bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/cell/specialized_cells/T_cell.rb

@@ -0,0 +1,60 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::T_cell
+#
+# This class describes a T cell (T lymphocyte).
+#
+# Usage example:
+#
+#   Bioroebe::T_cell.new
+#
+# =========================================================================== #
+# require 'bioroebe/cell/specialized_cells/T_cell.rb'
+# =========================================================================== #
+require 'bioroebe/cell/cell.rb'
+
+module Bioroebe
+
+class T_cell < ::Bioroebe::Cell # === Bioroebe::T_cell
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::T_cell[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::T_cell.new(ARGV)
+end # bioroebecell

data/lib/bioroebe/cleave_and_digest/cleave.rb

@@ -75,6 +75,8 @@ end
 if __FILE__ == $PROGRAM_NAME
   alias e puts
   _ = ARGV.join
-  e 'Input sequence is: '+_
+  e 'The input sequence is: '+_
+  e
   pp Bioroebe.cleave_with_trypsin(_)
+  e
 end # cleavewithtrypsin KRPKAKAGAGAUUGAUGAAGCCACA

data/lib/bioroebe/cleave_and_digest/digestion.rb

@@ -14,7 +14,7 @@
 # require 'bioroebe/cleave_and_digest/digestion.rb'
 # < Bioroebe::Digestion
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml

@@ -0,0 +1,93 @@
+# =========================================================================== #
+# Filename: 10090_Mus_musculus.yml
+#
+# The following dataset was obtained from:
+#
+#   https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=10090
+#
+#
+# UUU 17.2(422153)  UCU 16.2(398250)  UAU 12.2(298518)  UGU 11.4(279729)
+# UUC 21.8(535439)  UCC 18.1(444041)  UAC 16.1(394074)  UGC 12.3(301384)
+# UUA  6.7(165150)  UCA 11.8(289799)  UAA  1.0( 23403)  UGA  1.6( 40148)
+# UUG 13.4(329668)  UCG  4.2(103815)  UAG  0.8( 19126)  UGG 12.5(306619)
+#
+# CUU 13.4(329757)  CCU 18.4(450637)  CAU 10.6(260637)  CGU  4.7(114854)
+# CUC 20.2(495018)  CCC 18.2(446868)  CAC 15.3(375626)  CGC  9.4(229758)
+# CUA  8.1(198032)  CCA 17.3(423707)  CAA 12.0(293318)  CGA  6.6(161412)
+# CUG 39.5(969515)  CCG  6.2(151521)  CAG 34.1(836320)  CGG 10.2(250836)
+#
+# AUU 15.4(377698)  ACU 13.7(335039)  AAU 15.6(382284)  AGU 12.7(311331)
+# AUC 22.5(552184)  ACC 19.0(465115)  AAC 20.3(499149)  AGC 19.7(483013)
+# AUA  7.4(180467)  ACA 16.0(391437)  AAA 21.9(537723)  AGA 12.1(297135)
+# AUG 22.8(559953)  ACG  5.6(138180)  AAG 33.6(825270)  AGG 12.2(299472)
+#
+# GUU 10.7(262535)  GCU 20.0(491093)  GAU 21.0(515049)  GGU 11.4(280522)
+# GUC 15.4(377902)  GCC 26.0(637878)  GAC 26.0(638504)  GGC 21.2(520069)
+# GUA  7.4(182733)  GCA 15.8(388723)  GAA 27.0(661498)  GGA 16.8(411344)
+# GUG 28.4(696158)  GCG  6.4(157124)  GAG 39.4(965963)  GGG 15.2(372099)
+# =========================================================================== #
+
+UUU: 17.2
+UCU: 16.2
+UAU: 12.2
+UGU: 11.4
+UUC: 21.8
+UCC: 18.1
+UAC: 16.1
+UGC: 12.3
+UUA:  6.7
+UCA: 11.8
+UAA:  1.0
+UGA:  1.6
+UUG: 13.4
+UCG:  4.2
+UAG:  0.8
+UGG: 12.5
+CUU: 13.4
+CCU: 18.4
+CAU: 10.6
+CGU:  4.7
+CUC: 20.2
+CCC: 18.2
+CAC: 15.3
+CGC:  9.4
+CUA:  8.1
+CCA: 17.3
+CAA: 12.0
+CGA:  6.6
+CUG: 39.5
+CCG:  6.2
+CAG: 34.1
+CGG: 10.2
+AUU: 15.4
+ACU: 13.7
+AAU: 15.6
+AGU: 12.7
+AUC: 22.5
+ACC: 19.0
+AAC: 20.3
+AGC: 19.7
+AUA:  7.4
+ACA: 16.0
+AAA: 21.9
+AGA: 12.1
+AUG: 22.8
+ACG:  5.6
+AAG: 33.6
+AGG: 12.2
+GUU: 10.7
+GCU: 20.0
+GAU: 21.0
+GGU: 11.4
+GUC: 15.4
+GCC: 26.0
+GAC: 26.0
+GGC: 21.2
+GUA:  7.4
+GCA: 15.8
+GAA: 27.0
+GGA: 16.8
+GUG: 28.4
+GCG:  6.4
+GAG: 39.4
+GGG: 15.2

