def _compose_crosslink(self, index, result, features1, features2):
for f1, f2, col in result:
if f1 is None: continue
if self.no_color: col = colors.color2bw(col)
tf1 = features1.add_feature(f1, color=col, border=col)
tf2 = features2.add_feature(f2, color=col, border=col)
self.diagram.cross_track_links.append(CrossLink(tf1, tf2, col, col))
def test0(self):
"Test color2bw function on all named colors."
cols = list(colors.getAllNamedColors().values())
for col in cols:
gray = colors.color2bw(col)
r, g, b = gray.red, gray.green, gray.blue
assert r == g == b
def test0(self):
"Test color2bw function on all named colors."
cols = colors.getAllNamedColors().values()
for col in cols:
gray = colors.color2bw(col)
r, g, b = gray.red, gray.green, gray.blue
assert r == g == b
def draw_clusters(self):
print 'Creating cluster diagram.'
# create diagram
self.diagram = GenomeDiagram.Diagram(self.name)
# add tracks
max_len = max(len(c) for c in self.clusters)
normal_color = colors.grey if self.no_color else colors.black
mark_color = colors.black if self.no_color else colors.red
for cluster in self.clusters:
col = mark_color if cluster.marked else normal_color
track = self.diagram.new_track(1,
name=cluster.label,
greytrack=1, height=0.4,
greytrack_fontcolor=col,
greytrack_labels=1,
greytrack_fontsize=self.name_size,
scale=False,
start=0, end=max_len)
self.fsets.append(track.new_set())
# add crosslink features
if self.add_crosslinks:
self._compose_crosslinks()
# add CDS-es
for ci, cluster in enumerate(self.clusters):
gene_id = 0
for f in cluster.CDS:
known = False
fname = 'NONE'
if gene_id < len(cluster.genes):
fname = cluster.genes[gene_id]
fcolor = self.colors.get(fname, self.default_color)
if fname == 'NONE':
fname = self._feature_name(f, default='')
fcolor = self.default_color
else:
#decapitalize gene names if they are marked as proteins
# fname = fname[:1].lower() + fname[1:] if fname else ''
known = True
if self.no_color: fcolor = colors.color2bw(fcolor)
self.fsets[ci].add_feature(f, sigil="BIGARROW",
color=fcolor,
border=fcolor if self.no_border else colors.black,
name=fname, label=True,
label_position="middle",
label_size=self.gene_size if known else self.unknown_gene_size,
label_color=colors.black if known else colors.grey,
label_angle=self.gene_angle)
gene_id += 1
self.diagram.draw(format="linear", pagesize=self.pagesize, fragments=1,
start=0, end=max_len)
for ptype in ('PDF', 'EPS', 'SVG'):
dianame = '%s.%s' % (self.name, ptype.lower())
print 'Saving: %s' % dianame
self.diagram.write(dianame, ptype)
print 'Done.'
def test5(self):
"List and display all named colors and their gray equivalents."
canvas = reportlab.pdfgen.canvas.Canvas(
outputfile('test_lib_colors.pdf'))
#do all named colors
framePage(canvas, 'Color Demo - page %d' % canvas.getPageNumber())
all_colors = list(reportlab.lib.colors.getAllNamedColors().items())
all_colors.sort() # alpha order by name
canvas.setFont('Times-Roman', 10)
text = 'This shows all the named colors in the HTML standard (plus their gray and CMYK equivalents).'
canvas.drawString(72, 740, text)
canvas.drawString(200, 725, 'Pure RGB')
canvas.drawString(300, 725, 'B&W Approx')
canvas.drawString(400, 725, 'CMYK Approx')
y = 700
for (name, color) in all_colors:
canvas.setFillColor(colors.black)
canvas.drawString(100, y, name)
canvas.setFillColor(color)
canvas.rect(200, y - 10, 80, 30, fill=1)
canvas.setFillColor(colors.color2bw(color))
canvas.rect(300, y - 10, 80, 30, fill=1)
c, m, yel, k = colors.rgb2cmyk(color.red, color.green, color.blue)
CMYK = colors.CMYKColor(c, m, yel, k)
canvas.setFillColor(CMYK)
canvas.rect(400, y - 10, 80, 30, fill=1)
y = y - 40
if y < 100:
canvas.showPage()
framePage(canvas,
'Color Demo - page %d' % canvas.getPageNumber())
canvas.setFont('Times-Roman', 10)
y = 700
canvas.drawString(200, 725, 'Pure RGB')
canvas.drawString(300, 725, 'B&W Approx')
canvas.drawString(400, 725, 'CMYK Approx')
canvas.save()
def test5(self):
"List and display all named colors and their gray equivalents."
canvas = reportlab.pdfgen.canvas.Canvas(outputfile('test_lib_colors.pdf'))
#do all named colors
framePage(canvas, 'Color Demo - page %d' % canvas.getPageNumber())
all_colors = reportlab.lib.colors.getAllNamedColors().items()
all_colors.sort() # alpha order by name
canvas.setFont('Times-Roman', 10)
text = 'This shows all the named colors in the HTML standard (plus their gray and CMYK equivalents).'
canvas.drawString(72,740, text)
canvas.drawString(200,725,'Pure RGB')
canvas.drawString(300,725,'B&W Approx')
canvas.drawString(400,725,'CMYK Approx')
y = 700
for (name, color) in all_colors:
canvas.setFillColor(colors.black)
canvas.drawString(100, y, name)
canvas.setFillColor(color)
canvas.rect(200, y-10, 80, 30, fill=1)
canvas.setFillColor(colors.color2bw(color))
canvas.rect(300, y-10, 80, 30, fill=1)
c, m, yel, k = colors.rgb2cmyk(color.red, color.green, color.blue)
CMYK = colors.CMYKColor(c,m,yel,k)
canvas.setFillColor(CMYK)
canvas.rect(400, y-10, 80, 30, fill=1)
y = y - 40
if y < 100:
canvas.showPage()
framePage(canvas, 'Color Demo - page %d' % canvas.getPageNumber())
canvas.setFont('Times-Roman', 10)
y = 700
canvas.drawString(200,725,'Pure RGB')
canvas.drawString(300,725,'B&W Approx')
canvas.drawString(400,725,'CMYK Approx')
canvas.save()
def hex_base_color(self):
if self.force_bw:
return color2bw(HexColor(self.base_color))
else:
return HexColor(self.base_color)
def hex_base_color(self):
if self.force_bw:
return color2bw(HexColor(self.base_color))
else:
return HexColor(self.base_color)
