bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/string_matching/find_longest_substring.rb

@@ -15,17 +15,12 @@
 # =========================================================================== #
 # require 'bioroebe/string_matching/find_longest_substring.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class FindLongestSubstring < ::Bioroebe::CommandlineApplication # === Bioroebe::FindLongestSubstring
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === STRING1
   # ========================================================================= #
@@ -56,10 +51,7 @@ class FindLongestSubstring < ::Bioroebe::CommandlineApplication # === Bioroebe::
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @start_position
     # ======================================================================= #

data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb

@@ -19,19 +19,12 @@
 # =========================================================================== #
 # require 'bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class FindLongestSubstringViaLCSalgorithm < ::Bioroebe::CommandlineApplication # === Bioroebe::FindLongestSubstring
 
-  require 'bioroebe/toplevel_methods/matches.rb'
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -57,10 +50,7 @@ class FindLongestSubstringViaLCSalgorithm < ::Bioroebe::CommandlineApplication #
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @string1
     # ======================================================================= #
@@ -147,9 +137,9 @@ class FindLongestSubstringViaLCSalgorithm < ::Bioroebe::CommandlineApplication #
       e "  #{sfancy(lcs)}#{rev} (#{sfancy(lcs.size)}#{rev} characters)"
       e
     else
-      opnn; erev 'The gem '+sfancy('diff-lcs')+rev+' is not installed. '\
+      opnerev 'The gem '+sfancy('diff-lcs')+rev+' is not installed. '\
                  'Please install it if you'
-      opnn; erev 'wish to make use of this gem here.'
+      opnerev 'wish to make use of this gem here.'
     end
   end
 

data/lib/bioroebe/string_matching/hamming_distance.rb

@@ -14,7 +14,7 @@
 # require 'bioroebe/string_matching/hamming_distance.rb'
 # Bioroebe::HammingDistance.new(ARGV[0], ARGV[1])
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -40,8 +40,9 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
     # ======================================================================= #
     if block_given?
       case yield
+      # === :be_quiet
       when :be_quiet
-        @be_verbose = false
+        set_be_quiet
       end
     end
     run if run_already
@@ -59,12 +60,12 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
     @input = nil
     reset_spacer
     # ======================================================================= #
-    # === @be_verbose
+    # === :be_verbose
     #
     # The @be_verbose variable can also be set to :short, in which case
     # this class will only output a number.
     # ======================================================================= #
-    @be_verbose = true # If this is true then we will also show the amount of differences.
+    set_be_verbose # If this is true then we will also show the amount of differences.
   end
 
   # ========================================================================= #
@@ -208,7 +209,7 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
   # === report_result
   # ========================================================================= #
   def report_result
-    if @be_verbose and !(@be_verbose == :short)
+    if be_verbose? and !(be_verbose? == :short)
       _ = rev.dup
       if @n_differences > 1
         _ << 'These '+colourize_in_red(@n_differences)+rev+
@@ -224,7 +225,6 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
         _ << ', was found.'
       end
       e _
-      e
     end
     counter = 0
     # ======================================================================= #
@@ -261,15 +261,16 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
       # Finally, output the two different Arrays here. But only do so if
       # the verbosity level is not set to short.
       # ===================================================================== #
-      case @be_verbose
+      case be_verbose?
       when true, :default
+        padding_to_use = '  '
         e
-        e rev+inner_array1.join
-        e submatch.map {|entry|
+        e rev+padding_to_use+inner_array1.join
+        e padding_to_use+submatch.map {|entry|
           entry.gsub(/\|/,
             colourize_in_green('|')+rev)
         }.join
-        e rev+inner_array2.join
+        e rev+padding_to_use+inner_array2.join
         e
       # ===================================================================== #
       # === :short_style

data/lib/bioroebe/string_matching/levensthein.rb

@@ -15,7 +15,7 @@
 # require 'bioroebe/string_matching/levensthein.rb'
 # Bioroebe::Levensthein.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -23,11 +23,6 @@ class Levensthein < ::Bioroebe::CommandlineApplication # === Bioroebe::Levensthe
 
