def assemble(self): # Yes, everything with HEIGHT, so I'm working in a square. # May have the colors backwards. p=partLine(linetype=self.lineType) if self.pieces == 8: # No reason to do this as a special case, but it was working # first, so why mess with it. p.move(0,-blazon.Ordinary.HEIGHT) p.makeline(0,blazon.Ordinary.HEIGHT) p.hline(-blazon.Ordinary.HEIGHT) p.makeline(blazon.Ordinary.HEIGHT,-blazon.Ordinary.HEIGHT) p.closepath() p.move(-blazon.Ordinary.HEIGHT,0) p.makeline(blazon.Ordinary.HEIGHT,0) p.vline(blazon.Ordinary.HEIGHT) p.makeline(-blazon.Ordinary.HEIGHT,-blazon.Ordinary.HEIGHT) p.closepath() else: angle=2*math.pi/self.pieces pi_2=math.pi/2 for i in range(0,self.pieces,2): p.move(blazon.Ordinary.HEIGHT*math.cos(pi_2+i*angle), blazon.Ordinary.HEIGHT*math.sin(pi_2+i*angle)) p.makeline(0,0) p.makeline(blazon.Ordinary.HEIGHT*math.cos(pi_2+(i+1)*angle), blazon.Ordinary.HEIGHT*math.sin(pi_2+(i+1)*angle)) p.closepath() self.path=SVGdraw.path(p) self.path.attributes["fill-rule"]="evenodd"
def assemble(self): # Yes, everything with HEIGHT, so I'm working in a square. # May have the colors backwards. p = partLine(linetype=self.lineType) if self.pieces == 8: # No reason to do this as a special case, but it was working # first, so why mess with it. p.move(0, -blazon.Ordinary.HEIGHT) p.makeline(0, blazon.Ordinary.HEIGHT) p.hline(-blazon.Ordinary.HEIGHT) p.makeline(blazon.Ordinary.HEIGHT, -blazon.Ordinary.HEIGHT) p.closepath() p.move(-blazon.Ordinary.HEIGHT, 0) p.makeline(blazon.Ordinary.HEIGHT, 0) p.vline(blazon.Ordinary.HEIGHT) p.makeline(-blazon.Ordinary.HEIGHT, -blazon.Ordinary.HEIGHT) p.closepath() else: angle = 2 * math.pi / self.pieces pi_2 = math.pi / 2 for i in range(0, self.pieces, 2): p.move(blazon.Ordinary.HEIGHT * math.cos(pi_2 + i * angle), blazon.Ordinary.HEIGHT * math.sin(pi_2 + i * angle)) p.makeline(0, 0) p.makeline( blazon.Ordinary.HEIGHT * math.cos(pi_2 + (i + 1) * angle), blazon.Ordinary.HEIGHT * math.sin(pi_2 + (i + 1) * angle)) p.closepath() self.path = SVGdraw.path(p) self.path.attributes["fill-rule"] = "evenodd"
def assemble(self): p=partLine(linetype=self.lineType) height=float(blazon.Ordinary.HEIGHT)/self.pieces for i in range(0,self.pieces): p.move(-blazon.Ordinary.FESSPTX,-blazon.Ordinary.FESSPTY+i*height) p.makelinerel(blazon.Ordinary.WIDTH,height/2) p.makelinerel(-blazon.Ordinary.WIDTH,height/2) p.closepath() self.path=SVGdraw.path(p)
def assemble(self): p=partLine(linetype=self.lineType) width=float(blazon.Ordinary.WIDTH)/self.pieces for i in range(0,self.pieces): p.move(-blazon.Ordinary.FESSPTX+i*width,-blazon.Ordinary.FESSPTY) p.makelinerel(width/2,blazon.Ordinary.HEIGHT) p.makelinerel(width/2,-blazon.Ordinary.HEIGHT) p.closepath() self.path=SVGdraw.path(p)
def assemble(self): p = partLine(linetype=self.lineType) p.move(-blazon.Ordinary.FESSPTX, 35) p.makeline(0, -5, 1) p.makeline(blazon.Ordinary.FESSPTX, 35, shift=-1) p.relvline(blazon.Ordinary.FESSPTY) p.relhline(-blazon.Ordinary.WIDTH) p.closepath() self.path = SVGdraw.path(p) if self.inverted: self.path.attributes["transform"] = "rotate(180)"
