def errorsvg(msg):
s=SVGdraw.svg(width='5cm', height='1cm')
s.addElement(SVGdraw.text(0,0,msg))
d=SVGdraw.drawing()
d.svg=s
print d.toXml()
return s
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 errorsvg(msg):
s = SVGdraw.svg(width='5cm', height='1cm')
s.addElement(SVGdraw.text(0, 0, msg))
d = SVGdraw.drawing()
d.svg = s
print d.toXml()
return s
def writeTitle( self ):
"""write title into plot."""
if self.mTitle:
e = SVGdraw.text( self.mPageWidth / 2,
self.mTitleFontSize ,
self.mTitle,
self.mTitleFontSize,
self.mTitleFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "middle" )
self.addElement(e)
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
e.append( SVGdraw.text( x_label, y_label,
self.mTree.node(node_id).data.taxon,
self.mFontSize,
self.mFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
font_style = self.mFontStyle,
text_anchor = "left" ))
return e
def writeScale( self ):
"""write scales."""
current_x = self.mScaleX
current_y = self.mScaleY + self.mScaleHeight
nboxes = len(self.mColourThresholds)
# box size for legend in x-direction
# subtract size of right-most axis label so that it takes the
# same width as self.mDataWidth.
box_size_x = math.ceil( (self.mDataWidth -
(self.mScaleFontSize * len(self.mFormatNumberLegend % self.mColourThresholds[-1])))
/ nboxes )
# change font size such that it labels will fit between tick-marks
self.mScaleFontSize = min( self.mScaleFontSize,
(box_size_x * self.mScaleNumTicks * 1.5) / len(self.mFormatNumberLegend % self.mColourThresholds[-1]) )
for x in range(nboxes):
e = SVGdraw.rect( current_x,
current_y,
box_size_x,
self.mScaleBoxSizeY,
fill = "rgb(%i,%i,%i)" % self.mColours[x],
stroke = "rgb(%i,%i,%i)" % self.mColours[x])
self.addElement(e)
if x % self.mScaleNumTicks == 0:
e = SVGdraw.line( current_x,
current_y,
current_x,
current_y + self.mScaleBoxSizeY,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 5)
self.addElement(e)
e = SVGdraw.text( current_x,
current_y - self.mScaleBoxSizeY,
self.mFormatNumberLegend % self.mColourThresholds[x],
self.mScaleFontSize,
self.mScaleFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "start")
self.addElement(e)
current_x += box_size_x
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 writeFooter( self ):
"""write footer."""
current_x = self.mFooterX
current_y = self.mFooterY
if self.mFooter:
current_y += max( self.mFooterFontSize, self.mMaxBoxSize) + self.mSeparator
e = SVGdraw.text( self.mPageWidth / 2,
current_y + self.mFooterFontSize,
self.mFooter,
self.mFooterFontSize,
self.mFooterFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "middle")
self.addElement(e)
def writeGrid( self ):
"""add grid lines."""
