bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb}

@@ -2,18 +2,19 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# require 'bioroebe/www/sinatra/sinatra.rb'
+# require 'bioroebe/sinatra/sinatra_wrapper.rb'
+# Bioroebe.start_sinatra_interface
 # =========================================================================== #
+require 'bioroebe/sinatra/sinatra_interface.rb'
+
+module Bioroebe
+
 begin
   require 'cyberweb/and_sinatra_base.rb'
-  require 'sinatra'
 rescue LoadError; end
 
-module Bioroebe
-
-class Sinatra < ::Sinatra::Base
+class SinatraWrapper < ::Sinatra::Base # === Bioroebe::SinatraWrapper
 
-  require 'bioroebe/www/embeddable_interface.rb'
   set :port, ::Bioroebe::EmbeddableInterface::USE_THIS_PORT
 
   # ========================================================================= #
@@ -22,7 +23,7 @@ class Sinatra < ::Sinatra::Base
   @embeddable_interface = Bioroebe.embeddable_interface
 
   # ========================================================================= #
-  # === Bioroebe::Sinatra.embeddable_interface?
+  # === Bioroebe::SinatraWrapper.embeddable_interface?
   # ========================================================================= #
   def self.embeddable_interface?
     @embeddable_interface
@@ -32,366 +33,282 @@ class Sinatra < ::Sinatra::Base
   # === embeddable_interface?
   # ========================================================================= #
   def embeddable_interface?
-    ::Bioroebe::Sinatra.embeddable_interface?
+    ::Bioroebe::SinatraWrapper.embeddable_interface?
   end
 
+  # ========================================================================= #
+  # === LOCALHOST_TO_USE
+  # ========================================================================= #
+  LOCALHOST_TO_USE = ::Bioroebe::EmbeddableInterface.localhost_to_use?
+
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
   def initialize
     super()
     reset
-    target = Bioroebe::EmbeddableInterface.localhost_to_use?
-    use_this_port = ::Bioroebe::EmbeddableInterface::USE_THIS_PORT
-    Cyberweb.try_to_open_this_URL_via_the_browser(target, use_this_port) { :be_quiet }
+    Cyberweb.try_to_open_this_URL_via_the_browser(
+      LOCALHOST_TO_USE,
+      ::Bioroebe::EmbeddableInterface::USE_THIS_PORT
+    ) { :be_quiet }
   end
 
   # ========================================================================= #
-  # === p
+  # === /                                                          (main tag)
+  #
+  # This is the root tag, the root of our web-application.
   # ========================================================================= #
-  def p(
-      i, hash = {}
+  get('/') {
+    body = embeddable_interface?.return_root_string # Obtain the body-String here.
+    Cyberweb.html_template(
+      title: 'Bioroebe Web-API',
+      body:  body
     )
-    return HtmlTags.p(i, hash)
+  }
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
   end
 
