def testMultiplePaths():
"""
-
|
-
"""
t=Turtle()
t.penDown()
print(t.getPosition())
t.forward(205)
print(t.getPosition())
t.right(90)
t.forward(205)
print(t.getPosition())
t.right(90)
t.forward(105)
print(t.getPosition())
t.right(90)
t.forward(105)
print(t.getPosition())
t.penUp()
t.moveTo(Vector(300,300))
print(t.getPosition())
t.penDown()
t.forward(205)
print(t.getPosition())
t.finish()
#print (t.getXML())
s=Svg(0, 0, 2000, 2000)
s=t.addTurtlePathToSVG(s)
s.save('./testoutput/testTurtle.svg')
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 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)
def testLindenMayer():
s=Svg(0, 0, 2000, 2000)
commands='F+F-F-FF+F+F-F+F+F-F-FF+F+F-F+F+F-F-FF+F+F-F+F+F-F-FF+F+F-F'
t=Turtle()
t.moveTo(Vector(500,250))
t.penDown()
angle=90
distance=40
for cmd in commands:
print(cmd)
if cmd=='F':
t.forward(distance)
elif cmd=='+':
t.right(angle)
elif cmd=='-':
t.left(angle)
print(t.getPosition())
t.penDown()
print (t.getXML())
s=t.addTurtlePathToSVG(s)
s.save('./testoutput/testTurtle.svg')
def testLindenMayer():
s = Svg(0, 0, 2000, 2000)
commands = 'F+F-F-FF+F+F-F+F+F-F-FF+F+F-F+F+F-F-FF+F+F-F+F+F-F-FF+F+F-F'
t = Turtle()
t.moveTo(Vector(500, 250))
t.penDown()
angle = 90
distance = 40
for cmd in commands:
print(cmd)
if cmd == 'F':
t.forward(distance)
elif cmd == '+':
t.right(angle)
elif cmd == '-':
t.left(angle)
print(t.getPosition())
t.penDown()
print(t.getXML())
s = t.addTurtlePathToSVG(s)
s.save('./testoutput/testTurtle.svg')
def build_svg(self, outfile):
# background image
bg_image = PIL.Image.open(self.image_filename)
width, height = bg_image.size
# build a svg object, which size is the same as background
svg = Svg(width=width, height=height)
# add background image
png_link = bg_image.filename
if self.mode == 'online':
path = os.path.basename(self.image_filename).split('.')[0]
png_link = '{}/get/{}/image'.format(KEGGRest.KEGG_API_URL, path)
elif self.mode == 'base64':
with safe_open(self.image_filename, 'rb') as f:
png_link = 'data:image/png;base64,' + base64.b64encode(
f.read())
im = Image(x=0, y=0, width=width, height=height)
im.set_xlink_href(png_link)
svg.addElement(im)
for shape, position, url, title in self.conf_data:
a = A(target='new_window')
a.set_xlink_title(title)
a.set_xlink_href(KEGGRest.KEGG_BASE_URL + url)
# check gene, and add a highlighted rect or circle
color = get_gene_color(title, self.genedict)
child = self.add_child(shape, position, color)
if child:
a.addElement(child)
svg.addElement(a)
svg.save(outfile, encoding='UTF-8', standalone='no')
class SVGDrawingAlgorithm(object):
# options: shadow=True|False
def __init__(self, timeline, scene, view_properties, appearence, **kwargs):
self._timeline = timeline
self._scene = scene
self._appearence = appearence
self._view_properties = view_properties
self._svg = Svg(width=scene.width, height=scene.height)
self._small_font_style = self._get_small_font_style()
self._small_centered_font_style = self._get_small_centered_font_style()
self._larger_font_style = self._get_larger_font_style()