middlex = self.mDataMiddleX
middley = self.mDataMiddleY
## print separators
for c in range(len(self.contigs)):
contig = self.contigs[c]
pos = self.getPosition( contig, "+", 0)
angle = self.getAngle( pos )
x,y = self.getPosOnArc( angle, self.mRadius )
e = SVGdraw.line( middlex,
middley,
x,
y,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = self.mGridStrokeWidth )
self.addElement(e, self.mPlaneGrid )
if c < len(self.contigs) - 1:
next_angle = self.getAngle(self.getPosition( self.contigs[c+1], "+", 0 ) )
else:
next_angle = 360
x,y = self.getPosOnArc( angle + float(next_angle - angle) / 2, self.mRadiusStart / 2)
e = SVGdraw.text( x,
y,
contig,
self.mGridFontSize,
self.mGridFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "start" )
# do not rotate text:
# transform="rotate(%i,%i,%i)" % ( angle, x, y ))
self.addElement(e)
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, x1, x2, y ):
e = BranchDecoratorHorizontal.getElements( self, node_id, x1, x2, y )
text = self.getText( node_id )
d = x2 - x1
df = len(text) * (self.mFontSize / 2)
if df > d:
x = x1 - df
else:
x = x1 + (x2 - x1 - df) / 2
e.append( SVGdraw.text( x, y - 5,
text,
self.mFontSize,
self.mFont,
stroke = "rgb(%i,%i,%i)" % self.mFontColour,
text_anchor = "left" ))
return e
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 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 svgout(self,
stroke_width=0.3,
scale=20,
circle_radius=0.3,
startat=None,
coloriter=None,
crossings=True,
circradius=None,
circscale=1):
# if circradius is some positive number, try to draw a circular(!) diagram
# circscale is how much to scale the y-dimension by (how thick a circle)
# try:
# if type(SVGdraw)!=type(__builtins__):
# raise Exception("SVGdraw not a module?")
# return None
# except NameError:
# raise Exception("No SVGDraw found")
# return None
cols = [
'#000000', '#800000', '#808000', '#008080', '#000080', '#ff2000',
'#ffff20', '#20ffff', '#0020ff', '#ff0080', '#ff8000', '#8000ff',
'#80ff00'
]
if circradius:
sz = (2 * self.ymax * circscale + 2 + 2 * circradius)
svg = SVGdraw.svg(
width="%dpx" % (sz * scale),
height="%dpx" % (sz * scale),
viewBox=[-sz + self.xmodulus / 2.0, -sz, 2 * sz, 2 * sz])
def transform(x, y):
# Have to flip it over...
r = self.ymax * circscale + circradius - y * circscale
theta = 2 * math.pi * x / self.xmodulus - math.pi
return [
sz / 2 + r * math.cos(theta), sz / 2 + r * math.sin(theta)
]
else:
svg = SVGdraw.svg(
width="%dpx" % ((self.xmodulus + 2) * scale),
height="%dpx" % ((self.ymax + 2) * scale),
viewBox=[-1, -1, self.xmodulus + 2, self.ymax + 2])
def transform(x, y):
return [x, y]
defs = SVGdraw.defs(id="defs")
plusmask = SVGdraw.SVGelement("mask", attributes={"id": "plusmask"})
minusmask = SVGdraw.SVGelement("mask", attributes={"id": "minusmask"})
if circradius:
sz = 1 + 2 * self.ymax * circscale + 2 * circradius # Whatever, something big.
r = SVGdraw.rect(x=-sz,
y=-sz,
width=sz * 2,
height=sz * 2,
fill='white')
else:
r = SVGdraw.rect(x=-1,
y=-1,
width=self.xmodulus + 2,
height=self.ymax + 2,
fill='white')
plusmask.addElement(r)
minusmask.addElement(r)
defs.addElement(plusmask)
defs.addElement(minusmask)
svg.addElement(defs)
maingroup = SVGdraw.group(id="main")
# I've come to expect them this way up...
maingroup.attributes['transform']='scale(1,-1) translate(0,%d)'% \
(-self.ymax)
svg.addElement(maingroup)
# Positive slopes and negative slopes.
plus = SVGdraw.group(id="plus", mask="url(#plusmask)")
minus = SVGdraw.group(id="minus", mask="url(#minusmask)")
maingroup.addElement(plus)
maingroup.addElement(minus)
circgroup = SVGdraw.group(id="circgroup")
maingroup.addElement(circgroup)
strands = self.strands(self.pivots[0])
circuit = None
if coloriter is None:
if len(strands) > 1:
# Multistranded; color it by strand.
def multicoloriter():
counter = 0
lastcircuit = None
while True:
if circuit != lastcircuit:
lastcircuit = circuit
counter += 1
yield cols[counter % len(cols)]
coloriter = multicoloriter()
else:
def singlecoloriter(): # for singlestranders!