data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml

@@ -0,0 +1,72 @@
+#
+# Filename: 107243_Thlaspi_caerulescens.yml
+#
+# The following dataset was obtained from:
+#
+#   https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=107243
+#
+#
+UUU: 21.0
+UCU: 21.5
+UAU:  9.8
+UGU: 11.7
+UUC: 30.3
+UCC: 10.6
+UAC: 14.8
+UGC: 10.6
+UUA:  9.7
+UCA: 16.0
+UAA:  0.8
+UGA:  0.9
+UUG: 20.6
+UCG:  9.7
+UAG:  0.4
+UGG: 13.4
+CUU: 25.9
+CCU: 15.5
+CAU: 13.4
+CGU:  4.8
+CUC: 24.9
+CCC:  5.2
+CAC: 10.1
+CGC:  2.7
+CUA:  9.5
+CCA:  9.9
+CAA: 15.7
+CGA:  3.9
+CUG: 10.6
+CCG: 10.2
+CAG: 14.1
+CGG:  2.4
+AUU: 21.4
+ACU: 16.3
+AAU: 13.7
+AGU: 12.5
+AUC: 32.7
+ACC: 11.5
+AAC: 19.4
+AGC: 12.7
+AUA: 15.3
+ACA: 14.0
+AAA: 26.2
+AGA: 11.0
+AUG: 28.2
+ACG:  8.5
+AAG: 29.4
+AGG:  8.6
+GUU: 26.7
+GCU: 37.1
+GAU: 25.7
+GGU: 24.2
+GUC: 16.6
+GCC: 15.1
+GAC: 18.0
+GGC: 11.7
+GUA:  8.3
+GCA: 18.4
+GAA: 27.6
+GGA: 30.4
+GUG: 24.1
+GCG: 13.3
+GAG: 26.5
+GGG: 14.2

data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb

@@ -18,7 +18,7 @@
 # require 'bioroebe/codon_tables/frequencies/parse_frequency_table.rb'
 # Bioroebe::ParseFrequencyTable
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -315,7 +315,7 @@ GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'
   # ========================================================================= #
   # === Bioroebe::ParseFrequencyTable[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/codons/codon_table.rb

@@ -61,6 +61,9 @@ module Bioroebe
       i = 1 # :human
     end
     case be_verbose
+    # ======================================================================= #
+    # === :be_verbose
+    # ======================================================================= #
     when :be_verbose
       be_verbose = :be_verbose
     end
@@ -351,7 +354,10 @@ module Bioroebe
   # codon table. I recommend that you use this method - it is
   # more convenient than the other methods.
   # ========================================================================= #
-  def self.set_use_this_codon_table(i = :humans)
+  def self.set_use_this_codon_table(
+      i = :humans
+    )
+    require 'bioroebe/codons/codons.rb'
     set_codon_table_in_use(i)
     load_the_codon_table_dataset(i)
     determine_stop_codons_from_the_codon_table
@@ -399,7 +405,9 @@ module CodonTable
   #   x = Bioroebe::CodonTable.by_name("Vertebrate Mitochondrial")
   #
   # ========================================================================= #
-  def self.by_name(i = 'Vertebrate Mitochondrial')
+  def self.by_name(
+      i = 'Vertebrate Mitochondrial'
+    )
     ::Bioroebe.set_use_this_codon_table(i)
     return ::Bioroebe.codon_table_dataset?
   end; self.instance_eval { alias by_id by_name } # === Bioroebe::CodonTable.by_id