   require 'bioroebe/calculate/calculate_levensthein_distance.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_MATCH_COST
   #
@@ -85,7 +80,7 @@ class Levensthein < ::Bioroebe::CommandlineApplication # === Bioroebe::Levensthe
       # === :be_quiet
       # ===================================================================== #
       when :be_quiet
-        @be_verbose = false
+        set_be_quiet
       end
     end
     run if run_already
@@ -96,18 +91,11 @@ class Levensthein < ::Bioroebe::CommandlineApplication # === Bioroebe::Levensthe
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
-    # ======================================================================= #
-    # === @be_verbose
-    # ======================================================================= #
-    @be_verbose = true
-    # ======================================================================= #
-    # === @internal_hash
+    # === :be_verbose
     # ======================================================================= #
-    @internal_hash = {}
+    set_be_verbose
     # ======================================================================= #
     # === :string1
     # ======================================================================= #

data/lib/bioroebe/string_matching/simple_string_comparer.rb

@@ -21,7 +21,7 @@
 # =========================================================================== #
 # require 'bioroebe/string_matching/simple_string_comparer.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -63,6 +63,7 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
       &block
     )
     reset
+    set_commandline_arguments(i)
     case i
     when nil # Pass through in this case.
     when :dont_run_yet
@@ -109,6 +110,7 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
     @n_matches = 0
     set_match_token
     @non_match_token = '.' # This is the token that will be displayed for non-matches.
+    set_colour_for_a_match
   end
 
   # ========================================================================= #
@@ -127,10 +129,14 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
     else
       splitted = i
     end
+    if splitted and splitted.first.include?('|')
+      splitted = splitted.first
+    end
     splitted = splitted.split(N) unless splitted.is_a? Array
     splitted.map!(&:strip) # Get rid of trailing and leading newspaces.
     if splitted.is_a? Array
-      if splitted.size == 1
+      case splitted.size
+      when 1
         if splitted.first.include? '|'
           splitted = splitted.first.split('|')
         end
@@ -252,7 +258,11 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
     }.each_slice(80).to_a.map {|entry|
       entry.join
     }.map {|line|
-      line.gsub(/\|/, seagreen(match_token?)+rev) # Colourize the match-token in the colour seagreen.
+      line.gsub(
+        /\|/,
+        send(@colour_for_a_match.to_sym, match_token?)+
+        rev
+      ) # Colourize the match-token in the colour seagreen.
     }
     0.upto(array1.size-1) {|index|
       e array1[index]
@@ -263,6 +273,19 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
     e
   end; alias compare do_compare # === compare
 
+  # ========================================================================= #
+  # === set_colour_for_a_match
+  # ========================================================================= #
+  def set_colour_for_a_match(
+      i = :default
+    )
+    case i
+    when :default
+      i = :seagreen
+    end
+    @colour_for_a_match = i
+  end
+
   # ========================================================================= #
   # === consider_notifying_the_user_if_the_sequences_are_not_equal_in_length
   # ========================================================================= #
@@ -278,10 +301,30 @@ class SimpleStringComparer < ::Bioroebe::CommandlineApplication # === Bioroebe::
     end
   end
 
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = commandline_arguments_with_leading_hyphens?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # case tag
+      # ===================================================================== #
+      # === --colour-for-a-match=lightblue
+      # ===================================================================== #
+      when /^-?-?colour(-|_| )?for(-|_| )?a(-|_| )?match=(.+)$/ # === $4
+        set_colour_for_a_match($4.to_s.dup)
+      end
+    end
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
+    menu(commandline_arguments_with_leading_hyphens?)
     do_compare
   end
 
@@ -291,4 +334,5 @@ if __FILE__ == $PROGRAM_NAME
   Bioroebe::SimpleStringComparer.new(ARGV)
 end # sstringcompare
     # sstringcompare   "AAAAAAAAAAAAAATTTTTTTTTTTAAAAAAAAAAAATATA|GAAAAAAAAAAAAAAAATATTTTTTTTTTTTTTTTTTTTTT"
-    # scompare         "acgagagaccagtaacgagagaccagta|gtcaggagccagtagtcaggagccagta"
+    # scompare         "acgagagaccagtaacgagagaccagta|gtcaggagccagtagtcaggagccagta"
+    # scompare         "acgagagaccagtaacgagagaccagta|gtcaggagccagtagtcaggagccagta" --colour-for-a-match=lightblue

