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# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: Leighton Pritchard, The James Hutton Institute,
# Invergowrie, Dundee, Scotland, DD2 5DA, UK
# Leighton.Pritchard@hutton.ac.uk
################################################################################
"""Colors module.
Provides:
- ColorTranslator - class to convert tuples of integers and floats into
colors.Color objects
For drawing capabilities, this module uses reportlab to define colors:
http://www.reportlab.com
"""
# ReportLab imports
from reportlab.lib import colors
class ColorTranslator:
"""Class providing methods for translating representations of color into.
Examples
--------
>>> from Bio.Graphics import GenomeDiagram
>>> gdct=GenomeDiagram._Colors.ColorTranslator()
>>> print(gdct.float1_color((0.5, 0.5, 0.5)))
Color(.5,.5,.5,1)
>>> print(gdct.int255_color((1, 75, 240)))
Color(.003922,.294118,.941176,1)
>>> print(gdct.artemis_color(7))
Color(1,1,0,1)
>>> print(gdct.scheme_color(2))
Color(1,0,0,1)
>>> gdct.get_artemis_colorscheme()
{0: (Color(1,1,1,1), 'pathogenicity, adaptation, chaperones'), 1: (Color(.39,.39,.39,1), 'energy metabolism'), 2: (Color(1,0,0,1), 'information transfer'), 3: (Color(0,1,0,1), 'surface'), 4: (Color(0,0,1,1), 'stable RNA'), 5: (Color(0,1,1,1), 'degradation of large molecules'), 6: (Color(1,0,1,1), 'degradation of small molecules'), 7: (Color(1,1,0,1), 'central/intermediary/miscellaneous metabolism'), 8: (Color(.6,.98,.6,1), 'unknown'), 9: (Color(.53,.81,.98,1), 'regulators'), 10: (Color(1,.65,0,1), 'conserved hypotheticals'), 11: (Color(.78,.59,.39,1), 'pseudogenes and partial genes'), 12: (Color(1,.78,.78,1), 'phage/IS elements'), 13: (Color(.7,.7,.7,1), 'some miscellaneous information'), 14: (Color(0,0,0,1), ''), 15: (Color(1,.25,.25,1), 'secondary metabolism'), 16: (Color(1,.5,.5,1), ''), 17: (Color(1,.75,.75,1), '')}
>>> print(gdct.translate((0.5, 0.5, 0.5)))
Color(.5,.5,.5,1)
>>> print(gdct.translate((1, 75, 240)))
Color(.003922,.294118,.941176,1)
>>> print(gdct.translate(7))
Color(1,1,0,1)
>>> print(gdct.translate(2))
Color(1,0,0,1)
"""
def __init__(self, filename=None):
"""Initialize.
Argument filename is the location of a file containing
colorscheme information.
"""
self._artemis_colorscheme = {
0: (colors.Color(1, 1, 1), "pathogenicity, adaptation, chaperones"),
1: (colors.Color(0.39, 0.39, 0.39), "energy metabolism"),
2: (colors.Color(1, 0, 0), "information transfer"),
3: (colors.Color(0, 1, 0), "surface"),
4: (colors.Color(0, 0, 1), "stable RNA"),
5: (colors.Color(0, 1, 1), "degradation of large molecules"),
6: (colors.Color(1, 0, 1), "degradation of small molecules"),
7: (colors.Color(1, 1, 0), "central/intermediary/miscellaneous metabolism"),
8: (colors.Color(0.60, 0.98, 0.60), "unknown"),
9: (colors.Color(0.53, 0.81, 0.98), "regulators"),
10: (colors.Color(1, 0.65, 0), "conserved hypotheticals"),
11: (colors.Color(0.78, 0.59, 0.39), "pseudogenes and partial genes"),
12: (colors.Color(1, 0.78, 0.78), "phage/IS elements"),
13: (colors.Color(0.70, 0.70, 0.70), "some miscellaneous information"),
14: (colors.Color(0, 0, 0), ""),
15: (colors.Color(1, 0.25, 0.25), "secondary metabolism"),
16: (colors.Color(1, 0.5, 0.5), ""),
17: (colors.Color(1, 0.75, 0.75), ""),
} # Hardwired Artemis color scheme
self._colorscheme = {}
if filename is not None:
self.read_colorscheme(filename) # Imported color scheme
else:
self._colorscheme = self._artemis_colorscheme
def translate(self, color=None, colour=None):
"""Translate a color into a ReportLab Color object.
