def get_svg_groups(self, h_offset: int = 0, v_offset: int = 0, scaling: float = 1.,
screenwidth: int = 1024, colours: Dict[str, str] = None,
overview: bool = False, prefix: str = "dummy") -> List[Group]:
""" Returns all SVG elements required to draw the Cluster """
if not colours:
colours = {}
groups = []
group = Group()
self._add_label(group, v_offset)
line_y = 35 + v_offset
group.addElement(ShapeBuilder().createLine(10, line_y,
10 + (screenwidth * 0.75), line_y,
strokewidth=1, stroke="grey"))
groups.append(group)
# Add gene arrows
arrow_y = line_y + 5
offset = h_offset - self.start
if self.reversed:
offset = h_offset + self.end
for i, gene in enumerate(self.genes):
group = Group()
arrow = gene.get_arrow_polygon(scaling=scaling, offset=offset,
base=arrow_y,
colour=colours.get(gene.name, "white"))
if overview:
label = "all_"
else:
label = "h"
arrow.set_id("%s-%d_%s%d_%s_%s" % (prefix, self.query_cluster_number, label,
self.query_cluster_number, self.rank, i))
group.addElement(arrow)
# Can be used for domains
group.set_id("a%s_00%s" % (self.query_cluster_number, i))
groups.append(group)
return groups
def _add_label(self, group: Group, v_offset: int) -> Group:
acc = Text(self.full_description, 5, 20 + v_offset)
if self.prefix == "knownclusterblast":
desc = "%80s (%s), %s" % (self.description, self.similarity_string,
self.cluster_type)
acc = Text(
'<a xlink:href="https://mibig.secondarymetabolites.org/go/' +
self.accession +
'/%s" target="_blank">' % self.ref_cluster_number +
self.accession + '</a>: ' + desc, 5, 20 + v_offset)
elif self.prefix == "general":
acc = Text(
'<a xlink:href="https://antismash-db.secondarymetabolites.org/go/'
+ self.accession +
'/%s" target="_blank">' % self.ref_cluster_number +
self.full_description.replace(":", "</a>:", 1), 5,
20 + v_offset)
# Don't do any linking for subclusterblast
acc.set_class("clusterblast-acc")
group.addElement(acc)
group.setAttribute('label', self.accession)
group.setAttribute('description', self.full_description)
group.set_class('clusterblast-cluster')
return group
def _add_label(self, group: Group, v_offset: int) -> Group:
acc = Text(self.full_description, 5, 20 + v_offset)
if self.accession.startswith('BGC'):
acc = Text('<a xlink:href="http://mibig.secondarymetabolites.org/repository/'
+ self.accession + '/index.html#cluster-1" target="_blank">'
+ self.accession + '</a>: '
+ "%80s (%s)" % (self.description, self.similarity), 5, 20 + v_offset)
elif self.accession.split("_")[0] in get_antismash_db_accessions():
acc = Text('<a xlink:href="http://antismash-db.secondarymetabolites.org/output/'
+ self.accession + '/index.html#cluster-%s" target="_blank">' % self.ref_cluster_number[1:]
+ self.full_description.replace(":", "</a>:"), 5, 20 + v_offset)
acc.set_class("clusterblast-acc")
group.addElement(acc)
group.setAttribute('label', self.accession)
group.setAttribute('description', self.full_description)
group.set_class('clusterblast-cluster')
return group
def get_svg_groups(self, h_offset: int = 0, v_offset: int = 0, scaling: float = 1.,
screenwidth: int = 1024, colours: Dict[str, str] = None,
overview: bool = False, prefix: str = "dummy") -> List[Group]:
""" Returns all SVG elements required to draw the Cluster """
if not colours:
colours = {}
groups = []
group = Group()
acc = Text(self.description, 5, 20)
acc.set_class("clusterblast-acc")
group.addElement(acc)
line_y = 35 + v_offset
group.addElement(ShapeBuilder().createLine(10, line_y, 10 + (screenwidth * 0.75),
line_y, strokewidth=1, stroke="grey"))
group.setAttribute('label', self.description)
group.set_class('clusterblast-cluster')
groups.append(group)
base = line_y + 5
offset = h_offset + 10 - self.start # 10 for margin
for index, gene in enumerate(self.genes):
arrow = gene.get_arrow_polygon(scaling=scaling, offset=offset,
base=base, colour=colours.get(gene.name, "white"))
arrow.set_id("%s-%s_q%s_%s_%s" % (prefix, self.query_cluster_number, index, self.rank, "all"))
group.addElement(arrow)
return groups