bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/requires/require_colours.rb

@@ -11,7 +11,7 @@ module Bioroebe
   require 'bioroebe/colours/use_colours.rb'
 
   begin
-    require 'colours'
+    require 'colours/html_colours'
     @use_colours = true  # Keep track of the fact that we will make use of colours.
   rescue LoadError
     @use_colours = false # In this case we will disable colour-support.

data/lib/bioroebe/requires/require_the_bioroebe_project.rb

@@ -9,6 +9,10 @@
 # =========================================================================== #
 require 'bioroebe/project/project.rb'
 require 'bioroebe/version/version.rb'
+# =========================================================================== #
+# Require all the bioroebe-related constants next:
+# =========================================================================== #
+require 'bioroebe/requires/require_the_constants.rb'
 require 'bioroebe/colours/colours.rb'
 
 require 'bioroebe/base/prototype/prototype.rb'
@@ -35,11 +39,6 @@ require 'bioroebe/blosum/blosum.rb'
 # =========================================================================== #
 require 'bioroebe/regexes/regexes.rb'
 
-# =========================================================================== #
-# Require all the bioroebe-related constants next:
-# =========================================================================== #
-require 'bioroebe/requires/require_the_constants.rb'
-
 # =========================================================================== #
 # Require .rb files for yaml-support next:
 # =========================================================================== #
@@ -158,7 +157,6 @@ require 'bioroebe/requires/require_all_codon_files.rb'
 # =========================================================================== #
 # And the sinatra-interface:
 # =========================================================================== #
-# require 'bioroebe/requires/require_the_bioroebe_sinatra_components.rb'
-require 'bioroebe/www/sinatra/sinatra.rb'
+require 'bioroebe/requires/require_the_bioroebe_sinatra_components.rb'
 
 require 'bioroebe/sequence/protein.rb'

data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb

@@ -4,4 +4,4 @@
 # =========================================================================== #
 # require 'bioroebe/requires/require_the_bioroebe_sinatra_components.rb'
 # =========================================================================== #
-require 'bioroebe/www/sinatra/sinatra.rb'
+require 'bioroebe/sinatra/sinatra_wrapper.rb'

data/lib/bioroebe/requires/require_the_constants.rb

@@ -7,17 +7,5 @@
 # =========================================================================== #
 # require 'bioroebe/requires/require_the_constants.rb'
 # =========================================================================== #
-require 'bioroebe/constants/aminoacids_and_proteins.rb'
-require 'bioroebe/constants/base_directory.rb'
-require 'bioroebe/constants/carriage_return.rb'
-require 'bioroebe/constants/codon_tables.rb'
-require 'bioroebe/constants/database_constants.rb'
-require 'bioroebe/constants/files_and_directories.rb'
-require 'bioroebe/constants/misc.rb'
-require 'bioroebe/constants/newline.rb'
-require 'bioroebe/constants/nucleotides.rb'
-require 'bioroebe/constants/regex.rb'
-require 'bioroebe/constants/roebe.rb'
-require 'bioroebe/constants/row_terminator.rb'
-require 'bioroebe/constants/tabulator.rb'
-require 'bioroebe/constants/urls.rb'
+require 'bioroebe/constants/constants.rb'
+require 'bioroebe/constants/GUIs.rb'

data/lib/bioroebe/requires/require_yaml.rb

@@ -9,9 +9,9 @@
 #
 # Thus, this file allows us some flexibility for the bioroebe-project.
 #
-# Since as of the year 2019, using psych should have no real major
-# drawbacks really, so the BioRoebe project now defaults to psych
-# past 2019.
+# Since as of the year 2019, using psych should incur no real major
+# drawback anymore, so the BioRoebe project now defaults to psych
+# as of 2019.
 # =========================================================================== #
 # require 'bioroebe/requires/require_yaml.rb'
 # =========================================================================== #
@@ -44,7 +44,9 @@ module Bioroebe
   # Query method to determine which yaml engine is in use for the Bioroebe
   # project.
   # ========================================================================= #
-  def self.set_use_this_yaml_engine=(i = :default)
+  def self.set_use_this_yaml_engine=(
+      i = :default
+    )
     case i # case tag
     # ======================================================================= #
     # === :default
@@ -87,7 +89,7 @@ module Bioroebe
 
   # ========================================================================= #
   # Load psych or syck at once, whenever this file is loaded. By default
-  # this will load up psych past 2019.
+  # this will load up psych past the year 2019.
   # ========================================================================= #
   load_psych_or_syck
 

data/lib/bioroebe/sequence/alignment.rb

@@ -22,7 +22,7 @@
 # require 'bioroebe/sequence/alignment.rb'
 # Bioroebe::Alignment.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/sequence/dna.rb