colcounter = 0
colordiv = len(self.pivots) / 6
while True:
yield cols[int(colcounter / colordiv) % len(cols)]
colcounter += 1
coloriter = singlecoloriter()
for circuit in strands:
# If there's a startat parameter, and it appears in this list,
# slosh the list around so it's first
if startat and startat in circuit:
ind = circuit.index(startat)
circuit = circuit[ind:] + circuit[0:ind]
for i in range(0, len(circuit)):
here = circuit[i]
nxt = circuit[(i + 1) % len(circuit)]
col = coloriter.next()
if type(col) == int: # let iterator generate indexes
col = cols[col % len(cols)]
if circradius:
path = [here, nxt]
else:
path = self.pathbetween(here, nxt)
pathstring = ""
for j in range(0, len(path), 2):
# Had hoped that transform() would have been enough, but we need
# to go through all the intermediate lattice-points when doing
# circular plots, to curve around in the right direction.
if circradius:
betweens = self.pointsbetween(path[j], path[j + 1])
pathstring += " M %f %f " % tuple(
transform(path[j].x, path[j].y))
for k in range(0, len(betweens)):
pathstring+=" L %f %f "% \
tuple(transform(betweens[k].x,betweens[k].y))
pathstring+="L %f %f "% \
tuple(transform(path[j+1].x, path[j+1].y))
else:
pathstring+=" M %f %f L %f %f"% \
(tuple(transform(path[j].x,path[j].y)+
transform(path[j+1].x,path[j+1].y)))
pathelt = SVGdraw.path(pathstring,
stroke_width=stroke_width,
stroke=col,
fill="none")
if self.slopebetween(here, nxt) > 0:
plus.addElement(pathelt)
else:
minus.addElement(pathelt)
for i in self.pivots:
cr = transform(i.x, i.y)
c = SVGdraw.circle(cx=cr[0],
cy=cr[1],
r=circle_radius,
fill='black')
circgroup.addElement(c)
if not circradius:
# Mark the wraparound point.
circgroup.addElement(SVGdraw.path("M 0 -1 l 0 %d M %d -1 l 0 %d"% \
(self.ymax+2,self.xmodulus,
self.ymax+2),
stroke='black',
stroke_width=0.03))
# Somehow I want to *note* when a knot is single-strand or
# multistrand.
circgroup.addElement(
SVGdraw.text(x=0.2,
y=0,
text=str(len(strands)),
fill='#000408',
font_size=1,
font_family='sans-serif',
transform='scale(1,-1)'))
if crossings:
# Try multistrand crossings? (not working right)
# Need *ALL* the crossing points though.
oncircuit = []
for circuit in strands:
oncircuit.extend(self.oncircuit(circuit))
masked = set()
over = 0
masks = [minusmask, plusmask]
# How about this? For each horizontal line _that has intersections on it_,
# all crossings go in one direction, and that direction alternates.
#
# How do we find those lines?
points = []
for circuit in strands:
for i in range(0, len(circuit)):
here = circuit[i]
nxt = circuit[(i + 1) % len(circuit)]
points += self.pointsbetween(here, nxt)
heights = []
howmanyhits = dict()
for p in points:
howmanyhits[p] = howmanyhits.get(p, 0) + 1
howmanyhits = [(p, howmanyhits[p]) for p in howmanyhits.keys()]
howmanyhits = filter((lambda x: x[1] > 1), howmanyhits)
heights = [x[0].y for x in howmanyhits]
heights.sort()
# No "sort unique" so just keep track of the last one we saw and skip it.
# DOESN'T WORK EITHER BUT BETTER THAN BEFORE XXXXXX
# (testing with python ./knots.py -l 18 17 6 32 6 37) Works with more
# symmetrical designs.
last = None
for h in heights:
if h == last:
continue
last = h
mask = masks[over]
over = 1 - over
for x in range(0, self.xmodulus, 2):
p = Point((x if not h % 2 else x + 1), h, self)
if p in self.pivots:
continue # Skip pivot-points.
