def get_pairing_contents(self, index: int, width: int, height: int) -> str:
""" Generate an SVG comparing the query to a single hit cluster
Arguments:
index: the index of the hit
width: the width of the SVG
height: the height of the SVG
Returns:
a string containing the SVG XML
"""
svg = Svg(x=0, y=0, width=width, height=height)
viewbox = "0 0 %d %d" % (width, height)
svg.set_viewBox(viewbox)
svg.set_preserveAspectRatio("none")
max_length = max([len(self.query_cluster), len(self.hits[index])])
scaling = (width - 20) / max_length
for i, cluster in enumerate([self.query_cluster, self.hits[index]]):
for group in cluster.get_svg_groups(
v_offset=50 * i,
h_offset=(max_length - len(cluster)) // 2,
scaling=scaling,
colours=self.colour_lookup):
svg.addElement(group)
return svg.getXML()
def makePathSvg(self) -> Svg:
"""
Returns the main `Svg` object for Path view.
"""
viewbox = "0 0 %s %s" % (self.w, self.h)
path_svg = Svg(width=self.w, height=self.h)
path_svg.set_viewBox(viewbox)
path_svg.set_preserveAspectRatio("xMinYMid meet")
path_svg.setAttribute('id', "Cadnano_Path") # Main layer name
path_svg.addElement(self.defs)
path_svg.addElement(self.g_pathgridlines) # bottom layer
path_svg.addElement(self.g_patholigos)
path_svg.addElement(self.g_pathendpoints)
path_svg.addElement(self.g_pathvirtualhelices)
path_svg.addElement(self.g_pathvirtualhelixlabels) # top layer
path_svg.addElement(self.g_pathinsertions)
path_svg.addElement(self.g_pathskips)
if self.cn_doc.sequence_applied:
path_svg.addElement(self.g_pathsequences)
else:
print('No sequences were applied. Max oligo length: %s' % self.cn_doc.max_oligo_length, file=sys.stderr)
path_svg.save(self.output_path)
return path_svg
def get_overview_contents(self, width: int, height: int) -> str:
""" Generate an SVG comparing the query to all hit cluster
Arguments:
width: the width of the SVG
height: the height of the SVG
Returns:
a string containing the SVG XML
"""
svg = Svg(x=0, y=0, width=width, height=height)
viewbox = "0 0 %d %d" % (width, height)
svg.set_viewBox(viewbox)
svg.set_preserveAspectRatio("none")
scaling = (width - 20) / self.max_length # -20 for margins
offset = (self.max_length - len(self.query_cluster)) // 2
for group in self.query_cluster.get_svg_groups(
h_offset=offset,
scaling=scaling,
colours=self.colour_lookup,
overview=True,
prefix=self.prefix):
svg.addElement(group)
for index, cluster in enumerate(self.hits):
for group in cluster.get_svg_groups(
v_offset=50 * (index + 1),
h_offset=(self.max_length - len(cluster)) // 2,
scaling=scaling,
colours=self.colour_lookup,
overview=True,
prefix=self.prefix):
svg.addElement(group)
return svg.getXML()
def makeSliceSvg(self) -> Svg:
slice_svg = Svg(width=self.w, height=self.h)
viewbox = "0 0 %s %s" % (self.w, self.h)
slice_svg.set_viewBox(viewbox)
slice_svg.set_preserveAspectRatio("xMidYMid meet")
slice_svg.setAttribute('id', "Cadnano_Slice") # Main layer name
slice_svg.addElement(self.g_slicevirtualhelices) # bottom layer
slice_svg.addElement(self.g_slicevirtualhelixlabels) # top layer
slice_svg.save(self.output_path)