@@ -206,7 +206,9 @@ end
 end
 
 if __FILE__ == $PROGRAM_NAME
+  require 'colours'
+  alias e puts
   dna = Bioroebe::DNA.new(ARGV)
-  puts 'The DNA sequence is: '+dna.sequence?
-  puts 'The RNA sequence is: '+dna.to_rna
+  e Colours.rev+'The DNA sequence is: '+::Colours.steelblue(dna.sequence?)
+  e Colours.rev+'The RNA sequence is: '+::Colours.steelblue(dna.to_rna)
 end # dna ATCGATCGAAATTACCCCCCCC

data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb

@@ -11,7 +11,8 @@ module Bioroebe
 
 module NucleotideModule # === Bioroebe::NucleotideModule
 
-  require 'bioroebe/toplevel_methods/nucleotides.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+
   # ========================================================================= #
   # === Bioroebe::NucleotideModule.complementary_strand
   #
@@ -41,11 +42,12 @@ module NucleotideModule # === Bioroebe::NucleotideModule
        self.instance_eval { alias build_second_strand            complementary_strand } # === build_second_strand
        self.instance_eval { alias build_complementary_strand     complementary_strand } # === build_complementary_strand
 
-  require 'bioroebe/toplevel_methods/nucleotides.rb'
   # ========================================================================= #
   # === complementary_strand
   # ========================================================================= #
-  def complementary_strand(i = '')
+  def complementary_strand(
+      i = ''
+    )
     return ::Bioroebe.complementary_strand(i)
   end; alias complementary                  complementary_strand # === complementary
        alias build_complementary_dna_strand complementary_strand # === build_complementary_dna_strand
@@ -56,7 +58,7 @@ module NucleotideModule # === Bioroebe::NucleotideModule
   # === to_rna
   #
   # This method will simply return the RNA sequence corresponding to
-  # the DNA sequence.
+  # the DNA sequence at hand.
   # ========================================================================= #
   def to_rna(i = seq?)
     i.tr('T','U')
@@ -111,7 +113,7 @@ module NucleotideModule # === Bioroebe::NucleotideModule
   def gc_percentage(
       round_to_n_positions = 2
     )
-    sum = @sequence.count('G') + @sequence.count('C')
+    sum = @sequence.count('G') + @sequence.count('C') # Count G + C here.
     result = (sum * 100.0 / @sequence.size)
     if round_to_n_positions
       result = result.round(round_to_n_positions)
@@ -194,10 +196,19 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     end
     if optional_use_this_frame
       case optional_use_this_frame
+      # ===================================================================== #
+      # === :frame1
+      # ===================================================================== #
       when :frame1, :in_frame1
         _ = _.scan(/.../)
+      # ===================================================================== #
+      # === :frame2
+      # ===================================================================== #
       when :frame2, :in_frame2
         _ = _[1..-1].scan(/.../)
+      # ===================================================================== #
+      # === :frame3
+      # ===================================================================== #
       when :frame3, :in_frame3
         _ = _[2..-1].scan(/.../)
       else
@@ -218,7 +229,8 @@ module NucleotideModule # === Bioroebe::NucleotideModule
   # ========================================================================= #
   # === allow_only_valid_dna
   #
-  # Allow only valid DNA. It will discard anything that is not A, T, C or G.
+  # Allow only valid DNA. It will discard anything that is not A, T, C
+  # or G.
   #
   # "ATCGIIII".allow_only_valid_dna
   # ========================================================================= #
@@ -235,7 +247,9 @@ module NucleotideModule # === Bioroebe::NucleotideModule
     return return_string
   end; alias only_valid_dna_nucleotides allow_only_valid_dna # === only_valid_dna_nucleotides
 
-  require 'bioroebe/codons/codons.rb'
+  begin
+    require 'bioroebe/codons/codons.rb'
+  rescue LoadError; end
   # ========================================================================= #
   # === codon_to_aminoacid
   #
@@ -403,5 +417,5 @@ module NucleotideModule # === Bioroebe::NucleotideModule
 end; end
 
 if __FILE__ == $PROGRAM_NAME
-  NucleotideModule.new(ARGV)
+  Bioroebe::NucleotideModule.new(ARGV)
 end # nucleotide_module

data/lib/bioroebe/sequence/protein.rb

@@ -19,7 +19,7 @@ module Bioroebe
 
 class Protein < ::Bioroebe::Sequence # === Bioroebe::Protein
 
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   # ========================================================================= #
   # === ARRAY_THESE_METHODS_ARE_NOT_IN_USE_FOR_THIS_CLASS
@@ -364,7 +364,7 @@ end
 