data/lib/bioroebe/codons/codons.rb

@@ -21,8 +21,8 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/constants/codon_tables.rb'
   require 'bioroebe/regexes/regexes.rb'
+  require 'bioroebe/codons/codon_tables.rb'
   require 'bioroebe/codons/codon_table.rb'
   # require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
@@ -362,7 +362,7 @@ module Bioroebe
        self.instance_eval { alias decode_this_aminoacid_sequence codons_for_this_aminoacid? } # === Bioroebe.decode_this_aminoacid_sequence
        self.instance_eval { alias nucleotides_to_aminoacid       codons_for_this_aminoacid? } # === Bioroebe.nucleotides_to_aminoacid
 
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
   # ========================================================================= #
   # === Bioroebe.decode_this_aminoacid_sequence
   #
@@ -465,7 +465,7 @@ end
 
 if __FILE__ == $PROGRAM_NAME
   require 'colours/autoinclude'
-  require 'bioroebe/nucleotides/show_nucleotide_sequence.rb'
+  require 'bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb'
   puts Bioroebe.is_a_stop_codon? 'TAG'
   Bioroebe.initialize_codons
   puts Bioroebe.is_a_stop_codon? 'TAG'

data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb

@@ -46,7 +46,7 @@
 # =========================================================================== #
 # require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -85,15 +85,15 @@ class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # ===
   # ========================================================================= #
   def reset
     super()
-    reset_the_internal_hash
     # ======================================================================= #
-    # === @shall_we_replace_stop_codons
+    # === @internal_hash[:shall_we_replace_stop_codons]
     # ======================================================================= #
-    @shall_we_replace_stop_codons = :default
+    @internal_hash[:shall_we_replace_stop_codons] = :default
     # ======================================================================= #
     # === :with_trailer
     # ======================================================================= #
     @internal_hash[:with_trailer] = false
+    set_be_verbose
   end
 
   # ========================================================================= #
@@ -137,13 +137,6 @@ class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # ===
     @internal_hash[:with_trailer]
   end
 
-  # ========================================================================= #
-  # === report                                                   (report tag)
-  # ========================================================================= #
-  def report
-    e @result if be_verbose?
-  end
-
   # ========================================================================= #
   # === result?
   # ========================================================================= #
@@ -159,12 +152,12 @@ class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # ===
     menu( # Pass all arguments that start with -- next.
       commandline_arguments_starting_with_a_hyphen(i)
     )
-    case @shall_we_replace_stop_codons
+    case @internal_hash[:shall_we_replace_stop_codons]
     # ======================================================================= #
     # === :default
     # ======================================================================= #
     when :default
-      @shall_we_replace_stop_codons = true
+      @internal_hash[:shall_we_replace_stop_codons] = true
     end
     if i.is_a? Array
       i = reject_hyphens(i).join
@@ -205,6 +198,13 @@ class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # ===
     report
   end
 
+  # ========================================================================= #
+  # === report                                                   (report tag)
+  # ========================================================================= #
+  def report
+    e @result if be_verbose?
+  end
+
   # ========================================================================= #
   # === Bioroebe::ConvertThisCodonToThatAminoacid[]
   #
@@ -222,8 +222,11 @@ end
 # =========================================================================== #
 # === Bioroebe.convert_this_codon_to_that_aminoacid
 # =========================================================================== #
-def self.convert_this_codon_to_that_aminoacid(i = ARGV)
-  Bioroebe::ConvertThisCodonToThatAminoacid.new(i) { :be_quiet }
+def self.convert_this_codon_to_that_aminoacid(
+    i = ARGV,
+    &block
+  )
+  Bioroebe::ConvertThisCodonToThatAminoacid.new(i) { :be_quiet }.result?.to_s
 end; self.instance_eval { alias decode_this_codon               convert_this_codon_to_that_aminoacid } # === Bioroebe.decode_this_codon
      self.instance_eval { alias convert_dna_to_protein_sequence convert_this_codon_to_that_aminoacid } # === Bioroebe.convert_dna_to_protein_sequence
      self.instance_eval { alias translate_dna_into_aminoacid    convert_this_codon_to_that_aminoacid } # === Bioroebe.translate_dna_into_aminoacid

data/lib/bioroebe/codons/determine_optimal_codons.rb

@@ -16,7 +16,7 @@
 # =========================================================================== #
 # require 'bioroebe/codons/determine_optimal_codons.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb

