[BioRuby-cvs] bioruby/lib/bio/util/color_scheme buried.rb, NONE,
1.1 helix.rb, NONE, 1.1 hydropathy.rb, NONE, 1.1 nucleotide.rb,
NONE, 1.1 strand.rb, NONE, 1.1 taylor.rb, NONE, 1.1 turn.rb,
NONE, 1.1 zappo.rb, NONE, 1.1
Katayama Toshiaki
k at pub.open-bio.org
Sun Oct 23 04:40:43 EDT 2005
Update of /home/repository/bioruby/bioruby/lib/bio/util/color_scheme
In directory pub.open-bio.org:/tmp/cvs-serv18484/lib/bio/util/color_scheme
Added Files:
buried.rb helix.rb hydropathy.rb nucleotide.rb strand.rb
taylor.rb turn.rb zappo.rb
Log Message:
* Newly added Bio::ColorScheme module contributed by
Trevor Wennblom <trevor at corevx.com>
--- NEW FILE: helix.rb ---
#
# bio/util/color_scheme/helix.rb - Color codings for helix propensity
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: helix.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Helix < Score
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(percent, 1.0-percent, percent)
end
@colors = {}
@scores = {
'A' => 1.42,
'C' => 0.7,
'D' => 1.01,
'E' => 1.51,
'F' => 1.13,
'G' => 0.57,
'H' => 1.0,
'I' => 1.08,
'K' => 1.16,
'L' => 1.21,
'M' => 1.45,
'N' => 0.67,
'P' => 0.57,
'Q' => 1.11,
'R' => 0.98,
'S' => 0.77,
'T' => 0.83,
'U' => 0.0,
'V' => 1.06,
'W' => 1.08,
'Y' => 0.69,
'B' => 0.84,
'X' => 1.0,
'Z' => 1.31,
}
@min = 0.57
@max = 1.51
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: strand.rb ---
#
# bio/util/color_scheme/strand.rb - Color codings for strand propensity
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: strand.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Strand < Score
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(percent, 0.0, 1.0-percent)
end
@colors = {}
@scores = {
'A' => 0.83,
'C' => 1.19,
'D' => 0.54,
'E' => 0.37,
'F' => 1.38,
'G' => 0.75,
'H' => 0.87,
'I' => 1.6,
'K' => 0.74,
'L' => 1.3,
'M' => 1.05,
'N' => 0.89,
'P' => 0.55,
'Q' => 1.1,
'R' => 0.93,
'S' => 0.75,
'T' => 1.19,
'U' => 0.0,
'V' => 1.7,
'W' => 1.37,
'Y' => 1.47,
'B' => 0.72,
'X' => 1.0,
'Z' => 0.74,
}
@min = 0.37
@max = 1.7
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: turn.rb ---
#
# bio/util/color_scheme/turn.rb - Color codings for turn propensity
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: turn.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Turn < Score
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(percent, 1.0-percent, 1.0-percent)
end
@colors = {}
@scores = {
'A' => 0.66,
'C' => 1.19,
'D' => 1.46,
'E' => 0.74,
'F' => 0.6,
'G' => 1.56,
'H' => 0.95,
'I' => 0.47,
'K' => 1.01,
'L' => 0.59,
'M' => 0.6,
'N' => 1.56,
'P' => 1.52,
'Q' => 0.98,
'R' => 0.95,
'S' => 1.43,
'T' => 0.96,
'U' => 0,
'V' => 0.5,
'W' => 0.96,
'Y' => 1.14,
'B' => 1.51,
'X' => 1.0,
'Z' => 0.86,
}
@min = 0.47
@max = 1.56
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: taylor.rb ---
#
# bio/util/color_scheme/taylor.rb - Taylor color codings for amino acids
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: taylor.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Taylor < Simple
#########
protected
#########
@colors = {
'A' => 'CCFF00',
'C' => 'FFFF00',
'D' => 'FF0000',
'E' => 'FF0066',
'F' => '00FF66',
'G' => 'FF9900',
'H' => '0066FF',
'I' => '66FF00',
'K' => '6600FF',
'L' => '33FF00',
'M' => '00FF00',
'N' => 'CC00FF',
'P' => 'FFCC00',
'Q' => 'FF00CC',
'R' => '0000FF',
'S' => 'FF3300',
'T' => 'FF6600',
'U' => 'FFFFFF',
'V' => '99FF00',
'W' => '00CCFF',
'Y' => '00FFCC',
'B' => 'FFFFFF',
'X' => 'FFFFFF',
'Z' => 'FFFFFF',
}
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: hydropathy.rb ---
#
# bio/util/color_scheme/hydropathy.rb - Color codings for hydrophobicity
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: hydropathy.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