 if __FILE__ == $PROGRAM_NAME
   require 'colours/autoinclude'
-  require 'bioroebe/toplevel_methods/verbose.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
   protein = Bioroebe::Protein.new(ARGV)
   e protein.weight?
   e Colours.rev+'For the aminoacid sequence:'

data/lib/bioroebe/sequence/reverse_complement.rb

@@ -142,7 +142,7 @@ end
 end
 
 if __FILE__ == $PROGRAM_NAME
-  puts Bioroebe.reverse_complement(ARGV)
+  alias e puts
+  e Bioroebe.reverse_complement(ARGV)
 end # reversecomplement AAAACCCGGT
-    # reversecomplement  /Depot/Downloads/rosalind_revc.txt
-
+    # reversecomplement  /Depot/Downloads/rosalind_revc.txt

data/lib/bioroebe/sequence/rna.rb

@@ -21,6 +21,7 @@ class RNA < ::Bioroebe::Sequence # === Bioroebe::RNA
   include Bioroebe::InternalHashModule
 
   require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
   # ========================================================================= #
   # === initialize
@@ -49,9 +50,9 @@ class RNA < ::Bioroebe::Sequence # === Bioroebe::RNA
     # ======================================================================= #
     @internal_hash[:is_a_ribozyme] = false
     # ======================================================================= #
-    # === @name_of_the_gene
+    # === @internal_hash[:name_of_the_gene]
     # ======================================================================= #
-    @name_of_the_gene = nil # No name is assigned by default.
+    @internal_hash[:name_of_the_gene] = nil # No name is assigned by default.
   end
 
   # ========================================================================= #
@@ -60,7 +61,7 @@ class RNA < ::Bioroebe::Sequence # === Bioroebe::RNA
   # Use this method if you want to give the gene a specific name.
   # ========================================================================= #
   def set_name_of_the_gene(i)
-    @name_of_the_gene = i
+    @internal_hash[:name_of_the_gene] = i
   end; alias name=         set_name_of_the_gene # === name=
        alias set_name      set_name_of_the_gene # === set_name
        alias name_of_gene= set_name_of_the_gene # === name_of_gene=
@@ -70,7 +71,7 @@ class RNA < ::Bioroebe::Sequence # === Bioroebe::RNA
   # === name_of_gene?
   # ========================================================================= #
   def name_of_gene?
-    @name_of_the_gene
+    @internal_hash[:name_of_the_gene]
   end; alias name_of_gene name_of_gene? # === name_of_gene
        alias name?        name_of_gene? # === name?
 
@@ -84,7 +85,6 @@ class RNA < ::Bioroebe::Sequence # === Bioroebe::RNA
   end; alias to_RNA to_rna # === to_RNA
        alias to_T   to_rna # === to_T
 
-  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
   # ========================================================================= #
   # === to_aminoacids
   #
@@ -214,7 +214,8 @@ end
 end
 
 if __FILE__ == $PROGRAM_NAME
+  alias e puts
   rna = Bioroebe::RNA.new(ARGV)
-  puts 'The DNA sequence is: '+rna.sequence?
-  puts 'The RNA sequence is: '+rna.to_dna
-end # dna ATCGATCGAAATTACCCCCCCC
+  e 'The RNA sequence is: '+rna.to_dna
+  e 'The DNA sequence is: '+rna.sequence?
+end # rna ATCGATCGAAATTACCCCCCCC

data/lib/bioroebe/sequence/sequence.rb

@@ -33,6 +33,8 @@ class Sequence < ::Bioroebe::RawSequence
 
   alias e puts
 
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+
   # ========================================================================= #
   # === SHALL_WE_UPCASE
   #
@@ -276,7 +278,6 @@ class Sequence < ::Bioroebe::RawSequence
     @sequence.to_s.upcase.tr('T','U').count('U')
   end
 
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
   # ========================================================================= #
   # === save_sequence_to_this_file
   #
@@ -360,7 +361,7 @@ class Sequence < ::Bioroebe::RawSequence
     sanitize_dataset :rna
   end
 
-  require 'bioroebe/toplevel_methods/log_directory.rb'
+  require 'bioroebe/log_directory/log_directory.rb'
   # ========================================================================= #
   # === set_save_file
   #
@@ -598,7 +599,6 @@ class Sequence < ::Bioroebe::RawSequence
     @internal_hash[:type] == :protein
   end; alias is_protein? is_a_protein? # === is_protein?
 