@@ -19,7 +19,7 @@
 # require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
 # Bioroebe::PossibleCodonsForThisAminoacid.new(ARGV).report
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -187,7 +187,9 @@ class PossibleCodonsForThisAminoacid < ::Bioroebe::CommandlineApplication # ===
       result << 'this'
     end
     result << rev+
-              ' '+keys?.size.to_s+
+              ' '+
+              royalblue(keys?.size.to_s)+
+              rev+
               ' nucleotide '+codon_singular_or_plural+
               ":\n\n"
     result << "  #{sfancy(array_like_result?)}#{rev}\n\n"

data/lib/bioroebe/codons/show_codon_tables.rb

@@ -9,7 +9,7 @@
 # =========================================================================== #
 # require 'bioroebe/codons/show_codon_tables.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/codons/show_codon_usage.rb

@@ -17,13 +17,12 @@
 # require 'bioroebe/codons/show_codon_usage.rb'
 # Bioroebe::ShowCodonUsage.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCodonUsage
 
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
   require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
   # ========================================================================= #

data/lib/bioroebe/codons/show_this_codon_table.rb

@@ -24,7 +24,7 @@
 # require 'bioroebe/codons/show_this_codon_table.rb'
 # Bioroebe::ShowThisCodonTable.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -112,7 +112,6 @@ class ShowThisCodonTable < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    @internal_hash = {}
     # ======================================================================= #
     # === :title
     # ======================================================================= #
@@ -496,6 +495,7 @@ class ShowThisCodonTable < ::Bioroebe::CommandlineApplication
   def set_use_this_codon_table(
       i = DEFAULT_CODON_TABLE_TO_USE
     )
+    require 'bioroebe/codons/codon_table.rb'
     i = i.first if i.is_a? Array
     case i
     when 'human'

data/lib/bioroebe/codons/start_codons.rb

@@ -33,7 +33,9 @@ module Bioroebe
   #
   # This will designate the most important start codon.
   # ========================================================================= #
-  def self.set_start_codon(i = 'ATG')
+  def self.set_start_codon(
+      i = 'ATG'
+    )
     @start_codon = i
   end
 
@@ -99,7 +101,9 @@ end
 
 if __FILE__ == $PROGRAM_NAME
   alias e puts
+  require 'colours'
   # pp Bioroebe.is_a_start_codon? 'AUG' # => false
-  e 'The start codon in use is: '+
-     Bioroebe.start_codon?
+  e Colours.rev+
+    'The start codon in use is: '+
+     ::Colours.steelblue(Bioroebe.start_codon?)
 end

data/lib/bioroebe/colours/colour_schemes/README.md

@@ -1,4 +1,4 @@
-This directory will contain common, popular colours schemes for
+This directory will contain common, popular colour schemes for
 aminoacids and DNA/RNA.
 
 Most of these schemes have been created elsewhere first; the

data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb

@@ -8,7 +8,7 @@
 # =========================================================================== #
 module Bioroebe
 
-module ColourScheme
+module ColourScheme # === Bioroebe::ColourScheme
 
   # ========================================================================= #
   # === Bioroebe::ColourScheme::ARRAY_AVAILABLE_COLOUR_SCHEMES
@@ -28,10 +28,10 @@ module ColourScheme
     buried
     helix
     hydropathy
-    strand
-    turn
     nucleotide
+    strand
     taylor
+    turn
     zappo
   )
 

data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb

@@ -74,13 +74,13 @@
 # =========================================================================== #
 # require 'bioroebe/colour_schemes/colour_scheme.rb'
 # =========================================================================== #
-require 'bioroebe/colours/colour_schemes/simple.rb'
-require 'bioroebe/colours/colour_schemes/score.rb'
-
 module Bioroebe
 
 module ColourScheme # === Bioroebe::ColourScheme
 
+  require 'bioroebe/colours/colour_schemes/simple.rb'
+  require 'bioroebe/colours/colour_schemes/score.rb'
+
   # ========================================================================= #
   # === Consensus sub-classes
   #

data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb

@@ -28,6 +28,9 @@
 # require 'bioroebe/colour_schemes/colour_scheme_demo.rb'
 # =========================================================================== #
 require 'bioroebe/base/base.rb'
+
+module Bioroebe
+
 require 'bioroebe/colours/colour_schemes/colour_scheme.rb'
 require 'bioroebe/colours/colour_schemes/array_available_colour_schemes.rb'
 