tp1 = transform(p.x - 0.5, p.y - 0.5)
tp2 = transform(p.x - 0.5, p.y + 0.5)
tp3 = transform(p.x + 0.5, p.y + 0.5)
tp4 = transform(p.x + 0.5, p.y - 0.5)
tp = transform(p.x, p.y)
if circradius:
r = SVGdraw.circle(fill="black",
cx=tp[0],
cy=tp[1],
r=0.6)
else:
angle = 45
r=SVGdraw.polygon(fill="black",
points=[tp1,tp2,tp3,tp4],
transform="rotate(%f,%f,%f)"% \
(angle, tp[0], tp[1]))
mask.addElement(r)
# maingroup.addElement(r)
# If it's on the edge, duplicate it on the other side
# for ease of viewing.
if p.x == 0 and not circradius:
mask.addElement(
SVGdraw.rect(x=self.xmodulus - 0.5,
y=p.y - 0.5,
width=1,
height=1,
fill="#111",
transform="rotate(45,%d,%d)" %
(self.xmodulus, p.y)))
return svg
def doGrid(self, canvas, rows, verticalOffset, partHeight, columns, horizontalOffset, partWidth, gridsize, lineColor, fillColor, penWidth): polySize = str(gridsize) + self.units polyCount = 0 thebes = SVGdraw.text(20, 20, "Thebes") canvas.addElement(thebes) name = SVGdraw.text(200, 20, "Map For " + self.name) canvas.addElement(name) warning = SVGdraw.text(500, 20, "NOT IN GAME") canvas.addElement(warning) for polyRow in range(0, rows): polyTop = verticalOffset + polyRow*partHeight polyTopStr = str(polyTop) + self.units #do stuff for hexagons rowcolumns = columns rowoffset = 0 if self.type == 'hex': if polyRow % 2 == 0: if (self.width-(horizontalOffset+self.rightMargin-.01)) >= (columns*partWidth + gridsize): rowcolumns = columns + 1 else: rowoffset = gridsize/2 + gridsize/4 for polyColumn in range(0, rowcolumns): polyLeft = horizontalOffset + polyColumn*partWidth polyLeft += rowoffset polyLeftStr = str(polyLeft) + self.units polyCount += 1 if self.type == 'hex': nodeID = 100 * polyColumn + polyRow if (nodeID in self.nodes) or (self.drawAll): gridshape = hexagon(gridsize, polyLeft, polyTop, self.units, stroke=lineColor, fill=fillColor, stroke_width=penWidth) if self.drawNumbers: if (polyRow < 10): polyRowStr = "0" + str(polyRow) else: polyRowStr = str(polyRow) gridtext = SVGdraw.text(90 * (polyLeft + partHeight - .10), 90 * (polyTop + partHeight - .15),str(polyColumn)+polyRowStr,font_size=11); canvas.addElement(gridtext) canvas.addElement(gridshape) if nodeID in self.nodes: if self.drawDesc: gridname = SVGdraw.text(90 * (polyLeft + partHeight - .16), 90 * (polyTop + partHeight + .13),self.nodes[nodeID]["name"],font_size=9); canvas.addElement(gridname) griddesc = SVGdraw.text(90 * (polyLeft + partHeight - .2), 90 * (polyTop + partHeight + .02),self.nodes[nodeID]["desc"],font_size=8); canvas.addElement(griddesc) else: gridname = SVGdraw.text(90 * (polyLeft + partHeight - .16), 90 * (polyTop + partHeight + .02),self.nodes[nodeID]["name"],font_size=12); canvas.addElement(gridname) else: gridshape = SVGdraw.rect(polyLeftStr, polyTopStr, polySize, polySize, stroke=lineColor, fill=fillColor, stroke_width=penWidth) canvas.addElement(gridshape) return canvas
def writeFooter( self ):
"""write footer.
