bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/aminoacids/aminoacid_substitution.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe::AminoacidSubstitution
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -49,10 +44,7 @@ class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/aminoacids/codon_percentage.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::CodonPercentage
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -45,10 +40,7 @@ class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::Codon
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb

@@ -38,11 +38,6 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
   require 'bioroebe/misc/ruler.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_SEQUENCE
   #
@@ -73,10 +68,7 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/display_aminoacid_table.rb

@@ -79,6 +79,7 @@ class DisplayAminoacidTable < Bioroebe::CommandlineApplication # === Bioroebe::D
     if i.is_a? Array
       i = i.join(' ').strip
     end
+    i = ::Bioroebe.filter_away_invalid_aminoacids(i)
     @input = i
   end
 

data/lib/bioroebe/aminoacids/show_hydrophobicity.rb

@@ -27,11 +27,6 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
     HYDROPATHY_TABLE = YAML.load_file(FILE_HYDROPATHY_TABLE)
   end
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -142,7 +137,7 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
   # ========================================================================= #
   def opnn(i = nil)
     hash = {}
-    hash.merge!(namespace: NAMESPACE)
+    hash.merge!(namespace: namespace?)
     hash.merge!(i) if i
     super(hash)
   end

data/lib/bioroebe/base/colours_for_base/colours_for_base.rb

@@ -209,14 +209,6 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     return i
   end
 
-  # ========================================================================= #
-  # === sfancy
-  # ========================================================================= #
-  def sfancy(i = '')
-    return powderblue(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
-    return i
-  end
-
   # ========================================================================= #
   # === simp
   # ========================================================================= #
@@ -272,4 +264,22 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     @use_colours = true
   end
 
+  # ========================================================================= #
+  # === efancy
+  # ========================================================================= #
+  def efancy(i)
+    e sfancy(i)
+  end
+
+  # ========================================================================= #
+  # === sfancy
+  # ========================================================================= #
+  def sfancy(
+      i           = '',
+      use_colours = use_colours?
+    )
+    return powderblue(i) if use_colours and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/commandline_arguments.rb

@@ -78,6 +78,7 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     )
     i.reject {|entry| entry.start_with? '--' }
   end; alias return_commandline_arguments_without_hyphen return_entries_without_two_leading_hyphens # === return_commandline_arguments_without_hyphen
+       alias reject_hyphens                              return_entries_without_two_leading_hyphens # === reject_hyphens
 
   # ========================================================================= #
   # === select_commandline_arguments
@@ -111,6 +112,13 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     @commandline_arguments.join(' ').strip
   end
 
+  # ========================================================================= #
+  # === first_non_hyphen_argument?
+  # ========================================================================= #
+  def first_non_hyphen_argument?
+    return_entries_without_two_leading_hyphens.first
+  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+
   # ========================================================================= #
   # === select_entries_starting_with_two_hyphens
   #
@@ -125,20 +133,16 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     else
       []
     end
-  end; alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
-       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
-       alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
+  end; alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
        alias return_arguments_with_leading_hyphens                  select_entries_starting_with_two_hyphens # === return_arguments_with_leading_hyphens
        alias return_commandline_arguments_starting_with_hyphens     select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_hyphens
        alias return_commandline_arguments_starting_with_two_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_two_hyphens
-       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
+       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
+       alias commandline_arguments_containing_leading_hyphens?      select_entries_starting_with_two_hyphens # === commandline_arguments_containing_leading_hyphens?
+       alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
        alias commandline_arguments_starting_with_leading_hyphens?   select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_leading_hyphens?
-
-  # ========================================================================= #
-  # === first_non_hyphen_argument?
-  # ========================================================================= #
-  def first_non_hyphen_argument?
-    return_entries_without_two_leading_hyphens.first
-  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+       alias commandline_arguments_starting_with_a_hyphen?          select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_a_hyphen?
+       alias commandline_arguments_starting_with_a_hyphen           select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_a_hyphen
+       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
 
 end; end

data/lib/bioroebe/base/commandline_application/misc.rb

@@ -163,17 +163,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.cat(i)
   end
 
-  # ========================================================================= #
-  # === codon_to_aminoacid
-  # ========================================================================= #
-  def codon_to_aminoacid(i)
-    unless Bioroebe.respond_to? :codon_to_aminoacid
-      require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
-    end
-    ::Bioroebe.codon_to_aminoacid(i)
-  end; alias nucleotides_to_aminoacid codon_to_aminoacid # === nucleotides_to_aminoacid
-       alias codons_to_aminoacid      codon_to_aminoacid # === codons_to_aminoacid
-
   # ========================================================================= #
   # === without_extname
   #
@@ -329,23 +318,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.return_ubiquitin_sequence(i)
   end
 