   # ========================================================================= #
-  # === Convert into DNA                    (2 tag, second entry, reverse_complement tag)
+  # === Query how many stop codons are in a given DNA sequence
+  #
+  # This method will determine how many stop codons are in the given
+  # sequence.
+  #
+  #   http://localhost:4568/n_stop_codons_in_this_sequence
+  #
+  # Example:
+  #
+  #   http://localhost:4568/n_stop_codons_in_this_sequence/ATGCUUUUUUUUUTAG
+  #
+  # ========================================================================= #
+  %w(
+    /n_stop_codons_in_this_sequence/*
+    /n_stop/*
+    /nstop/*
+  ).each {|entry|
+    get(entry) {
+      the_params = params[:splat]
+      if the_params.is_a? Array
+        the_params = the_params.join(' ')
+      end
+      if params.has_key? 'user_input'
+        the_params = params['user_input']
+      end
+      the_params = the_params.strip.upcase if the_params
+      the_result = ::Bioroebe.return_n_stop_codons_in_this_sequence(the_params)
+      if the_params.empty?
+        the_result = return_intro_for_n_stop_codons_in_this_sequence+
+        p(
+          '<b> Please input a DNA sequence which will be '\
+          'investigated next.</b>'
+        )+
+        return_paragraph_of_hyperlinks
+      else
+        the_result = return_intro_for_n_stop_codons_in_this_sequence+
+        p('This sequence contains <b style="font-size: larger; color: blueviolet">'+
+          the_result.to_s+'</b> stop '\
+          'codons.'
+        )+
+        p(
+          '(The <b>input-sequence</b> was <b style="color: darkgreen">'+
+          the_params.to_s+'</b>)'
+        )
+      end
+      the_result << return_form_for_n_stop_codons_in_this_sequence(entry.delete('*'))
+      the_result << hyperlinks_paragraph
+      the_result
+    }
+  }
+
+  # ========================================================================= #
+  # === /palindromes
+  #
+  # http://localhost:4568/palindromes
+  # ========================================================================= #
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.each {|target|
+    get(target) {
+      embeddable_interface?.return_header_for_palindromes+
+      HtmlTags.p(
+        'Input how many nucleotides shall be part of '\
+        'a palindrome (input an even number)'
+      )+
+      embeddable_interface?.return_form_for_palindromes_action+
+      embeddable_interface?.footer
+    }
+  }
+
+  # ========================================================================= #
+  # http://localhost:4568/random_aminoacids_source
+  # ========================================================================= #
+  ['/random_aminoacids_source'].each {|target|
+    get(target) {
+      body = HtmlTags.p('The source is:')+
+             '<pre>'+
+             ::Bioroebe.return_source_code_of_this_method(method(:random_aminoacids))+
+             '</pre>'+
+             footer
+      Cyberweb.html_template(
+      title: 'Source code to random_aminoacids()',
+      body:  body
+    )
+    }
+  }
+
+  # ========================================================================= #
+  # === not_found
+  # ========================================================================= #
+  not_found {
+    Cyberweb.html_template(
+      title: 'API was not found',
+      body:  p('This particular <b>API</b> was not found.')+
+             p('You may try any of the following variants instead:')+
+             embeddable_interface?.return_index_of_hyperlinks
+    ).to_s
+  }
+
+  # ========================================================================= #
+  # === Convert into a chunked display
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4568/reverse_complement
+  #   http://localhost:4568/chunked
   #
   # Example:
   #
-  #   http://localhost:4568/reverse_complement/ATGCUUUUUUUUUU
+  #   http://localhost:4568/chunked/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
-  get('/reverse_complement/*') {
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
+    get(target+'/*') {
+      the_params = params[:splat]
+      if the_params.is_a? Array
+        the_params = the_params.join(' ')
+      end
+      if params.has_key? 'user_input'
+        the_params = params['user_input']
+      end
+      the_params = the_params.strip.upcase if the_params
+      the_result = ::Bioroebe.chunked_display(the_params)
+      if the_params.empty?
+        the_result = p(
+                       '<b> Please input a DNA sequence</b>'
+                     )+
+                     return_paragraph_of_hyperlinks
+      else
+        the_result = p('Converted into a chunked display:')+
+                     HtmlTags.pre(
+                       '<b>'+the_result+'</b>',
+                       css_style: 'color: darkblue; margin:1em; font-size: larger;'
+                     )+
+                     return_paragraph_of_hyperlinks
+      end
+      Cyberweb.html_template(
+        title: 'To chunked display',
+        body:  the_result
+      )
+    }
+  }
+
+  # ========================================================================= #
+  # === Codon Frequencies
+  #
+  # Example:
+  #
+  #   http://localhost:4568/frequency_per_thousand/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/frequency_per_thousand/*') {
     the_params = params[:splat]
-    if the_params.is_a? Array
-      the_params = the_params.join(' ')
-    end
-    if params.has_key? 'user_input'
-      the_params = params['user_input']
-    end
+    the_params = the_params.join(' ') if the_params.is_a? Array
+    the_params = params['user_input'] if params.has_key? 'user_input'
     the_params = the_params.strip.upcase if the_params
-    if the_params.is_a? Array
-      the_params = the_params.flatten.first
-    end
-    the_reverse_complement = ::Bioroebe.reverse_complement(the_params)
-    if the_reverse_complement.is_a? Array
-      the_reverse_complement = the_reverse_complement.first.to_s
-    end
+    the_params = the_params.flatten.first if the_params.is_a? Array
     the_result = ''.dup
     if the_params.empty?
       the_result << return_intro_for_reverse_complement_conversion+
         p(
-          '<b> Please input a DNA sequence which will be '\
-          'reverse-complemented into DNA.</b>'
+          '<b>Please input a DNA sequence.</b>'
         )+
         return_paragraph_of_hyperlinks
     else
       _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
-      the_result << _+p(
-        "The reverse complement of <b>5'-#{the_params.to_s}</b> is:"
-      )
-      the_result << p(
-        "<b>5'-#{the_reverse_complement}</b>",
-        css_style: 'margin:1em; font-size: larger; color: blueviolet'
+      the_result << HtmlTags.pre(
+        Bioroebe.frequency_per_thousand(the_params)
       )
     end
-    the_result << embeddable_interface?.return_form_for_reverse_complement_action
+    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
     the_result << embeddable_interface?.hyperlinks_paragraph
     the_result
   }
 