# Hydropathy index
# Kyte, J., and Doolittle, R.F., J. Mol. Biol.
# 1157, 105-132, 1982
module Bio::ColorScheme
class Hydropathy < Score
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(percent, 0.0, 1.0-percent)
end
@colors = {}
@scores = {
'A' => 1.8,
'C' => 2.5,
'D' => -3.5,
'E' => -3.5,
'F' => 2.8,
'G' => -0.4,
'H' => -3.2,
'I' => 4.5,
'K' => -3.9,
'L' => 3.8,
'M' => 1.9,
'N' => -3.5,
'P' => -1.6,
'Q' => -3.5,
'R' => -4.5,
'S' => -0.8,
'T' => -0.7,
'U' => 0.0,
'V' => 4.2,
'W' => -0.9,
'Y' => -1.3,
'B' => -3.5,
'X' => -0.49,
'Z' => -3.5,
}
@min = -3.9
@max = 4.5
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: zappo.rb ---
#
# bio/util/color_scheme/zappo.rb - Zappo color codings for amino acids
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: zappo.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Zappo < Simple
#########
protected
#########
@colors = {
'A' => 'FFAFAF',
'C' => 'FFFF00',
'D' => 'FF0000',
'E' => 'FF0000',
'F' => 'FFC800',
'G' => 'FF00FF',
'H' => 'FF0000',
'I' => 'FFAFAF',
'K' => '6464FF',
'L' => 'FFAFAF',
'M' => 'FFAFAF',
'N' => '00FF00',
'P' => 'FF00FF',
'Q' => '00FF00',
'R' => '6464FF',
'S' => '00FF00',
'T' => '00FF00',
'U' => 'FFFFFF',
'V' => 'FFAFAF',
'W' => 'FFC800',
'Y' => 'FFC800',
'B' => 'FFFFFF',
'X' => 'FFFFFF',
'Z' => 'FFFFFF',
}
@colors.default = 'FFFFFF' # return white by default
end
end
--- NEW FILE: nucleotide.rb ---
#
# bio/util/color_scheme/nucleotide.rb - Color codings for nucleotides
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: nucleotide.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Nucleotide < Simple
#########
protected
#########
@colors = {
'A' => '64F73F',
'C' => 'FFB340',
'G' => 'EB413C',
'T' => '3C88EE',
'U' => '3C88EE',
}
@colors.default = 'FFFFFF' # return white by default
end
NA = Nuc = Nucleotide
end
--- NEW FILE: buried.rb ---
#
# bio/util/color_scheme/buried.rb - Color codings for buried amino acids
#
# Copyright (C) 2005 Trevor Wennblom <trevor at corevx.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: buried.rb,v 1.1 2005/10/23 08:40:41 k Exp $
#
require 'bio/util/color_scheme'
module Bio::ColorScheme
class Buried < Score
#########
protected
#########
def self.score_to_rgb_hex(score, min, max)
percent = score_to_percent(score, min, max)
rgb_percent_to_hex(0.0, 1.0-percent, percent)
end
@colors = {}
@scores = {
'A' => 0.66,
'C' => 1.19,
'D' => 1.46,
'E' => 0.74,
'F' => 0.6,
'G' => 1.56,
'H' => 0.95,
'I' => 0.47,
'K' => 1.01,
'L' => 0.59,
'M' => 0.6,
'N' => 1.56,
'P' => 1.52,
'Q' => 0.98,
'R' => 0.95,
'S' => 1.43,
'T' => 0.96,
'U' => 0,
'V' => 0.5,
'W' => 0.96,
'Y' => 1.14,
'B' => 1.51,
'X' => 1.0,
'Z' => 0.86,
}
@min = 0.05
@max = 4.6
@scores.each { |k,s| @colors[k] = score_to_rgb_hex(s, @min, @max) }
@colors.default = 'FFFFFF' # return white by default
end
end
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