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 makePathInsertionsGroup(self) -> G:
part = self.cn_doc.part
id_coords = self.mapIdnumsToYcoords()
_BW = self._base_width
_hBW = _BW/2
_BH = self._base_height
_hBH = _BH/2
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3
g = G()
g.setAttribute('id', "PathInsertions")
g.setAttribute('font-size', "5")
g.setAttribute("font-family", "'SourceSansPro-Regular'")
g.setAttribute("text-anchor", "middle")
insertions = self.cn_doc.insertions
for id_num in sorted(insertions.keys(), reverse=True):
fwd_ins_y = id_coords[id_num] - _BH
rev_ins_y = id_coords[id_num]
for ins_idx, ins_len, fwd_col, rev_col in insertions[id_num][::-1]:
ins_g = G()
ins_g.setAttribute('id', "Ins %s[%s]" % (id_num, ins_idx))
ins_x = _BW*ins_idx + _pX
ins_fwd, ins_rev = part.hasStrandAtIdx(id_num, ins_idx)
if ins_fwd:
u = Use()
u.setAttribute('xlink:href', '#insertion')
u.setAttribute('x', ins_x)
u.setAttribute('y', fwd_ins_y)
fwd_style = 'fill:none; stroke:%s; stroke-width:2' % fwd_col
u.set_style(fwd_style)
ins_g.addElement(u)
t = Text('%s' % ins_len, ins_x+_hBW, fwd_ins_y)
t.set_style('fill:#999999')
ins_g.addElement(t)
if ins_rev:
u = Use()
u.setAttribute('xlink:href', '#insertion')
u.setAttribute('x', ins_x)
u.setAttribute('y', rev_ins_y)
rev_style = 'fill:none; stroke:%s; stroke-width:2' % rev_col
u.set_style(rev_style)
u.set_transform('rotate(180,%s,%s)' % (ins_x+_hBW, rev_ins_y+_hBH))
ins_g.addElement(u)
t = Text('%s' % ins_len, ins_x+_hBW, rev_ins_y+_BH*1.3)
t.set_style('fill:#999999')
ins_g.addElement(t)
g.addElement(ins_g)
# print(g.getXML())
return g
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
def _draw_text(self, my_text, rect, style, center_text=False):
my_text = self._encode_text(my_text)
x, y = self._calc_text_pos(rect, center_text)
label = Text(my_text, x, y)
label.set_style(style.getStyle())
label.set_lengthAdjust("spacingAndGlyphs")
return label
def makePathSequencesGroup(self) -> G:
"""
Creates and returns a 'G' object for Path oligo sequences.
"""
_BW = self._base_width
_BH = self._base_height
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3
id_coords = self.mapIdnumsToYcoords()
oligo_list = self.cn_doc.getOligoList()
g = G()
g.setAttribute('id', 'PathOligoSequences')
g.setAttribute('font-size', '8')
g.setAttribute('font-family', 'Monaco')
i = 0
for color, is_circular, strands in oligo_list:
g_oligo = G()
g_oligo.setAttribute('id', "oligo_seq_%s" % i)
i += 1
for id_num, idx5, idx3, isfwd, seq in strands:
x = _pX + idx5*_BW + _BW/4 if isfwd else _pX + idx5*_BW - _BW/4
y = id_coords[id_num] - _BH*1.1 if isfwd else id_coords[id_num] + _BH*2.2
t = Text('%s' % seq, x, y)
t.set_style('fill:%s66' % color)
strand_width = (idx3-idx5+1)*_BW if isfwd else (idx5-idx3+1)*_BW
t.setAttribute('textLength', strand_width)
if not isfwd:
t.set_transform('rotate(180,%s,%s)' % (x+_BW/2, y-_BH/2))
g_oligo.addElement(t)
g.addElement(g_oligo)
return g
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 makePathVhLabelGroup(self) -> G:
"""
Creates and returns a 'G' object for Path VirtualHelix Labels.
"""
g = G()
g.setAttribute('id', "VirtualHelixLabels")
g.setAttribute('font-size', "%s" % self._path_vh_fontsize)
if self.useCS6font:
g.setAttribute("font-family", "'SourceSansPro-Regular'")
else:
g.setAttribute("font-family", "'Source Sans Pro', sans-serif")
g.setAttribute("text-anchor", "middle")
for i in range(len(self.cn_doc.vh_order)):
id_num = self.cn_doc.vh_order[i]
x = self.PATH_X_PADDING
y = self.PATH_Y_PADDING + self._path_vh_margin*i + self._path_radius_scaled/2.
t = Text('%s' % id_num, x, y)
t.setAttribute('id', "label_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(t)
return g
def makeSliceVhLabelGroup(self, transform) -> G:
"""
Creates and returns a 'G' object for Slice VirtualHelix Labels.
"""
_SLICE_SCALE = self._scale
g = G()
g.setAttribute('id', "VirtualHelixLabels")
g.setAttribute('font-size', "%s" % self._slice_vh_fontsize)
if self.useCS6font:
g.setAttribute("font-family", "'SourceSansPro-Regular'")
else:
g.setAttribute("font-family", "'Source Sans Pro', sans-serif")
g.setAttribute("text-anchor", "middle")
for id_num in self.cn_doc.vh_order[::-1]:
vh_x, vh_y = self.cn_doc.vh_origins[id_num]
x = vh_x # + self.cn_doc.x_offset
y = -vh_y + self.cn_doc.vh_radius/2.
t = Text('%s' % id_num, x*_SLICE_SCALE, y*_SLICE_SCALE - 1)
t.setAttribute('id', "label_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(t)
g.set_transform(transform)
return g
def _text(self, the_text, x, y):
encoded_text = self._encode_text(the_text)
return Text(encoded_text, x, y)
def draw_bits_as_string(svg, id, x, y, prefix, numBits, bits):
ob = SvgText(prefix + ":" + bits_to_string(numBits, bits), x, y, id=id)
ob.set_style(nameStyle)
svg.addElement(ob)
def draw_bits(svg, id, x, y, prefix, numBits, bits, activeBits=None):
# prefix is assumed to be a single character
if (showBitsAs == "text"):
draw_bits_as_string(svg, id, x, y, prefix, numBits, bits)
return
ob = SvgText(prefix, x, y, id=id)
ob.set_style(nameStyle)
svg.addElement(ob)
x += dc.bitPrefixSkip
y -= dc.bitHgt - 1
if (activeBits == None):
infBit = 1
for bitNum in range(numBits):
bitPos = numBits - 1 - bitNum
bit = bits & (1 << bitPos)
if (activeBits != None):
infBit = activeBits & (1 << bitPos)
if (bitGroupSizes == None): groupNum = 0
else: groupNum = bitNum // bitGroupSizes[0]
bitX = bitNum * dc.bitWdt + groupNum * dc.bitGroupSepWdt
ob = SvgRect(x + bitX,
y,
dc.bitWdt,
dc.bitHgt,
id="%s_bit%d" % (id, bitNum))
ob.set_stroke(dc.bitOutlineColor)
ob.set_stroke_width(dc.bitOutlineThickness)
if (infBit == 0): ob.set_fill(dc.bitXColor)
elif (bit == 0): ob.set_fill(dc.bit0Color)
else: ob.set_fill(dc.bit1Color)
svg.addElement(ob)
