# 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)