try:
self._shadow_flag = kwargs["shadow"]
except KeyError:
self._shadow_flag = False
def write(self, path):
"""
write the SVG code into the file with filename path. No
checking is done if file/path exists
"""
self._svg.save(path, encoding=ENCODING)
def draw(self):
for element in self._get_elements():
self._svg.addElement(element)
def _get_elements(self):
elements = [self._define_shadow_filter(), self._get_bg()]
elements.extend(self._get_events())
elements.extend(self._get_legend())
return elements
def _get_events(self):
return [
self._draw_event(event, rect)
for (event, rect) in self._scene.event_data
]
def _get_legend(self):
categories = self._extract_categories()
return [
item for item in [self._draw_legend(categories)]
if self._legend_should_be_drawn(categories)
]
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 _draw_background(self):
svg_color = self._map_svg_color(self._appearence.get_bg_colour())
return ShapeBuilder().createRect(0,
0,
self._scene.width,
self._scene.height,
fill=svg_color)
def _draw_era_strip(self, era):
svg_color = self._map_svg_color(era.get_color())
x, width = self._calc_era_strip_metrics(era)
return ShapeBuilder().createRect(x,
INNER_PADDING,
width,
self._scene.height -
2 * INNER_PADDING,
fill=svg_color,
strokewidth=0)
def _draw_era_text(self, era):
x, y = self._calc_era_text_metrics(era)
return self._draw_label(era.get_name(), x, y,
self._small_centered_font_style)
def _calc_era_strip_metrics(self, era):
period = era.get_time_period()
x = self._scene.x_pos_for_time(period.start_time)
width = min(self._scene.x_pos_for_time(period.end_time),
self._scene.width) - x
return x, width
def _calc_era_text_metrics(self, era):
period = era.get_time_period()
_, width = self._calc_era_strip_metrics(era)
x = self._scene.x_pos_for_time(period.start_time) + width // 2
y = self._scene.height - OUTER_PADDING
return x, y
def _draw_minor_strip_divider_line(self, time):
return self._draw_vertical_line(self._scene.x_pos_for_time(time),
"lightgrey")
def _draw_minor_strip_label(self, strip_period):
label = self._scene.minor_strip.label(strip_period.start_time)
x = self._calc_x_for_minor_strip_label(strip_period)
y = self._calc_y_for_minor_strip_label()
return self._draw_label(label, x, y, self._small_font_style)
def _calc_x_for_minor_strip_label(self, strip_period):
return (self._scene.x_pos_for_time(strip_period.start_time) +
self._scene.x_pos_for_time(
strip_period.end_time)) // 2 - SMALL_FONT_SIZE_PX
def _calc_y_for_minor_strip_label(self):
return self._scene.divider_y - OUTER_PADDING
def _draw_label(self, label, x, y, style):
text = self._text(label, x, y)
text.set_style(style.getStyle())
return text
def _draw_major_strip_divider_line(self, time):
return self._draw_vertical_line(self._scene.x_pos_for_time(time),
"black")
def _draw_vertical_line(self, x, colour):
return ShapeBuilder().createLine(x,
0,
x,
self._scene.height,
strokewidth=0.5,
stroke=colour)
def _draw_major_strip_label(self, tp):
label = self._scene.major_strip.label(tp.start_time, True)