The footer contains the legend.
"""
total_branch_length = (max(self.mNodeWidthsEnd) - min(self.mNodeWidthsStart)) / self.mBranchScaleFactor
self.mFooterX = self.getHeaderWidth()
self.mFooterY = self.getHeaderHeight() + self.mDataHeight + self.mSeparatorHeight
ruler_start = self.mFooterX
ruler_end = self.mFooterX + int(total_branch_length * self.mBranchScaleFactor)
if "ruler" in self.mRulerElements:
## full length ruler with tick marks and labels
e = SVGdraw.line( ruler_start,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
## get reasonable intervalls
increment = self.mRulerIncrement * self.mBranchScaleFactor
## adjust increment for extremely long trees
if (ruler_end - ruler_start) / increment > 1000:
increment = (ruler_end - ruler_start) / 1000.0
self.mRulerIncrement = increment / self.mBranchScaleFactor
if "right-ticks" in self.mRulerElements:
x = ruler_end
while x >= ruler_start:
e = SVGdraw.line( x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
x -= self.mRulerIncrement * self.mBranchScaleFactor
self.mFooterY += 2 * self.mRulerTickSize + 1 + self.mSeparatorHeight
if "left-ticks" in self.mRulerElements:
x = ruler_start
while x <= ruler_end:
e = SVGdraw.line( x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
x += increment
self.mFooterY += 2 * self.mRulerTickSize + 1 + self.mSeparatorHeight
if "scale" in self.mRulerElements:
w = int(self.mRulerIncrement * self.mBranchScaleFactor)
e = SVGdraw.line( ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end - w,
self.mFooterY + self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
e = SVGdraw.line( ruler_end,
self.mFooterY,
ruler_end,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
e = SVGdraw.line( ruler_end - w,
self.mFooterY,
ruler_end - w,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke = "rgb(%i,%i,%i)" % BLACK,
stroke_width = 1 )
self.addElement( e )
e = SVGdraw.text( ruler_end - w / 2,
self.mFooterY + 2 * self.mRulerTickSize + 1 + self.mRulerFontSize ,
self.mRulerFormat % self.mRulerIncrement,
self.mRulerFontSize,
self.mRulerFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "middle" )
self.addElement(e)
self.mFooterY += 2 * self.mRulerTickSize + 1 + self.mRulerFontSize
e, self.mFooterX, self.mFooterY = self.mDecoratorExternalNodes.getLegend( self.mFooterX, self.mFooterY )
self.addElements(e)
e, self.mFooterX, self.mFooterY = self.mDecoratorInternalNodes.getLegend( self.mFooterX, self.mFooterY )
self.addElements(e)
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
def toSVG(self):
#modification du maximum en X : depend du nombre d'element
global XMAX
XMAX = len(self.infos)*(BAR_THICKNESS+SPACE)
# creation du document
doc=SVGdraw.drawing()
svg=SVGdraw.svg(None, '100%','100%')
# creation des patterns pour les axes et la grille
axeX = SVGdraw.pattern(id="axeX",width="20",height="10",patternUnits="userSpaceOnUse")
axeX.addElement(SVGdraw.path("M 0 0, L 0 10","none","black","0.25"))
axeX.addElement(SVGdraw.path("M 10 10, V 5","none","lightgray","0.25"))
axeY = SVGdraw.pattern(id="axeY",width="10",height="20",patternUnits="userSpaceOnUse")