-  # ========================================================================= #
-  # === be_verbose?
-  # ========================================================================= #
-  def be_verbose?
-    @be_verbose
-  end; alias verbose? be_verbose? # === be_verbose?
-
-  # ========================================================================= #
-  # === be_silent
-  # ========================================================================= #
-  def be_silent
-    @be_verbose = false
-  end; alias be_quiet          be_silent # === be_quiet
-       alias set_be_silent     be_silent # === set_be_silent
-       alias set_be_quiet      be_silent # === set_be_quiet
-       alias do_not_be_verbose be_silent # === do_not_be_verbose
-
   # ========================================================================= #
   # === leading_five_prime
   #
@@ -392,19 +364,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     )
   end
 
-  # ========================================================================= #
-  # === set_be_verbose
-  # ========================================================================= #
-  def set_be_verbose(i = true)
-    case i
-    when :be_verbose
-      i = true
-    when :be_quiet
-      i = false
-    end
-    @be_verbose = i
-  end
-
   # ========================================================================= #
   # === colourize_this_dna_sequence
   #
@@ -435,14 +394,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     return i.delete('[0-9]')
   end
 
-  require 'bioroebe/toplevel_methods/open_in_browser.rb'
-  # ========================================================================= #
-  # === open_in_browser
-  # ========================================================================= #
-  def open_in_browser(this_url)
-    ::Bioroebe.open_in_browser(this_url)
-  end
-
   # ========================================================================= #
   # === load_bioroebe_yaml_file
   #
@@ -482,4 +433,70 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
   end; alias three_aminoacid_letter_code_to_one_aminoacid_letter_code three_to_one # === three_aminoacid_letter_code_to_one_aminoacid_letter_code
        alias three_letters_to_one_letter                              three_to_one # === three_letters_to_one_letter
 
+  require 'bioroebe/toplevel_methods/open_in_browser.rb'
+  # ========================================================================= #
+  # === open_in_browser
+  # ========================================================================= #
+  def open_in_browser(this_url)
+    ::Bioroebe.open_in_browser(this_url)
+  end; alias open_in_browser_tab open_in_browser # === open_in_browser_tab
+
+  require 'bioroebe/toplevel_methods/verbose.rb'
+  # ========================================================================= #
+  # === verbose_truth
+  #
+  # Delegate towards the module Bioroebe::VerboseTruth here.
+  # ========================================================================= #
+  def verbose_truth(i)
+    ::Bioroebe::VerboseTruth[i]
+  end
+
+  # ========================================================================= #
+  # === codon_to_aminoacid
+  # ========================================================================= #
+  def codon_to_aminoacid(i)
+    unless Bioroebe.respond_to? :codon_to_aminoacid
+      require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
+    end
+    ::Bioroebe.codon_to_aminoacid(i).to_s
+  end; alias nucleotides_to_aminoacid codon_to_aminoacid # === nucleotides_to_aminoacid
+       alias codons_to_aminoacid      codon_to_aminoacid # === codons_to_aminoacid
+
+  # ========================================================================= #
+  # === be_verbose?
+  # ========================================================================= #
+  def be_verbose?
+    @be_verbose
+  end; alias verbose? be_verbose? # === be_verbose?
+
+  # ========================================================================= #
+  # === be_silent
+  # ========================================================================= #
+  def be_silent
+    @be_verbose = false
+  end; alias be_quiet          be_silent # === be_quiet
+       alias set_be_silent     be_silent # === set_be_silent
+       alias set_be_quiet      be_silent # === set_be_quiet
+       alias do_not_be_verbose be_silent # === do_not_be_verbose
+
+  # ========================================================================= #
+  # === set_be_verbose
+  # ========================================================================= #
+  def set_be_verbose(i = true)
+    case i
+    # ======================================================================= #
+    # === :be_verbose
+    # ======================================================================= #
+    when :be_verbose,
+         :default
+      i = true
+    # ======================================================================= #
+    # === :be_quiet
+    # ======================================================================= #
+    when :be_quiet
+      i = false
+    end
+    @be_verbose = i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/opn.rb