# If the label is not visible when it is positioned in the middle
# of the period, we move it so that as much of it as possible is
# visible without crossing strip borders.
# since there is no function like textwidth() for SVG, just take into account that text can be overwritten
# do not perform a special handling for right border, SVG is unlimited
x = (max(0, self._scene.x_pos_for_time(tp.start_time)) + min(
self._scene.width, self._scene.x_pos_for_time(tp.end_time))) // 2
y = LARGER_FONT_SIZE_PX + OUTER_PADDING
return self._draw_label(label, x, y, self._larger_font_style)
def _draw_divider_line(self):
return ShapeBuilder().createLine(0,
self._scene.divider_y,
self._scene.width,
self._scene.divider_y,
strokewidth=0.5,
stroke="grey")
def _draw_lines_to_non_period_events(self, group, view_properties):
for (event, rect) in self._scene.event_data:
if rect.Y < self._scene.divider_y:
line, circle = self._draw_line_to_non_period_event(
view_properties, event, rect)
group.addElement(line)
group.addElement(circle)
def _draw_line_to_non_period_event(self, view_properties, event, rect):
x = self._scene.x_pos_for_time(event.mean_time())
y = rect.Y + rect.Height // 2
stroke = {
True: "red",
False: "black"
}[view_properties.is_selected(event)]
line = ShapeBuilder().createLine(x,
y,
x,
self._scene.divider_y,
stroke=stroke)
circle = ShapeBuilder().createCircle(x, self._scene.divider_y, 2)
return line, circle
def _draw_now_line(self):
return self._draw_vertical_line(self._scene.x_pos_for_now(), "darkred")
def _now_line_is_visible(self):
x = self._scene.x_pos_for_now()
return x > 0 and x < self._scene.width
def _get_event_border_color(self, event):
return self._map_svg_color(darken_color(self._get_event_color(event)))
def _get_event_box_color(self, event):
return self._map_svg_color(self._get_event_color(event))
def _get_box_indicator_color(self, event):
return self._map_svg_color(
darken_color(self._get_event_color(event), 0.6))
def _get_event_color(self, event):
if event.category:
return event.category.color
else:
return event.get_default_color()
def _map_svg_color(self, color):
"""
map (r,g,b) color to svg string
"""
return "#%02X%02X%02X" % color[:3]
def _legend_should_be_drawn(self, categories):
return self._appearence.get_legend_visible() and len(categories) > 0
def _extract_categories(self):
return sort_categories(
unique_based_on_eq(event.category
for (event, _) in self._scene.event_data
if event.category))
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 _draw_categories_box(self, nbr_of_categories):
return ShapeBuilder().createRect(
self._get_categories_box_x(),
self._get_categories_box_y(nbr_of_categories),
self._get_categories_box_width(),
self._get_categories_box_height(nbr_of_categories),
fill='white')
def _get_categories_box_width(self):
# reserve 15% for the legend
return int(self._scene.width * 0.15)
def _get_categories_item_height(self):
return SMALL_FONT_SIZE_PX + OUTER_PADDING
def _get_categories_box_height(self, nbr_of_categories):
return nbr_of_categories * (self._get_categories_item_height(
) + INNER_PADDING) + 2 * OUTER_PADDING - INNER_PADDING
def _get_categories_box_x(self):
return self._scene.width - self._get_categories_box_width(
) - OUTER_PADDING
def _get_categories_box_y(self, nbr_of_categories):
return self._scene.height - self._get_categories_box_height(
nbr_of_categories) - OUTER_PADDING
def _draw_category(self, width, item_height, x, y, cat):
return (self._draw_category_color_box(item_height, x, y, cat),
self._draw_category_label(width, item_height, x, y, cat))
def _draw_category_color_box(self, item_height, x, y, cat):
base_color = self._map_svg_color(cat.color)
border_color = self._map_svg_color(darken_color(cat.color))
return ShapeBuilder().createRect(x + OUTER_PADDING,
y,
item_height,
item_height,
fill=base_color,
stroke=border_color)
def _draw_category_label(self, width, item_height, x, y, cat):
return self._svg_clipped_text(
cat.name,
(x + OUTER_PADDING + INNER_PADDING + item_height, y,
width - OUTER_PADDING - INNER_PADDING - item_height, item_height),
self._get_small_font_style())
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 _draw_event_rect(self, event, rect):
boxBorderColor = self._get_event_border_color(event)
if event.is_container() and EXTENDED_CONTAINER_HEIGHT.enabled():
svg_rect = ShapeBuilder().createRect(
rect.X,
rect.Y - Y_RECT_OFFSET,
rect.GetWidth(),
rect.GetHeight() + Y_RECT_OFFSET,
stroke=boxBorderColor,
fill=self._get_event_box_color(event))
else:
svg_rect = ShapeBuilder().createRect(
rect.X,
rect.Y,
rect.GetWidth(),
rect.GetHeight(),
stroke=boxBorderColor,
fill=self._get_event_box_color(event))
if self._shadow_flag:
svg_rect.set_filter("url(#filterShadow)")
return svg_rect
def _draw_contents_indicator(self, event, rect):
"""
The data contents indicator is a small triangle drawn in the upper
right corner of the event rectangle.