Arguments:
- color - Color defined as an int, a tuple of three ints 0->255
or a tuple of three floats 0 -> 1, or a string giving
one of the named colors defined by ReportLab, or a
ReportLab color object (returned as is).
- colour - Backwards compatible alias using UK spelling (which
will over-ride any color argument).
Returns a colors.Color object, determined semi-intelligently
depending on the input values
"""
# Let the UK spelling (colour) override the USA spelling (color)
if colour is not None:
color = colour
if color is None:
raise ValueError("Passed color (or colour) must be a valid color type")
elif isinstance(color, int):
color = self.scheme_color(color)
elif isinstance(color, colors.Color):
return color
elif isinstance(color, str):
# Assume its a named reportlab color like "red".
color = colors.toColor(color)
elif isinstance(color, tuple) and isinstance(color[0], float):
color = self.float1_color(color)
elif isinstance(color, tuple) and isinstance(color[0], int):
color = self.int255_color(color)
return color
def read_colorscheme(self, filename):
r"""Load colour scheme from file.
Reads information from a file containing color information and stores
it internally.
Argument filename is the location of a file defining colors in
tab-separated format plaintext as::
INT \t RED \t GREEN \t BLUE \t Comment
Where RED, GREEN and BLUE are intensities in the range 0 -> 255, e.g.::
2 \t 255 \t 0 \t 0 \t Red: Information transfer
"""
with open(filename).readlines() as lines:
for line in lines:
data = line.strip().split("\t")
try:
label = int(data[0])
red, green, blue = int(data[1]), int(data[2]), int(data[3])
if len(data) > 4:
comment = data[4]
else:
comment = ""
self._colorscheme[label] = (
self.int255_color((red, green, blue)),
comment,
)
except ValueError:
raise ValueError(
"Expected INT \t INT \t INT \t INT \t string input"
) from None
def get_artemis_colorscheme(self):
"""Return the Artemis color scheme as a dictionary."""
return self._artemis_colorscheme
def artemis_color(self, value):
"""Artemis color (integer) to ReportLab Color object.
Arguments:
- value: An int representing a functional class in the Artemis
color scheme (see www.sanger.ac.uk for a description),
or a string from a GenBank feature annotation for the
color which may be dot delimited (in which case the
first value is used).
Takes an int representing a functional class in the Artemis color
scheme, and returns the appropriate colors.Color object
"""
try:
value = int(value)
except ValueError:
if value.count("."): # dot-delimited
value = int(value.split(".", 1)[0]) # Use only first integer
else:
raise
if value in self._artemis_colorscheme:
return self._artemis_colorscheme[value][0]
else:
raise ValueError("Artemis color out of range: %d" % value)
def get_colorscheme(self):
"""Return the user-defined color scheme as a dictionary."""
return self._colorscheme
def scheme_color(self, value):
"""Map a user-defined color integer to a ReportLab Color object.
- value: An int representing a single color in the user-defined
color scheme
Takes an int representing a user-defined color and returns the
appropriate colors.Color object.
"""
if value in self._colorscheme:
return self._colorscheme[value][0]
else:
raise ValueError("Scheme color out of range: %d" % value)
def int255_color(self, values):
"""Map integer (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as
integers in the range 0->255
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 255 and returns an appropriate colors.Color object.
"""
red, green, blue = values
factor = 1 / 255.0
red, green, blue = red * factor, green * factor, blue * factor
return colors.Color(red, green, blue)
def float1_color(self, values):
"""Map float (red, green, blue) tuple to a ReportLab Color object.
- values: A tuple of (red, green, blue) intensities as floats
in the range 0 -> 1
Takes a tuple of (red, green, blue) intensity values in the range
0 -> 1 and returns an appropriate colors.Color object.
"""
red, green, blue = values
return colors.Color(red, green, blue)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest(verbose=2)
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