def assemble(self): p=partLine(linetype=self.lineType) p.move(-blazon.Ordinary.FESSPTX,35) p.makeline(0,-5,1) p.makeline(blazon.Ordinary.FESSPTX,35,shift=-1) p.relvline(blazon.Ordinary.FESSPTY) p.relhline(-blazon.Ordinary.WIDTH) p.closepath() self.path=SVGdraw.path(p) if self.inverted: self.path.attributes["transform"]="rotate(180)"
def assemble(self): p=partLine(linetype=self.lineType) breadth=math.sqrt(blazon.Ordinary.HEIGHT**2 + blazon.Ordinary.WIDTH**2) unit=breadth/self.pieces for i in range(0,self.pieces): p.move(-breadth/2+i*unit, -breadth/2) p.makelinerel(unit/2, breadth) p.makelinerel(unit/2, -breadth) p.closepath() self.path=SVGdraw.path(p) self.path.attributes["transform"]=" rotate(45)"
def assemble(self): p=partLine() p.lineType=self.lineType p.move(-blazon.Ordinary.WIDTH-blazon.Ordinary.FESSPTX,-blazon.Ordinary.HEIGHT-blazon.Ordinary.FESSPTY) p.hline(0) p.makeline(0,blazon.Ordinary.HEIGHT) p.hline(blazon.Ordinary.WIDTH) p.vline(0) p.makeline(-blazon.Ordinary.WIDTH,0) p.closepath() self.path=SVGdraw.path(p) self.path.attributes["fill-rule"]="evenodd"
def assemble(self): p = partLine(linetype=self.lineType) breadth = math.sqrt(blazon.Ordinary.HEIGHT**2 + blazon.Ordinary.WIDTH**2) unit = breadth / self.pieces for i in range(0, self.pieces): p.move(-breadth / 2 + i * unit, -breadth / 2) p.makelinerel(unit / 2, breadth) p.makelinerel(unit / 2, -breadth) p.closepath() self.path = SVGdraw.path(p) self.path.attributes["transform"] = " rotate(45)"
def assemble(self): p = partLine() p.lineType = self.lineType p.move(0, blazon.Ordinary.HEIGHT) p.makeline(0, 0, align=1) p.makeline(-blazon.Ordinary.WIDTH, -blazon.Ordinary.WIDTH) p.vline(blazon.Ordinary.HEIGHT) p.closepath() self.path1 = SVGdraw.path(p) p = partLine() p.lineType = self.lineType p.move(0, blazon.Ordinary.HEIGHT) p.makeline(0, 0, align=1, shift=1) p.makeline(blazon.Ordinary.WIDTH, -blazon.Ordinary.WIDTH) p.vline(blazon.Ordinary.HEIGHT) p.closepath() self.path2 = SVGdraw.path(p) if self.inverted: # Have to rearrange the colors too self.colors = (self.colors[2], self.colors[1], self.colors[0]) self.path1.attributes["transform"] = "rotate(180)" self.path2.attributes["transform"] = "rotate(180)"
def assemble(self): p = partLine() p.lineType = self.lineType p.move(-blazon.Ordinary.WIDTH - blazon.Ordinary.FESSPTX, -blazon.Ordinary.HEIGHT - blazon.Ordinary.FESSPTY) p.hline(0) p.makeline(0, blazon.Ordinary.HEIGHT) p.hline(blazon.Ordinary.WIDTH) p.vline(0) p.makeline(-blazon.Ordinary.WIDTH, 0) p.closepath() self.path = SVGdraw.path(p) self.path.attributes["fill-rule"] = "evenodd"