"""
corner_x = rect.X + rect.Width
points = "%d,%d %d,%d %d,%d" % \
(corner_x - DATA_INDICATOR_SIZE, rect.Y,
corner_x, rect.Y,
corner_x, rect.Y + DATA_INDICATOR_SIZE)
color = self._get_box_indicator_color(event)
indicator = ShapeBuilder().createPolygon(points,
fill=color,
stroke=color)
# TODO (low): Transparency ?
return indicator
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
def _create_clip_path(self, rect):
path_id, path = self._calc_clip_path(rect)
clip = ClipPath()
clip.addElement(path)
clip.set_id(path_id)
self._svg.addElement(self._create_defs(clip))
return path_id
def _calc_clip_path(self, rect):
rx, ry, width, height = rect
if rx < 0:
width += rx
rx = 0
pathId = "path%d_%d_%d" % (rx, ry, width)
p = Path(pathData="M %d %d H %d V %d H %d" %
(rx, ry + height, rx + width, ry, rx))
return pathId, p
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 _calc_text_pos(self, rect, center_text=False):
rx, ry, width, height = rect
# In SVG, negative value should be OK, but they
# are not drawn in Firefox. So add a special handling here.
if rx < 0:
width += rx
x = 0
else:
x = rx + INNER_PADDING
if center_text:
x += (width - 2 * INNER_PADDING) // 2
y = ry + height - INNER_PADDING
return x, y
def _text(self, the_text, x, y):
encoded_text = self._encode_text(the_text)
return Text(encoded_text, x, y)
def _encode_text(self, text):
return xmlescape(text)
def _define_shadow_filter(self):
return self._create_defs(self._get_shadow_filter())
def _create_defs(self, definition):
d = Defs()
d.addElement(definition)
return d
def _get_small_font_style(self):
return self._get_font_style(SMALL_FONT_SIZE_PX, 'left', (2, 2))
def _get_small_centered_font_style(self):
return self._get_font_style(SMALL_FONT_SIZE_PX, 'middle', (2, 2))
def _get_larger_font_style(self):
return self._get_font_style(LARGER_FONT_SIZE_PX, 'left', "")
def _get_font_style(self, size, anchor, dash_array):
style = StyleBuilder()
style.setStrokeDashArray(dash_array)
style.setFontFamily(fontfamily="Verdana")
style.setFontSize("%dpx" % size)
style.setTextAnchor(anchor)
return style
def _get_shadow_filter(self):
filterShadow = Filter(x="-.3", y="-.5", width=1.9, height=1.9)
filtBlur = FeGaussianBlur(stdDeviation="4")
filtBlur.set_in("SourceAlpha")
filtBlur.set_result("out1")
filtOffset = FeOffset()
filtOffset.set_in("out1")
filtOffset.set_dx(4)
filtOffset.set_dy(-4)
filtOffset.set_result("out2")
filtMergeNode1 = FeMergeNode()
filtMergeNode1.set_in("out2")
filtMergeNode2 = FeMergeNode()
filtMergeNode2.set_in("SourceGraphic")
filtMerge = FeMerge()
filtMerge.addElement(filtMergeNode1)
filtMerge.addElement(filtMergeNode2)
filterShadow.addElement(
filtBlur
) # here i get an error from python. It is not allowed to add a primitive filter
filterShadow.addElement(filtOffset)
filterShadow.addElement(filtMerge)
filterShadow.set_id("filterShadow")
return filterShadow