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 makePathDefs(self) -> Defs:
"""
Creates Defs object for reusable `Insertion` and `Skip` elements.
"""
_BW, _BH = self._base_width, self._base_height
_hBW, _hBH = _BW/2, _BH/2
_67BW, _67BH = _BW/1.5, _BH/1.5
p = Path()
p.appendMoveToPath(_hBW, _hBH)
p.appendQuadraticCurveToPath(-_67BW, -_BH, 0, -_BH)
p.appendQuadraticCurveToPath(_67BW, 0, 0, _BH)
p.set_stroke_linecap("round")
g_insertion = G()
g_insertion.setAttribute('id', "insertion")
g_insertion.addElement(p)
d = 0.5 # small delta to compensate for round endcap
line1 = Line(d, d, _BW-d, _BH-d, style="stroke:#cc0000; stroke-width:2")
line2 = Line(_BW-d, d, d, _BH-d, style="stroke:#cc0000; stroke-width:2")
line1.set_stroke_linecap("round")
line2.set_stroke_linecap("round")
g_skip = G()
g_skip.setAttribute('id', "skip")
g_skip.addElement(line1)
g_skip.addElement(line2)
path_defs = Defs()
path_defs.addElement(g_insertion)
path_defs.addElement(g_skip)
return path_defs
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 _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 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 makeSliceVhGroup(self) -> Tuple:
"""
Creates and returns a 'G' object for Slice Virtual Helices.
"""
_SLICE_SCALE = self._scale
vh_radius = self.cn_doc.vh_radius * _SLICE_SCALE
g = G()
g.setAttribute('id', "VirtualHelices")
minx = 99999
miny = 99999
maxx = -99999
maxy = -99999
for id_num in self.cn_doc.vh_order[::-1]:
vh_x, vh_y = self.cn_doc.vh_origins[id_num]
x = vh_x * _SLICE_SCALE # + self.cn_doc.x_offset
y = -vh_y * _SLICE_SCALE # + self.cn_doc.y_offset
minx = min(minx, x)
miny = min(miny, y)
maxx = max(maxx, x)
maxy = max(maxy, y)
c = Circle(x, y, vh_radius)
circle_style = 'fill:#f2ca9a; stroke:#cc6600; stroke-width:1;'
c.set_style(circle_style)
c.setAttribute('id', "circle_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(c)
minx = minx-vh_radius*2
miny = miny-vh_radius*2
width = round(maxx-minx+vh_radius*2, 3)
height = round(maxy-miny+vh_radius*2, 3)
transform = 'translate(%.3f %.3f)' % (-minx, -miny)
g.set_transform(transform)
return g, width, height, transform
def __init__(self, x, y, z, YZgridCoord):
self.x = float(x)*SCALING_FACTOR
self.y = float(y)*SCALING_FACTOR
self.z = float(z)*SCALING_FACTOR
print(str(self.z) + ' prism')
self.startCoord = [YZgridCoord[0], YZgridCoord[1] + self.y + SPACING]
self.out = G()
def genHoneycomb(self):
outComb = G()
circleStyle = StyleBuilder()
#circleStyle.setStrokeWidth(0.5)
circleStyle.setStroke('orange')
circleStyle.setFilling('#edd239')
CORNER = self.hCSlice.getBottomRight()
circleY = []
circleY.append(CORNER[1] + (ROW_SPACE - CIRCLE_RADIUS))
for g in range(0, self.row):
circleX = CORNER[0] - CIRCLE_RADIUS
if (g != 0 and g % 2 != 0):
circleY.append(circleY[g-1] + 2*CIRCLE_RADIUS)
elif (g!= 0 and g % 2 == 0):
circleY.append(circleY[g-1] + 2*(ROW_SPACE - CIRCLE_RADIUS))
#initCircle = Circle(circleX, circleY[g], CIRCLE_RADIUS)
#outComb.addElement(initCircle)
for i in range(0, self.col):
newShift = TransformBuilder()
xShift = -i*CIRCLE_RADIUS*math.sqrt(3)
yShift = 0
if i % 2 != 0 and g % 2 != 0:
yShift = CIRCLE_RADIUS
elif i % 2 != 0 and g % 2 == 0:
yShift = -1*CIRCLE_RADIUS
newShift.setTranslation(str(xShift) + ' ' + str(yShift))
a = Circle(circleX, circleY[g], CIRCLE_RADIUS)
a.set_transform(newShift.getTransform())
outComb.addElement(a)
outComb.set_style(circleStyle.getStyle())
return outComb
def _draw_legend(self, categories):
"""
Draw legend for the given categories.