def assemble(self): p=partLine() p.lineType=self.lineType p.move(0,blazon.Ordinary.HEIGHT) p.makeline(0,0,align=1) p.makeline(-blazon.Ordinary.WIDTH, -blazon.Ordinary.WIDTH) p.vline(blazon.Ordinary.HEIGHT) p.closepath() self.path1=SVGdraw.path(p) p=partLine() p.lineType=self.lineType p.move(0,blazon.Ordinary.HEIGHT) p.makeline(0,0,align=1,shift=1) p.makeline(blazon.Ordinary.WIDTH, -blazon.Ordinary.WIDTH) p.vline(blazon.Ordinary.HEIGHT) p.closepath() self.path2=SVGdraw.path(p) if self.inverted: # Have to rearrange the colors too self.colors=(self.colors[2],self.colors[1],self.colors[0]) self.path1.attributes["transform"]="rotate(180)" self.path2.attributes["transform"]="rotate(180)"
def assemble(self): # Can't really do this by rotating Bendy, since the round corner is # on the other side. p=partLine(linetype=self.lineType) fullwidth=math.sqrt(2)*blazon.Ordinary.HEIGHT if self.pieces>3: width=fullwidth*.87/self.pieces # Compensate for round corner. else: width=fullwidth/self.pieces for i in range(1,self.pieces+2,2): p.rect(-fullwidth/2+i*width, -blazon.Ordinary.HEIGHT, width, 2*blazon.Ordinary.HEIGHT) self.path=SVGdraw.path(p) self.path.attributes["transform"]="rotate(45)"
def assemble(self): # Can't really do this by rotating Bendy, since the round corner is # on the other side. p = partLine(linetype=self.lineType) fullwidth = math.sqrt(2) * blazon.Ordinary.HEIGHT if self.pieces > 3: width = fullwidth * .87 / self.pieces # Compensate for round corner. else: width = fullwidth / self.pieces for i in range(1, self.pieces + 2, 2): p.rect(-fullwidth / 2 + i * width, -blazon.Ordinary.HEIGHT, width, 2 * blazon.Ordinary.HEIGHT) self.path = SVGdraw.path(p) self.path.attributes["transform"] = "rotate(45)"
def assemble(self): """For internal use, to simplify assembly of subclasses""" p=partLine(linetype=self.lineType) # Start to support partition lines width=float(blazon.Ordinary.WIDTH)/self.pieces for i in range(1,self.pieces-1,2): p.rect(-blazon.Ordinary.FESSPTX+i*width,-blazon.Ordinary.HEIGHT, width,2*blazon.Ordinary.HEIGHT) if not self.pieces%2: # Make the last one extra-big, so things don't show through # if the line-type isn't plain. p.rect(-blazon.Ordinary.FESSPTX+(self.pieces-1)*width, -blazon.Ordinary.HEIGHT, 2*width,2*blazon.Ordinary.HEIGHT) self.path=SVGdraw.path(p)
def assemble(self): p = partLine(linetype=self.lineType) # OK, let's map things on the *square* HEIGHTxHEIGHT # Because HEIGHT > WIDTH!!! fullwidth = math.sqrt(2) * blazon.Ordinary.HEIGHT # Oh, this is going to be much easier to do orthogonally and rotating. if self.pieces > 3: width = fullwidth * .87 / self.pieces # Compensate for round corner. else: # Otherwise Per Bend doesn't work. width = fullwidth / self.pieces for i in range(0, self.pieces + 2, 2): p.rect(fullwidth / 2 - i * width, -blazon.Ordinary.HEIGHT, width, 2 * blazon.Ordinary.HEIGHT) self.path = SVGdraw.path(p) self.path.attributes["transform"] = "rotate(-45)"
def assemble(self): p=partLine(linetype=self.lineType) # OK, let's map things on the *square* HEIGHTxHEIGHT # Because HEIGHT > WIDTH!!! fullwidth=math.sqrt(2)*blazon.Ordinary.HEIGHT # Oh, this is going to be much easier to do orthogonally and rotating. if self.pieces>3: width=fullwidth*.87/self.pieces # Compensate for round corner. else: # Otherwise Per Bend doesn't work. width=fullwidth/self.pieces for i in range(0,self.pieces+2,2): p.rect(fullwidth/2-i*width, -blazon.Ordinary.HEIGHT, width,2*blazon.Ordinary.HEIGHT) self.path=SVGdraw.path(p) self.path.attributes["transform"]="rotate(-45)"