axeY.addElement(SVGdraw.path("M 0 0, L 10 0","none","black","0.25"))
axeY.addElement(SVGdraw.path("M 5 10, L 10 10","none","lightgray","0.25"))
grid = SVGdraw.pattern(id="grid",width="10",height="10",patternUnits="userSpaceOnUse")
grid.addElement(SVGdraw.path("M 0 0, L 10 0, L 10 10,L 0 10, L 0 0","none","lightgray","0.25"))
defs=SVGdraw.defs()
defs.addElement(axeX)
defs.addElement(axeY)
defs.addElement(grid)
svg.addElement(defs)
group=SVGdraw.group(transform="translate(130,130) scale(1,-1)")
# dessin de la grille de fond
group.addElement(SVGdraw.rect(0,0,XMAX,YMAX,"url(#grid)","lightgray","0.25"))
# dessin des axes
group.addElement(SVGdraw.rect(0,-10,XMAX,10,"url(#axeX)"))
group.addElement(SVGdraw.rect(-10,0,10,YMAX,"url(#axeY)"))
group.addElement(SVGdraw.line(0,0,XMAX,0,"black",1))
group.addElement(SVGdraw.line(0,0,0,YMAX,"black",1))
# dessin des fleches des axes
group.addElement(SVGdraw.polygon([[-3,YMAX],[3,YMAX],[0,YMAX+10]], "black","white"))
group.addElement(SVGdraw.polygon([[XMAX,-3],[XMAX,3],[XMAX+10,0]], "black","white"))
textgroup=SVGdraw.group(transform="scale(1,-1)")
# graduations
for y in range(0,YMAX+STEP,STEP):
textgroup.addElement(SVGdraw.text(-STEP,y, str(y), 8, text_anchor="middle", transform="translate(0,%d)"%(-y*2)))
textgroup.addElement(SVGdraw.text(0,YMAX+SPACE, r"%", 8, transform="translate(0,%d)"%(-(YMAX+SPACE)*2)))
# ajout de la legende principale
legendText = "Repertoire %s - taille %.02f ko"%(self.rootName,float(self.totalSize/1024.0))
textgroup.addElement(SVGdraw.text(XMAX,YMAX+3*SPACE, legendText,12, "verdana",
text_anchor="end", fill="darkblue",transform="translate(0,%d)"%(-(YMAX+3*SPACE)*2)))
group.addElement(textgroup)
# tri des elements selon la taille occupee
self.infos.sort(self.tupleCmp)
xincr=0
#self.infos
for (name,size) in self.infos:
# calcul du pourcentage de place occupe
pourcent = (100.0*float(size))/float(self.totalSize)
height=int(pourcent*YMAX/100);
# insertion du texte de l'emplacement sur le disque et de la taille occupee en Ko
legendText = "%s (%### ###.02f ko)"%(name,float(size/1024.0))
legend = SVGdraw.text(xincr+BAR_THICKNESS/2, -10,legendText,8,"verdana",text_anchor="begin",fill="blue")
legend.attributes["transform"]="scale(1,-1) translate(0,20) rotate(45,%d,-10)"%(xincr+BAR_THICKNESS/2)
group.addElement(legend)
#insertion de la barre representant le pourcentage
group.addElement(SVGdraw.rect(xincr,0,BAR_THICKNESS, height,"green","black",opacity=0.5))
#insertion de la taille en pourcentage a gauche de la barre
pourcentText=SVGdraw.text(xincr+BAR_THICKNESS/2, height+SPACE,"%02.01f%% "%pourcent,6,
"arial", text_anchor="middle", fill="black")
pourcentText.attributes["transform"]="scale(1,-1) translate(0,-%d)"%((height+SPACE)*2)
group.addElement(pourcentText)
# augmentation du l'abscisse en X
xincr = xincr+BAR_THICKNESS+SPACE
svg.addElement(group)
doc.setSVG(svg)
doc.toXml(self.svgURL)
def svgout(self,stroke_width=0.3,scale=20,circle_radius=0.3,
startat=None,coloriter=None,crossings=True,circradius=None,circscale=1):