Box in lower right corner
Motivation for positioning in right corner:
SVG text cannot be centered since the text width cannot be calculated
and the first part of each event text is important.
ergo: text needs to be left aligned.
But then the probability is high that a lot of text is at the left
bottom
ergo: put the legend to the right.
+----------+
| Name O |
| Name O |
+----------+
"""
group = G()
group.addElement(self._draw_categories_box(len(categories)))
cur_y = self._get_categories_box_y(len(categories)) + OUTER_PADDING
for cat in categories:
color_box, label = self._draw_category(
self._get_categories_box_width(),
self._get_categories_item_height(),
self._get_categories_box_x(), cur_y, cat)
group.addElement(color_box)
group.addElement(label)
cur_y = cur_y + self._get_categories_item_height() + INNER_PADDING
return group
def drawSideFacePair(topCorners, bottomCorners, color):
pointList = []
pointList2 = []
output = G()
XYStyle1 = StyleBuilder()
#XYStyle1.setStroke('black')
#XYStyle1.setStrokeWidth(1.5)
XYStyle1.setFilling(color)
#XYStyle1.setFillOpacity(0.8)
XYStyle2 = StyleBuilder()
XYStyle2.setStroke(color)
XYStyle2.setStrokeWidth(0.5)
XYStyle2.setFilling(color)
pointList.append(strPathStart(topCorners[2]))
pointList.append(strPathPoint(topCorners[3]))
pointList.append(strPathPoint(bottomCorners[3]))
pointList.append(strPathPoint(bottomCorners[2]))
svgCode1 = pGram(pointList)
pointList2.append(strPathStart(topCorners[0]))
pointList2.append(strPathPoint(topCorners[1]))
pointList2.append(strPathPoint(bottomCorners[1]))
pointList2.append(strPathPoint(bottomCorners[0]))
svgCode2 = pGram(pointList2)
rightFace = Path(svgCode1)
rightFace.set_style(XYStyle1.getStyle())
leftFace = Path(svgCode2)
leftFace.set_style(XYStyle2.getStyle())
output.addElement(leftFace)
output.addElement(rightFace)
return output
def drawFrontFacePair(topCorners, bottomCorners, color):
pointList = []
pointList2 = []
output = G()
YZStyle1 = StyleBuilder()
#YZStyle1.setStroke('black')
#YZStyle1.setStrokeWidth(1.5)
YZStyle1.setFilling(color)
YZStyle1.setFillOpacity(0.75)
YZStyle2 = StyleBuilder()
YZStyle2.setStroke('black')
YZStyle2.setStrokeWidth(0.5)
YZStyle2.setFillOpacity(0.75)
YZStyle2.setFilling('#ffffff')
pointList.append(strPathStart(topCorners[1]))
pointList.append(strPathPoint(topCorners[2]))
pointList.append(strPathPoint(bottomCorners[2]))
pointList.append(strPathPoint(bottomCorners[1]))
svgCode1 = pGram(pointList)
pointList2.append(strPathStart(topCorners[0]))
pointList2.append(strPathPoint(topCorners[3]))
pointList2.append(strPathPoint(bottomCorners[3]))
pointList2.append(strPathPoint(bottomCorners[0]))
svgCode2 = pGram(pointList2)
frontFace = Path(svgCode1)
frontFace.set_style(YZStyle1.getStyle())
backFace = Path(svgCode2)
backFace.set_style(YZStyle2.getStyle())
output.addElement(backFace)
output.addElement(frontFace)
return output
def _get_bg(self):
"""
Draw background color
Draw background Era strips and labels
Draw major and minor strips, lines to all event boxes and baseline.
Both major and minor strips have divider lines and labels.