data/lib/bioroebe/string_matching/smith_waterman.rb

@@ -86,9 +86,11 @@ class SmithWaterman # === Bioroebe::SmithWaterman
     alignment.each_with_index { |pos, i|
       next if i == 0
       case alignment[i-1][2]
+      # === :down
       when :down
         la << [ str_a_arr[pos[0]-1] ].pack('U*')
         lb << '-'
+      # === :right
       when :right
         la << '-'
         lb << [ str_b_arr[pos[1]-1] ].pack('U*')
@@ -171,7 +173,9 @@ class SmithWaterman # === Bioroebe::SmithWaterman
   # ========================================================================= #
   # === assign_cell
   # ========================================================================= #
-  def assign_cell(i, j)
+  def assign_cell(
+      i, j
+    )
     score = (str_a_arr[i-1] == str_b_arr[j-1]) ? SCORE_MATCH : SCORE_MISS      
     value = [
       0,
@@ -263,14 +267,15 @@ end; end
 
 if __FILE__ == $PROGRAM_NAME
   # Determine our two main sequences next:
+  alias e puts
   _ = Bioroebe::SmithWaterman.new(
     'ACACACTA',
     'AGCACACA'
   )
   _.do_perform_the_alignment
-  puts
-  puts _.mat.inspect
-  puts _.alignment_inspect
-  puts _.alignment.inspect
-  puts "Highest SCORE = #{_.score}"
+  e
+  e _.mat.inspect
+  e _.alignment_inspect
+  e _.alignment.inspect
+  e "Highest SCORE = #{_.score}"
 end # rb smith_waterman.rb

data/lib/bioroebe/svg/glyph.rb

@@ -93,7 +93,8 @@ class Glyph # === Bioroebe::SVG::Glyph
   # :y_round = y-axis radius of the ellipse used to round off the corners of the rectangle (default = 1)
   # :style = an arbitrary SVG compliant style string eg "fill-opacity:0.4;" 
   # :x = x coordinate of the feature in pixels, usually added by the Bioroebe::SVG::Page object
-  # :y = y coordinate of the feature in pixels, usually added by the Bioroebe::SVG::Page object
+  # :y = y coordinate of the feature in pixels, usually
+  #      added by the Bioroebe::SVG::Page object
   #
   # Will return:
   #
@@ -654,8 +655,10 @@ class Glyph # === Bioroebe::SVG::Glyph
   # ========================================================================= #
   def self.gradient(gradient)
     type, color = case gradient
+    # === :red_white_h
     when :red_white_h
       [:linear, 'red']
+    # === :green_white_h
     when :green_white_h
       [:linear, 'green']
     when :blue_white_h

data/lib/bioroebe/svg/mini_feature.rb

@@ -105,7 +105,7 @@ class MiniFeature # === Bioroebe::SVG::MiniFeature
     # ======================================================================= #
     # === @block_gaps
     # ======================================================================= #
-    @block_gaps     = []
+    @block_gaps = []
   end
 
 end; end; end

data/lib/bioroebe/svg/page.rb

@@ -69,9 +69,14 @@ class Page # === Bioroebe::SVG::Page
     @track_top = 30
     # ======================================================================= #
     # === @tracks
+    #
+    # Array of track objects with loads of features in it.
+    # ======================================================================= #
+    @tracks = []
     # ======================================================================= #
-    @tracks = [] # Array of track objects with loads of features in it.
-    @scale_start = 1.0/0.0
+    # === @scale_start
+    # ======================================================================= #
+    @scale_start = 1.0 / 0.0
     @scale_stop  = -1.0/0.0
     @nt_per_percent = 1
   end
@@ -181,7 +186,7 @@ class Page # === Bioroebe::SVG::Page
   # Adds a new Bioroebe::SVG::Track object to the current Bioroebe::SVG::Page
   # object.
   #
-  #==args
+  # Arguments:
   #
   #* :glyph = one of Bioroebe::SVG::Glyphs#glyphs currently 
   # [:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
@@ -236,9 +241,11 @@ class Page # === Bioroebe::SVG::Page
   #        :opacity => 1
   #        }, ]
   # }
-  #* :utr_stroke = the outline colour of the utr part of the glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
-  #* :utr_stroke_width = The width of the outline stroke for the utr part of the glyph (default = 1)
-  #* :exon_fill_color = the fill colour of the utr part of the glyph (default = 'red'), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients or a custom definition of a gradient 
+  # * :utr_stroke = the outline colour of the utr part of
+  #                 the glyph (default = "black"), can be
+  #                 any SVG colour eg rgb(256,0,0) or #FF0000
+  # * :utr_stroke_width = The width of the outline stroke for the utr part of the glyph (default = 1)
+  # * :exon_fill_color = the fill colour of the utr part of the glyph (default = 'red'), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bioroebe::SVG::Glyph#gradients or a custom definition of a gradient 
   # [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
   #or a custom definition of a gradient
   # {:type => :radial, 
@@ -278,7 +285,11 @@ class Page # === Bioroebe::SVG::Page
     # ======================================================================= #
     # Sort out the colour/gradient options
     # ======================================================================= #
-    [:fill_color, :exon_fill_color, :utr_fill_color].each { |colour_tag|
+    [
+      :fill_color,
+      :exon_fill_color,
+      :utr_fill_color
+    ].each { |colour_tag|
       if Glyph.gradients.include?(args[colour_tag])
         @svg.gradient(Glyph.gradient(args[colour_tag]))
         args[colour_tag] = "url(##{args[colour_tag]})"