# if circradius is some positive number, try to draw a circular(!) diagram
# circscale is how much to scale the y-dimension by (how thick a circle)
# try:
# if type(SVGdraw)!=type(__builtins__):
# raise Exception("SVGdraw not a module?")
# return None
# except NameError:
# raise Exception("No SVGDraw found")
# return None
cols=['#000000',
'#800000', '#808000', '#008080', '#000080',
'#ff2000', '#ffff20', '#20ffff', '#0020ff',
'#ff0080', '#ff8000', '#8000ff', '#80ff00']
if circradius:
sz=(2*self.ymax*circscale+2+2*circradius)
svg=SVGdraw.svg(width="%dpx"%(sz*scale), height="%dpx"%(sz*scale),
viewBox=[-sz+self.xmodulus/2.0, -sz, 2*sz, 2*sz])
def transform(x,y):
# Have to flip it over...
r=self.ymax*circscale+circradius-y*circscale
theta=2*math.pi*x/self.xmodulus-math.pi
return [sz/2+r*math.cos(theta), sz/2+r*math.sin(theta)]
else:
svg=SVGdraw.svg(width="%dpx"%((self.xmodulus+2)*scale),
height="%dpx"%((self.ymax+2)*scale),
viewBox=[-1, -1, self.xmodulus+2,
self.ymax+2])
def transform(x,y):
return [x,y]
defs=SVGdraw.defs(id="defs")
plusmask=SVGdraw.SVGelement("mask",
attributes={"id":"plusmask"})
minusmask=SVGdraw.SVGelement("mask",
attributes={"id":"minusmask"})
if circradius:
sz=1+2*self.ymax*circscale+2*circradius # Whatever, something big.
r=SVGdraw.rect(x=-sz, y=-sz, width=sz*2,height=sz*2,fill='white')
else:
r=SVGdraw.rect(x=-1,y=-1,width=self.xmodulus+2,height=self.ymax+2,
fill='white')
plusmask.addElement(r)
minusmask.addElement(r)
defs.addElement(plusmask)
defs.addElement(minusmask)
svg.addElement(defs)
maingroup=SVGdraw.group(id="main")
# I've come to expect them this way up...
maingroup.attributes['transform']='scale(1,-1) translate(0,%d)'% \
(-self.ymax)
svg.addElement(maingroup)
# Positive slopes and negative slopes.
plus=SVGdraw.group(id="plus",mask="url(#plusmask)")
minus=SVGdraw.group(id="minus",mask="url(#minusmask)")
maingroup.addElement(plus)
maingroup.addElement(minus)
circgroup=SVGdraw.group(id="circgroup")
maingroup.addElement(circgroup)
strands=self.strands(self.pivots[0])
circuit=None
if coloriter is None:
if len(strands)>1:
# Multistranded; color it by strand.
def multicoloriter():
counter=0
lastcircuit=None
while True:
if circuit != lastcircuit:
lastcircuit=circuit
counter+=1
yield cols[counter%len(cols)]
coloriter=multicoloriter()
else:
def singlecoloriter(): # for singlestranders!
colcounter=0
colordiv=len(self.pivots)/6
while True:
yield cols[int(colcounter/colordiv)%len(cols)]
colcounter+=1
coloriter=singlecoloriter()
for circuit in strands:
# If there's a startat parameter, and it appears in this list,
# slosh the list around so it's first
if startat and startat in circuit:
ind=circuit.index(startat)
circuit=circuit[ind:]+circuit[0:ind]
for i in range(0,len(circuit)):
here=circuit[i]
nxt=circuit[(i+1)%len(circuit)]
col=coloriter.next()
if type(col)==int: # let iterator generate indexes
col=cols[col%len(cols)]
if circradius:
path=[here,nxt]
else:
path=self.pathbetween(here,nxt)
pathstring=""
for j in range(0,len(path),2):