Draw now line if it is visible
"""
group = G()
group.addElement(self._draw_background())
for era in self._timeline.get_all_periods():
group.addElement(self._draw_era_strip(era))
group.addElement(self._draw_era_text(era))
for strip in self._scene.minor_strip_data:
group.addElement(
self._draw_minor_strip_divider_line(strip.end_time))
group.addElement(self._draw_minor_strip_label(strip))
for strip in self._scene.major_strip_data:
group.addElement(
self._draw_major_strip_divider_line(strip.end_time))
group.addElement(self._draw_major_strip_label(strip))
group.addElement(self._draw_divider_line())
self._draw_lines_to_non_period_events(group, self._view_properties)
if self._now_line_is_visible():
group.addElement(self._draw_now_line())
return group
def makePathSkipsGroup(self) -> G:
"""
Creates and returns a 'G' object for Path VirtualHelix Labels.
Elements are sorted in reverse order so they are listed in
ascending order in Illustrator.
"""
_BW = self._base_width
_BH = self._base_height
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3
id_coords = self.mapIdnumsToYcoords()
part = self.cn_doc.part
g = G()
g.setAttribute('id', "PathSkips")
skips = self.cn_doc.skips
for id_num in sorted(skips.keys(), reverse=True):
fwd_skip_y = id_coords[id_num] - _BH
rev_skip_y = id_coords[id_num]
for skip_idx, _ in skips[id_num][::-1]:
skip_g = G()
skip_g.setAttribute('id', "Skip %s[%s]" % (id_num, skip_idx))
skip_x = _BW*skip_idx + _pX
skip_fwd, skip_rev = part.hasStrandAtIdx(id_num, skip_idx)
if skip_fwd:
u = Use()
u.setAttribute('xlink:href', '#skip')
u.setAttribute('x', skip_x)
u.setAttribute('y', fwd_skip_y)
skip_g.addElement(u)
if skip_rev:
u = Use()
u.setAttribute('xlink:href', '#skip')
u.setAttribute('x', skip_x)
u.setAttribute('y', rev_skip_y)
skip_g.addElement(u)
g.addElement(skip_g)
return g
def makerow(self):
frameStyle = StyleBuilder()
frameStyle.setStrokeWidth(1.5)
frameStyle.setStroke('black')
frameStyle.setFilling('white')
out = G()
yCoord = 10 + (FRAMELEN + 20) * self.i
for z in range(0, 4):
newFrame = Rect(10 + (FRAMELEN + 20) * z, yCoord, FRAMELEN,
FRAMELEN)
newFrame.set_style(frameStyle.getStyle())
out.addElement(newFrame)
self.rowCoords.append([10 + (FRAMELEN + 20) * z, yCoord])
return out
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 makePathVhGroup(self) -> G:
"""
Creates and returns a 'G' object for Path Virtual Helices.
"""
g = G()
g.setAttribute('id', "VirtualHelices")
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
c = Circle(x, y, self.cn_doc.vh_radius*self._scale)
circle_style = 'fill:#f2ca9a; stroke:#cc6600; stroke-width:1;'
c.set_style(circle_style)
c.setAttribute('id', "circle_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(c)
return g
def _draw_event(self, event, rect):
if self._scene.center_text():
style = self._small_centered_font_style
else:
style = self._small_font_style
group = G()
group.addElement(self._draw_event_rect(event, rect))
text_rect = rect.Get()
if event.is_container() and EXTENDED_CONTAINER_HEIGHT.enabled():
text_rect = rect.Get()
text_rect = (text_rect[0], text_rect[1] - Y_TEXT_OFFSET, text_rect[2], text_rect[3])
group.addElement(self._svg_clipped_text(event.text, text_rect, style,
