2Name:
tx = re.sub( species, "%s" % self.mMapSpecies2Name[species], t)
else:
tx = t
colour = self.getColour( node_id, x, y )
if self.mPlotLabel:
ee = SVGdraw.text( x_label, y_label,
tx,
self.mFontSize,
self.mFont,
stroke = "rgb(%i,%i,%i)" % colour,
text_anchor = "left" )
if self.mMapTaxon2URL != None:
url = self.mMapTaxon2URL(t)
if url:
l = SVGdraw.link( url )
l.addElement( ee )
e.append( l )
else:
e.append(ee)
else:
e.append( ee )
return e
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):
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)