# Had hoped that transform() would have been enough, but we need
# to go through all the intermediate lattice-points when doing
# circular plots, to curve around in the right direction.
if circradius:
betweens=self.pointsbetween(path[j],path[j+1])
pathstring+=" M %f %f "%tuple(transform(path[j].x,path[j].y))
for k in range(0,len(betweens)):
pathstring+=" L %f %f "% \
tuple(transform(betweens[k].x,betweens[k].y))
pathstring+="L %f %f "% \
tuple(transform(path[j+1].x, path[j+1].y))
else:
pathstring+=" M %f %f L %f %f"% \
(tuple(transform(path[j].x,path[j].y)+
transform(path[j+1].x,path[j+1].y)))
pathelt=SVGdraw.path(pathstring,stroke_width=stroke_width,
stroke=col,fill="none")
if self.slopebetween(here,nxt)>0:
plus.addElement(pathelt)
else:
minus.addElement(pathelt)
for i in self.pivots:
cr=transform(i.x, i.y)
c=SVGdraw.circle(cx=cr[0], cy=cr[1], r=circle_radius,
fill='black')
circgroup.addElement(c)
if not circradius:
# Mark the wraparound point.
circgroup.addElement(SVGdraw.path("M 0 -1 l 0 %d M %d -1 l 0 %d"% \
(self.ymax+2,self.xmodulus,
self.ymax+2),
stroke='black',
stroke_width=0.03))
# Somehow I want to *note* when a knot is single-strand or
# multistrand.
circgroup.addElement(SVGdraw.text(x=0.2,y=0,
text=str(len(strands)),
fill='#000408',
font_size=1,
font_family='sans-serif',
transform='scale(1,-1)'))
if crossings:
# Try multistrand crossings? (not working right)
# Need *ALL* the crossing points though.
oncircuit=[]
for circuit in strands:
oncircuit.extend(self.oncircuit(circuit))
masked=set()
over=0
masks=[minusmask,plusmask]
# How about this? For each horizontal line _that has intersections on it_,
# all crossings go in one direction, and that direction alternates.
#
# How do we find those lines?
points=[]
for circuit in strands:
for i in range(0,len(circuit)):
here=circuit[i]
nxt=circuit[(i+1)%len(circuit)]
points+=self.pointsbetween(here,nxt)
heights=[]
howmanyhits=dict()
for p in points:
howmanyhits[p]=howmanyhits.get(p,0)+1
howmanyhits=[(p,howmanyhits[p]) for p in howmanyhits.keys()]
howmanyhits=filter((lambda x: x[1]>1), howmanyhits)
heights=[x[0].y for x in howmanyhits]
heights.sort()
# No "sort unique" so just keep track of the last one we saw and skip it.
# DOESN'T WORK EITHER BUT BETTER THAN BEFORE XXXXXX
# (testing with python ./knots.py -l 18 17 6 32 6 37) Works with more
# symmetrical designs.
last=None
for h in heights:
if h==last:
continue
last=h
mask=masks[over]
over=1-over
for x in range(0,self.xmodulus,2):
p=Point((x if not h%2 else x+1),h,self)
if p in self.pivots:
continue # Skip pivot-points.
tp1=transform(p.x-0.5, p.y-0.5)
tp2=transform(p.x-0.5, p.y+0.5)
tp3=transform(p.x+0.5, p.y+0.5)
tp4=transform(p.x+0.5, p.y-0.5)
tp=transform(p.x, p.y)
if circradius:
r=SVGdraw.circle(fill="black",
cx=tp[0], cy=tp[1], r=0.6)
else:
angle=45
r=SVGdraw.polygon(fill="black",
points=[tp1,tp2,tp3,tp4],
transform="rotate(%f,%f,%f)"% \
(angle, tp[0], tp[1]))
mask.addElement(r)
# maingroup.addElement(r)
# If it's on the edge, duplicate it on the other side
# for ease of viewing.
if p.x==0 and not circradius:
mask.addElement(SVGdraw.rect(x=self.xmodulus-0.5,
y=p.y-0.5,
width=1, height=1,
fill="#111",
transform=
"rotate(45,%d,%d)"%
(self.xmodulus,p.y)))
return svg