self._scene.center_text()))
if event.has_data():
group.addElement(self._draw_contents_indicator(event, rect))
return group
def makePathGridlinesGroup(self) -> G:
size = self.cn_doc.max_vhelix_length
_BW = self._base_width
_BH = self._base_height
g = G()
g.setAttribute('id', "GridLines")
for i in range(len(self.cn_doc.vh_order)):
id_num = self.cn_doc.vh_order[i]
x = self.PATH_X_PADDING + self._path_radius_scaled*3
y = self.PATH_Y_PADDING + self._path_vh_margin*i
h_lines = " ".join("M %s,%s h %s" % (x, y-_BH+j*_BH, _BW*size) for j in range(3))
v_lines = " ".join("M %s,%s v %s" % (x+j*_BW, y-_BH, _BH*2) for j in range(int(size)+1))
p = Path(h_lines + " " + v_lines)
grid_style = 'fill:none; stroke:#666666; stroke-width:0.25'
p.set_style(grid_style)
p.setAttribute('id', "grid_"+self.cn_doc.vh_props['name'][id_num])
g.addElement(p)
return g
def makePathEndpointsGroup(self) -> G:
_BW = self._base_width
_BH = self._base_height
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3
id_coords = self.mapIdnumsToYcoords()
ends5p, ends3p = self.cn_doc.getOligoEndpointsList()
g = G()
g.setAttribute('id', "Endpoints")
i = 0
for color, idnum5p, idx5p, isfwd5p in ends5p:
if isfwd5p:
x = _pX + idx5p*_BW + _BW*.25
y = id_coords[idnum5p] - _BH + _BH*.05
else:
x = _pX + idx5p*_BW
y = id_coords[idnum5p] + _BH*.05
r = Rect(x=x, y=y, width=_BW*0.75, height=_BH*.9)
endpoint_style = 'fill:%s; stroke:none; stroke-width:0.5' % color
r.set_style(endpoint_style)
r.setAttribute('id', "end5p_%s" % i)
i += 1
g.addElement(r)
j = 0
for color, idnum3p, idx3p, isfwd3p in ends3p:
if isfwd3p:
x = _pX + idx3p*_BW
y = id_coords[idnum3p] - _BH
x1, y1 = x, y
x2, y2 = x1+_BW*0.75, y1+_BH/2
x3, y3 = x, y1+_BH
else:
x = _pX + idx3p*_BW
y = id_coords[idnum3p]
x1, y1 = x+_BW, y
x2, y2 = x+_BW*0.25, y1+_BH/2
x3, y3 = x+_BW, y+_BH
pts = "%s,%s %s,%s %s,%s %s,%s" % (x1, y1, x2, y2, x3, y3, x1, y1)
p = Polygon(points=pts)
end3p_style = 'fill:%s; stroke:none; stroke-width:0.5' % color
p.set_style(end3p_style)
p.setAttribute('id', "end3p_%s" % j)
j += 1
g.addElement(p)
return g
def makePathOligosGroup(self) -> G:
id_coords = self.mapIdnumsToYcoords()
oligo_list = self.cn_doc.getOligoList()
_BW = self._base_width
_BH = self._base_height
_pX = self.PATH_X_PADDING + self._path_radius_scaled*3 + _BW/2
g = G()
g.setAttribute('id', "Oligos")
i = 0
for color, is_circular, strands in oligo_list:
prev_id, prev5, prev3, prevX, prevY = None, None, None, 0, 0
path_lines = []
if is_circular:
strands.append(strands[0])
for id_num, idx5, idx3, isfwd, _ in strands:
x = _pX + idx5*_BW
if idx5 < idx3: # top strand
y = id_coords[id_num] - _BH/2
else:
y = id_coords[id_num] + _BH/2
dx = (idx3-idx5)*_BW
if prev_id is not None and id_num != prev_id:
# c dx1 dy1, dx2 dy2, dx dy
if isfwd:
x1 = x + abs(y-prevY)*0.03
else:
x1 = x - abs(y-prevY)*0.03
y1 = (y+prevY)/2
path_lines.append("Q %s %s, %s %s" % (x1, y1, x, y))
path_lines.append("h %s" % dx)
else:
path_lines.append("M %s, %s h %s" % (x, y, dx))
prev_id, prev5, prev3, prevX, prevY = id_num, idx5, idx3, x, y
p = Path(" ".join(path_lines))
oligo_style = 'fill:none; stroke:%s; stroke-width:2' % color
p.set_style(oligo_style)