-  require 'bioroebe/toplevel_methods/infer.rb'
   # ========================================================================= #
   # === infer_type
   #

data/lib/bioroebe/shell/configuration/use_silent_startup.yml

@@ -1 +1 @@
-use_silent_startup: false
+false

data/lib/bioroebe/shell/help/class.rb

@@ -6,13 +6,13 @@
 #
 # This class will show the help options for the Bioroebe project.
 # =========================================================================== #
-require 'bioroebe/base/base.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class Shell
 
-class Help < Base
+class Help < ::Bioroebe::CommandlineApplication
 
   # ========================================================================= #
   # === N_LEFT_PADDING
@@ -27,13 +27,20 @@ class Help < Base
   # ========================================================================= #
   DEFAULT_MIDDLE_PADDING = 25
 
+  # ========================================================================= #
+  # === RAW_TITLE
+  # ========================================================================= #
+  RAW_TITLE = 'BioShell Help Options:'
+
   # ========================================================================= #
   # === TITLE
   #
   # This constant specifies the title that we will use for the
-  # bioshell help options.
+  # bioshell help options. Since as of November 2023 this
+  # constant is not as important anymore, as we return the
+  # title dynamically, via RAW_TITLE. 
   # ========================================================================= #
-  TITLE = "#{::Bioroebe.rev}BioShell Help Options:"
+  TITLE = "#{::Bioroebe.rev}#{RAW_TITLE}"
 
   # ========================================================================= #
   # === initialize
@@ -47,8 +54,10 @@ class Help < Base
       run_already = true
     )
     reset
-    @use_colours = use_colours
+    set_use_colours(use_colours)
     # ======================================================================= #
+    # === Handle blocks next
+    #
     # The user may pass in a block, which usually means that the user
     # wants to display only some subcommands.
     # ======================================================================= #
@@ -74,6 +83,13 @@ class Help < Base
         end
       end
     end
+    case run_already
+    # ======================================================================= #
+    # === :do_not_run_yet
+    # ======================================================================= #
+    when :do_not_run_yet
+      run_already = false
+    end
     run if run_already
   end
 
@@ -81,6 +97,7 @@ class Help < Base
   # === reset
   # ========================================================================= #
   def reset
+    super()
     # ======================================================================= #
     # === @_
     # ======================================================================= #
@@ -108,6 +125,13 @@ class Help < Base
     @middle_padding
   end
 
+  # ========================================================================= #
+  # === title?
+  # ========================================================================= #
+  def title?
+    RAW_TITLE
+  end
+
   # ========================================================================= #
   # === expanded_middle_padding?
   #
@@ -132,13 +156,6 @@ class Help < Base
     true
   end
 
-  # ========================================================================= #
-  # === Bioroebe::Shell::Help[]
-  # ========================================================================= #
-  def self.[](i = '')
-    new(i)
-  end
-
   # ========================================================================= #
   # === build_help_string
   #
@@ -148,7 +165,7 @@ class Help < Base
     # ======================================================================= #
     # Add the title first
     # ======================================================================= #
-    add TITLE+N # Add a newline to start with.
+    add "#{title?}#{N}" # Add a newline to start with.
     # ======================================================================= #
     # a tag
     # ======================================================================= #
@@ -337,6 +354,17 @@ class Help < Base
         'or -3, too.'
   end
 
+  # ========================================================================= #
+  # === show_help
+  #
+  # This method will show the help subsection for the BioShell.
+  # ========================================================================= #
+  def show_help(
+      display_this = @_
+    )
+    e "#{display_this}#{N}"
+  end; alias display_result show_help # === display_result
+
   # ========================================================================= #
   # === add                                                         (add tag)
   # ========================================================================= #
@@ -420,13 +448,27 @@ class Help < Base
   end
 
   # ========================================================================= #
-  # === show_help
-  #
-  # This method will show the help subsection for the BioShell.
+  # === result?
   # ========================================================================= #
-  def show_help(display_this = @_)
-    e "#{display_this}#{N}"
-  end; alias display_result show_help # === display_result
+  def result?
+    @_
+  end
+
+  # ========================================================================= #
+  # === set_use_colours
+  # ========================================================================= #
+  def set_use_colours(
+      i = true
+    )
+    case i
+    # ======================================================================= #
+    # === :do_not_use_colours
+    # ======================================================================= #
+    when :do_not_use_colours
+      i = false
+    end
+    set_will_we_use_colours(i)
+  end
 
   # ========================================================================= #
   # === run
@@ -436,6 +478,13 @@ class Help < Base
     show_help
   end
 
+  # ========================================================================= #
+  # === Bioroebe::Shell::Help[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
 end; end; end
 
 if __FILE__ == $PROGRAM_NAME