data/lib/bioroebe/svg/svgee.rb

@@ -7,14 +7,14 @@
 # The Bioroebe::SVG::SVGEE class takes argument information in
 # a hash and creates SVG Markup tags, which it will draw.
 # =========================================================================== #
-require 'bioroebe/svg/primitive.rb'
-
 module Bioroebe
 
 class SVG
 
 class SVGEE # === Bioroebe::SVG::SVGEE
 
+  require 'bioroebe/svg/primitive.rb'
+
   # ========================================================================= #
   # === initialize
   #
@@ -31,8 +31,8 @@ class SVGEE # === Bioroebe::SVG::SVGEE
   def initialize(args = {})
     reset
     opts = {
-      :width  => '100%',
-      :height => '100%'
+      width:  '100%',
+      height: '100%'
     }
     if args
       opts.merge!(args) unless args.empty?
@@ -98,15 +98,15 @@ class SVGEE # === Bioroebe::SVG::SVGEE
   # ========================================================================= #
   # === update_height
   # ========================================================================= #
-  def update_height(new_height)
-    @height = new_height
+  def update_height(i)
+    @height = i
   end
 
   # ========================================================================= #
   # === update_width
   # ========================================================================= #
-  def update_width(new_width)
-    @width = new_width
+  def update_width(i)
+    @width = i
   end
 
   # ========================================================================= #
@@ -285,7 +285,7 @@ class SVGEE # === Bioroebe::SVG::SVGEE
   end
 
   # ========================================================================= #
-  # === draw (draw tag)
+  # === draw                                                       (draw tag)
   #
   # Produces the svg text to display all the features on a Page.
   # ========================================================================= #
@@ -304,10 +304,15 @@ if __FILE__ == $PROGRAM_NAME
   # ========================================================================= #
   # === How to use SVGEE
   # ========================================================================= #
-  puts 'How to use SVGEE:'
+  alias e puts
+  e 'How to use SVGEE:'
   s = Bioroebe::SVG::SVGEE.new
   s.gradient(
-    :radial => 'grad1', :cx => 50, :cy => 50, :r => 50, :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0},  {:offset => 100, :color => 'rgb(0,0,255)', :opacity => 1},]
+    :radial => 'grad1',
+    :cx => 50,
+    :cy => 50,
+    :r => 50,
+    :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0},  {:offset => 100, :color => 'rgb(0,0,255)', :opacity => 1},]
   )
   s.circle(:x_center => 40, :y_center => 40, :radius => 20, :fill_color => "url(#grad1)")
   s.circle(:x_center => 250, :y_center => 250, :radius => 20, :fill_color => "url(#grad1)", :link => {:href => "http://www.bbc.co.uk"})
@@ -317,10 +322,14 @@ if __FILE__ == $PROGRAM_NAME
   s.line(:x1 => 10, :y1 => 10, :x2 => 145, :y2 => 145, :stroke_width => 5, :stroke => 'blue')
   s.polyline(:points => '2,2 400,440 600,440', :stroke_width => 10, :stroke => "#f00", :fill => "none")
   s.text(
-    :x => 100, :y => 100, :fill => 'red', :text => 'Look! It is a circle!', :style => 'letter-spacing:2;font-family:Arial'
+    :x => 100,
+    :y => 100,
+    :fill => 'red',
+    :text => 'Look! It is a circle!',
+    :style => 'letter-spacing:2;font-family:Arial'
   )
   s.text(:x => 100, :y => 400, :fill => 'green', :text => "This one is a link", :link => {:href => "http://www.bbc.co.uk"})
   prim.update(x_center: 200)
   s.add_primitive(prim)  #add one of the returned, updated Primitive objects 
-  puts s.draw
+  e s.draw
 end