@@ -22,18 +22,11 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.use_opn?
   end
 
-  # ========================================================================= #
-  # === opne
-  # ========================================================================= #
-  def opne(i = '')
-    opnn; e i
-  end
-
   # ========================================================================= #
   # === opnn
   # ========================================================================= #
   def opnn(
-      i = @namespace,
+      i = namespace?,
       &block
     )
     if use_opn?
@@ -44,4 +37,11 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     end
   end
 
+  # ========================================================================= #
+  # === opne
+  # ========================================================================= #
+  def opne(i = '')
+    opnn; erev i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/reset.rb

@@ -20,7 +20,8 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     # ======================================================================= #
     # === @namespace
     # ======================================================================= #
-    @namespace = Bioroebe::Base::NAMESPACE
+    # @namespace = Bioroebe::Base::NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @commandline_arguments
     # ======================================================================= #
@@ -30,7 +31,7 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     #
     # By default, CommandlineApplication will report a lot of stuff.
     # ======================================================================= #
-    @be_verbose  = true
+    set_be_verbose
     # ======================================================================= #
     # === @use_colours
     # ======================================================================= #

data/lib/bioroebe/base/misc.rb

@@ -10,6 +10,13 @@ class Base
 
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
 
+  # ========================================================================= #
+  # === namespace?
+  # ========================================================================= #
+  def namespace?
+    @namespace
+  end
+
   # ========================================================================= #
   # === is_palindrome?
   # ========================================================================= #
@@ -91,4 +98,32 @@ class Base
     ::Bioroebe.project_yaml_directory?
   end; alias yaml_directory? project_yaml_directory? # === yaml_directory?
 
+  # ========================================================================= #
+  # === infer_the_namespace
+  #
+  # This will assume the true namespace from the inspectable name.
+  # ========================================================================= #
+  def infer_the_namespace
+    _ = inspect.to_s.delete('<')
+    _ = _.split(':0').first if _.include?(':0')
+    if _.include? ' '
+      _ = _.split(' ').first.delete('#')
+      if _.include? ':'
+        _ = _.split(':')[0 .. -2].reject {|entry| entry.empty? }.join('::')
+      end
+    end
+    _.delete!('#') if _.include?('#')
+    @namespace = _ # And assign it here.
+  end
+
+  # ========================================================================= #
+  # === word_wrap
+  # ========================================================================= #
+  def word_wrap(
+      text,
+      line_width = 80
+    )
+    return text.scan(/\S.{0,#{line_width}}\S(?=\s|$)|\S+/).join(N)
+  end
+
 end; end

data/lib/bioroebe/base/prototype/misc.rb

@@ -12,13 +12,23 @@ class Base
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
   require 'bioroebe/toplevel_methods/rds.rb'
 
+  # ========================================================================= #
+  # === return_the_first_line_of_this_file
+  # ========================================================================= #
+  def return_the_first_line_of_this_file(i)
+    if File.exist? i
+      return File.open(i) {|this_file| this_file.readline.strip }
+    end
+    return i
+  end
+
   require 'bioroebe/toplevel_methods/is_on_roebe.rb'
   # ========================================================================= #
   # === is_on_roebe?
   # ========================================================================= #
   def is_on_roebe?
     ::Bioroebe.is_on_roebe?
-  end
+  end; alias on_roebe? is_on_roebe? # === on_roebe?
 
   # ========================================================================= #
   # === main_encoding?

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

@@ -26,11 +26,6 @@ class ParseFrequencyTable < ::Bioroebe::CommandlineApplication # === Bioroebe::P
 
   require 'open-uri'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === AUTOMATICALLY_CREATE_A_LOCAL_YAML_FILE_IF_IT_DOES_NOT_YET_EXIST
   #
@@ -100,10 +95,7 @@ GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @use_this_url
     #
@@ -129,7 +121,7 @@ GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'
   # === menu                                                       (menu tag)
   # ========================================================================= #
   def menu(
-      i = @commandline_arguments
+      i = commandline_arguments?
     )
     if i.is_a? Array
       i.each {|entry| menu(entry) }

data/lib/bioroebe/codons/codons.rb

@@ -24,7 +24,7 @@ module Bioroebe
   require 'bioroebe/constants/codon_tables.rb'
   require 'bioroebe/regexes/regexes.rb'
   require 'bioroebe/codons/codon_table.rb'
-  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
+  # require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
   # ========================================================================= #
   # === @stop_codons