p.setAttribute('id', "oligo_%s" % i)
p.setAttribute("stroke-linejoin", "round")
i += 1
g.addElement(p)
return g
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 genLabels(self):
labels = G()
labelStyle = StyleBuilder()
labelStyle.setTextAnchor('middle')
labelStyle.setFontSize(10)
lineStyle = StyleBuilder()
lineStyle.setStroke('#a9a9a9')
dimLabelA = str(self.dimA) + ' nm'
dimLabelB = str(self.dimB) + ' nm'
# horizontal label
cornerHL = self.view.getTopLeft()
cornerHR = self.view.getTopRight()
hLabelStart = [cornerHL[0], cornerHL[1] + 5]
hLabelEnd = [cornerHR[0], cornerHR[1] + 5]
hLine = Line(hLabelStart[0], hLabelStart[1], hLabelEnd[0], hLabelEnd[1])
hLabel = Text(dimLabelA, (hLabelStart[0] + hLabelEnd[0])/2, hLabelEnd[1] + 20)
hLine.set_style(lineStyle.getStyle())
hLabel.set_style(labelStyle.getStyle())
cornerVL = self.view.getTopLeft()
cornerVR = self.view.getBottomLeft()
vLabelStart = [cornerVL[0] - 5, cornerVL[1]]
vLabelEnd = [cornerVR[0] - 5, cornerVR[1]]
vLine = Line(vLabelStart[0], vLabelStart[1], vLabelEnd[0], vLabelEnd[1])
vLabel = Text(dimLabelB, vLabelEnd[0] - 30, (vLabelStart[1] + vLabelEnd[1])/2)
vLine.set_style(lineStyle.getStyle())
vLabel.set_style(labelStyle.getStyle())
labels.addElement(hLine)
labels.addElement(hLabel)
labels.addElement(vLine)
labels.addElement(vLabel)
#center = [self.gridCoord[0] + self.dimA*SCALING_FACTOR/2, self.gridCoord[1] + self.dimB*SCALING_FACTOR + LABEL_SHIFT]
#dimLabel = str(self.dimA) + 'nm x ' +str(self.dimB) + 'nm'
#labels = Text(dimLabel, center[0], center[1])
#labels.set_style(labelStyle.getStyle())
return labels
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 genLabels(self):
labels = G()
labelStyle = StyleBuilder()
labelStyle.setTextAnchor('middle')
labelStyle.setFontSize(10)
lineStyle = StyleBuilder()
lineStyle.setStroke('#a9a9a9')
dimLabelA = str(self.x/SCALING_FACTOR) + ' nm'
dimLabelB = str(self.z/SCALING_FACTOR) + ' nm'
# horizontal label
cornerHL = self.hCSlice.getTopLeft()
cornerHR = self.hCSlice.getTopRight()
hLabelStart = [cornerHL[0], cornerHL[1] + 5]
hLabelEnd = [cornerHR[0], cornerHR[1] + 5]
hLine = Line(hLabelStart[0], hLabelStart[1], hLabelEnd[0], hLabelEnd[1])
hLabel = Text(dimLabelA, (hLabelStart[0] + hLabelEnd[0])/2, hLabelEnd[1] + 20)
hLine.set_style(lineStyle.getStyle())
hLabel.set_style(labelStyle.getStyle())
cornerVL = self.hCSlice.getTopLeft()
cornerVR = self.hCSlice.getBottomLeft()
vLabelStart = [cornerVL[0] - 5, cornerVL[1]]
vLabelEnd = [cornerVR[0] - 5, cornerVR[1]]
vLine = Line(vLabelStart[0], vLabelStart[1], vLabelEnd[0], vLabelEnd[1])
vLabel = Text(dimLabelB, vLabelEnd[0] - 30, (vLabelStart[1] + vLabelEnd[1])/2)
vLine.set_style(lineStyle.getStyle())
vLabel.set_style(labelStyle.getStyle())
labels.addElement(hLine)
labels.addElement(hLabel)
labels.addElement(vLine)
labels.addElement(vLabel)
return labels
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.region_number, index, self.rank, "all"))
group.addElement(arrow)
return groups
def _svg_clipped_text(self, text, rect, style, center_text=False):
group = G()
group.set_clip_path("url(#%s)" % self._create_clip_path(rect))
group.addElement(self._draw_text(text, rect, style, center_text))
return group