data/lib/bioroebe/svg/track.rb

@@ -19,7 +19,6 @@ class Track # === Bioroebe::SVG::Track
 
   attr_reader :args
   attr_reader :glyph
-  attr_reader :max_y
 
   attr_accessor :features
   attr_accessor :feature_rows
@@ -157,11 +156,28 @@ class Track # === Bioroebe::SVG::Track
     # === @feature_height
     # ======================================================================= #
     @feature_height = @args[:feature_height]
-    @number_of_rows = 1
     @max_y = args[:max_y]
     @min_width = args[:min_width]
+    reset
   end
 
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    # ======================================================================= #
+    # === @number_of_rows
+    # ======================================================================= #
+    @number_of_rows = 1
+  end
+
+  # ========================================================================= #
+  # === max_y?
+  # ========================================================================= #
+  def max_y?
+    @max_y
+  end; alias max_y max_y? # === max_y
+
   # ========================================================================= #
   # === scale?
   # ========================================================================= #
@@ -209,13 +225,13 @@ class Track # === Bioroebe::SVG::Track
       current_row = 1
       begin
         found = true
-        rows[current_row].each_with_index do |f2, j|
+        rows[current_row].each_with_index { |f2, j|
           if overlaps(f1, f2, page)
             found = false
             current_row += 1
             break
           end
-        end
+        }
       end until found
       @feature_rows[i] = current_row
       rows[current_row] << f1

data/lib/bioroebe/taxonomy/chart.rb

@@ -13,7 +13,7 @@
 #   x = Bioroebe::Taxonomy::Chart.new; x.find_id 55
 #
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -87,7 +87,7 @@ class Chart < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   # === Bioroebe::Taxonomy::Chart[]
   # ========================================================================= #
-  def [](i)
+  def [](i = ARGV)
     i = i.to_sym unless i.is_a? Fixnum # For now these are symbols.
     return @hash[i]
   end; alias find_id [] # === find_id

data/lib/bioroebe/taxonomy/class_methods.rb

@@ -8,14 +8,12 @@ module Bioroebe
 
 module Taxonomy # === Bioroebe::Taxonomy
 
+  require 'bioroebe/colours/colours.rb'
   require 'bioroebe/taxonomy/shared.rb'
-  require 'bioroebe/colours/rev.rb'
   require 'bioroebe/taxonomy/constants.rb'
 
-  require 'bioroebe/toplevel_methods/extract.rb'
-  require 'bioroebe/toplevel_methods/time_and_date.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
   require 'bioroebe/toplevel_methods/taxonomy.rb'
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
 
   extend Colours::E
   extend Colours
@@ -57,9 +55,10 @@ module Taxonomy # === Bioroebe::Taxonomy
     }
   end
 
-  require 'bioroebe/toplevel_methods/download_and_fetch_data.rb' # Needed for wget-like functionality.
   # ========================================================================= #
   # === Bioroebe::Taxonomy.download_directory?
+  #
+  # This method is needed for wget-like functionality.
   # ========================================================================= #
   def self.download_directory?
     DOWNLOAD_DIR
@@ -98,7 +97,7 @@ module Taxonomy # === Bioroebe::Taxonomy
   # Get rid of some .sql files through this method here.
   # ========================================================================= #
   def self.cleanup
-    e 'Trying to remove some files now.'
+    erev 'Trying to remove some files now.'
     i = 'names.sql'
     remove_file(i) if File.exist? i
     i = 'nodes.sql'

data/lib/bioroebe/taxonomy/constants.rb

@@ -10,7 +10,7 @@ module Taxonomy
 
 module Constants # === Bioroebe::Taxonomy::Constants
 
-  require 'bioroebe/toplevel_methods/log_directory.rb'
+  require 'bioroebe/log_directory/log_directory.rb'
 
   # ========================================================================= #
   # === FILE_USE_THIS_DATABASE

data/lib/bioroebe/taxonomy/info/info.rb

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