def assemble(self): p=partLine(linetype=self.lineType) height=float(blazon.Ordinary.HEIGHT)/self.pieces #"Chevronny of n" doesn't make all that much sense anyway. for i in range(0,self.pieces+2,2): p.move(-blazon.Ordinary.FESSPTX, blazon.Ordinary.FESSPTY-(i-2)*height) p.makelinerel(blazon.Ordinary.FESSPTX,-25,align=1) p.makelinerel(blazon.Ordinary.FESSPTX,25) p.relvline(-height) p.makelinerel(-blazon.Ordinary.FESSPTX,-25,align=1) p.makelinerel(-blazon.Ordinary.FESSPTX,25) p.closepath() self.path=SVGdraw.path(p) if (self.inverted): self.path.attributes['transform']=" rotate(180)"
def assemble(self): p = partLine(linetype=self.lineType) height = float(blazon.Ordinary.HEIGHT) / self.pieces #"Chevronny of n" doesn't make all that much sense anyway. for i in range(0, self.pieces + 2, 2): p.move(-blazon.Ordinary.FESSPTX, blazon.Ordinary.FESSPTY - (i - 2) * height) p.makelinerel(blazon.Ordinary.FESSPTX, -25, align=1) p.makelinerel(blazon.Ordinary.FESSPTX, 25) p.relvline(-height) p.makelinerel(-blazon.Ordinary.FESSPTX, -25, align=1) p.makelinerel(-blazon.Ordinary.FESSPTX, 25) p.closepath() self.path = SVGdraw.path(p) if (self.inverted): self.path.attributes['transform'] = " rotate(180)"
def assemble(self): p=partLine(linetype=self.lineType) height=float(blazon.Ordinary.HEIGHT)/self.pieces # Problem. Optical center is at 0. Geometric center is a little lower, # owing to the placement of the coordinates. for i in range(1,self.pieces-1,2): p.rect(-blazon.Ordinary.WIDTH, -blazon.Ordinary.FESSPTY+i*height, 3*blazon.Ordinary.WIDTH, height) # Last piece is extra-wide because everything is shifted up to correct # for optical center. Only matters when pieces is even. # Also compensates for non-plain lines. if not self.pieces%2: p.rect(-blazon.Ordinary.WIDTH, -blazon.Ordinary.FESSPTY+(self.pieces-1)*height, 3*blazon.Ordinary.WIDTH, 3*height) self.path=SVGdraw.path(p) # Shift to bring center into place. self.path.attributes["transform"]=" translate(0,%.4f)"%\ -(blazon.Ordinary.HEIGHT/2 - blazon.Ordinary.FESSPTY)
def assemble(self): p=partLine(linetype=self.lineType) p.move(-blazon.Ordinary.FESSPTX,35) p.makeline(0,-5,1) p.makeline(blazon.Ordinary.FESSPTX,35,shift=-1) p.relvline(blazon.Ordinary.HEIGHT) p.relhline(-blazon.Ordinary.WIDTH) p.closepath() self.path=SVGdraw.path(p) trns="" try: trns+=" "+self.transform except AttributeError: pass if self.inverted: trns+=" rotate(180)" if trns: self.path.attributes['transform']=trns
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 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 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 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 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