@@ -35,13 +38,11 @@ Bioroebe::ColourScheme::ARRAY_AVAILABLE_COLOUR_SCHEMES.each {|this_scheme|
   require "bioroebe/colours/colour_schemes/#{this_scheme}.rb"
 }
 
-module Bioroebe
-
 class ColourSchemeDemo < ::Bioroebe::Base
 
   require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
-  require 'bioroebe/toplevel_methods/nucleotides.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   # ========================================================================= #
   # === TITLE

data/lib/bioroebe/colours/colour_schemes/helix.rb

@@ -57,7 +57,9 @@ class Helix < Score # === Bioroebe::ColourScheme::Helix
   # ========================================================================= #
   # === Bioroebe::ColourScheme::Helix.score_to_rgb_hex
   # ========================================================================= #
-  def self.score_to_rgb_hex(score, min, max)
+  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

data/lib/bioroebe/colours/colour_schemes/hydropathy.rb

@@ -62,7 +62,9 @@ class Hydropathy < Score # === Bioroebe::ColourScheme::Hydropathy
   # ======================================================================= #
   # === Bioroebe::ColourScheme::Hydropathy.score_to_rgb_hex
   # ======================================================================= #
-  def self.score_to_rgb_hex(score, min, max)
+  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

data/lib/bioroebe/colours/colour_schemes/score.rb

@@ -21,6 +21,9 @@ class Score # === Bioroebe::ColourScheme::Score
   # ========================================================================= #
   @colours = {}
   @colours.default = 'FFFFFF' # Use white colour by default.
+  # ========================================================================= #
+  # === @scores
+  # ========================================================================= #
   @scores = {
     'A' => 0.83,
   }
@@ -41,7 +44,11 @@ class Score # === Bioroebe::ColourScheme::Score
   # ========================================================================= #
   # === Bioroebe::ColourScheme::Score.rgb_percent_to_hex
   # ========================================================================= #
-  def self.rgb_percent_to_hex(red, green, blue)
+  def self.rgb_percent_to_hex(
+      red,
+      green,
+      blue
+    )
     Score.percent_to_hex(red)+   # R
     Score.percent_to_hex(green)+ # G
     Score.percent_to_hex(blue)   # B
@@ -50,7 +57,11 @@ class Score # === Bioroebe::ColourScheme::Score
   # ========================================================================= #
   # === Bioroebe::ColourScheme::Score.score_to_rgb_hex
   # ========================================================================= #
-  def self.score_to_rgb_hex(score, min, max)
+  def self.score_to_rgb_hex(
+      score,
+      min,
+      max
+    )
     percent = score_to_percent(score, min, max)
     Score.rgb_percent_to_hex(percent, 0.0, 1.0-percent)
   end

data/lib/bioroebe/colours/colour_schemes/strand.rb

@@ -57,7 +57,9 @@ class Strand < Score # === Bioroebe::ColourScheme::Strand
   # ======================================================================= #
   # === Bioroebe::ColourScheme::Strand.score_to_rgb_hex
   # ======================================================================= #
-  def self.score_to_rgb_hex(score, min, max)
+  def self.score_to_rgb_hex(
+      score, min, max
+    )
     percent = score_to_percent(score, min, max)
     rgb_percent_to_hex(percent, percent, 1.0-percent)
   end

data/lib/bioroebe/colours/colour_schemes/turn.rb

@@ -57,7 +57,9 @@ class Turn < Score # === Bioroebe::ColourScheme::Turn
   # ======================================================================= #
   # === Bioroebe::ColourScheme::Turn.score_to_rgb_hex
   # ======================================================================= #
-  def self.score_to_rgb_hex(score, min, max)
+  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