   # ========================================================================= #
-  # http://localhost:4568/to_dna_source
+  # === chunked_display
+  #
+  # http://localhost:4568/chunked_display
+  # http://localhost:4568/chunked
+  # http://localhost:4568/upcase
   # ========================================================================= #
-  get([
-        '/to_dna_source',
-        '/to_aa_source'
-      ]){
-    sanitized_URL_part = request.path_info.to_s.sub('_source','').
-                         delete('/').to_sym
-    file, line_number = ::Bioroebe.method(sanitized_URL_part).source_location
-    if File.exist? file
-      readlines = File.readlines(file)
-      source_code = readlines[(line_number - 1) .. -1].join
-      Cyberweb::HtmlTemplate[
-        title: sanitized_URL_part.to_s+' source code',
-        body:  embeddable_interface?.return_intro_for_to_dna_conversion+
-        p(
-          'The source code for the <b>/'+sanitized_URL_part.to_s+
-          '</b> functionality is: '
-        )+
-        '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
-        source_code+
-        '</pre>'+
-        embeddable_interface?.hyperlink_paragraph
-      ].to_s
-    else
-      "Can not read the file's content."
-    end
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
+    get(target) {
+      embeddable_interface?.return_header_to_chunked_display+
+      embeddable_interface?.footer
+    }
   }
 
   # =========================================================================== #
-  # Example:
+  # === /to_dna
   #
-  #   http://localhost:4568/shuffleseq
+  # Usage Examples:
+  #
+  #   http://localhost:4568/to_dna
+  #   http://localhost:4568/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
   #
   # =========================================================================== #
-  get('/shuffleseq'){
-    embeddable_interface?.method_shuffleseq
+  get('/to_dna'){
+    embeddable_interface?.return_sinatra_to_dna
   }
 
   # ========================================================================= #
-  # === /shuffleseq
-  #
-  # http://localhost:4568/shuffleseq
+  # http://localhost:4568/to_aa
+  # http://localhost:4568/to_aminoacids
   # ========================================================================= #
-  ['/shuffleseq'].each {|target|
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.each {|target|
     get(target) {
-      Cyberweb::HtmlTemplate[
-        title: 'Shuffleseq - Shuffle a sequence',
-        body:  '<pre>'+
-               ::Bioroebe.shuffleseq(method(:reverse_complement))+
-               '</pre>'+
-               footer
-      ].to_s
+      Cyberweb.html_template(
+        title: 'To aminoacid conversion',
+        body:   return_header_to_aminoacid_conversion+
+                return_explanation_of_how_to_use_the_aminoacid_conversion+
+                return_form_for_to_aa_action+
+                footer
+      ).to_s
     }
   }
 
   # ========================================================================= #
-  # === shuffleseq
+  # === /mirror_source
+  #
+  # http://localhost:4568/mirror_source
   # ========================================================================= #
-  get('/shuffleseq/*') {
-    the_params = params[:splat]
-    if the_params.is_a? Array
-      the_params = the_params.join(' ')
-    end
-    the_params = the_params.dup
-    if the_params
-      the_params = the_params.strip.upcase
-    end
-    the_result = ::Bioroebe.shuffleseq(the_params)
-    body = embeddable_interface?.return_intro_for_shuffleseq.dup
-    if the_params.empty?
-      body <<
-        p(
-          '<b> Please input a DNA sequence.</b>'
-        )+
-        return_paragraph_of_hyperlinks
-    else
-      body <<
-        HtmlTags.p(
-          'The shuffled sequence of <b>'+the_params.to_s+'</b> is:'
-        )+
-        HtmlTags.p(
-          '<b>'+the_result.to_s+'</b>',
-          css_style: 'margin:1em; font-size: larger; color: blueviolet'
-        )
-    end
-    body << embeddable_interface?.return_form_for_shuffleseq_action
-    body << embeddable_interface?.hyperlinks_paragraph
-    Cyberweb::HtmlTemplate[
-      title: 'Shuffleseq - Shuffle a sequence',
-      body:  body
-    ].to_s
-  }
-
-  get('/test') {
-    return_index_of_hyperlinks
-  }
-
-  # ========================================================================= #
-  # === Bioroebe::Sinatra.e
-  # ========================================================================= #
-  def self.e(i = '')
-    ::Bioroebe.e(i)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::Sinatra.erev
-  # ========================================================================= #
-  def self.erev(i = '')
-    ::Bioroebe.erev(i)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::Sinatra.start_sinatra_interface
-  #
-  # This method can be used to start the sinatra interface.
-  # ========================================================================= #
-  def self.start_sinatra_interface
-    erev 'Trying to start the sinatra-interface of Bioroebe next.'
-    e
-    erev 'This should use the following URL:'
-    e
-    erev "  #{sfancy(Bioroebe::EmbeddableInterface.localhost_to_use?)}"
-    e
-    ::Bioroebe::Sinatra.run!
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::Sinatra.sfancy
-  # ========================================================================= #
-  def self.sfancy(i = '')
-    ::Bioroebe.sfancy(i)
-  end
-
-  # ========================================================================= #
-  # http://localhost:4568/reverse_complement_source
-  # ========================================================================= #
-  ['/reverse_complement_source'].each {|target|
-    get(target) {
-      body = HtmlTags.p('The source is:')+
-             '<pre>'+
-             ::Bioroebe.return_source_code_of_this_method(method(:reverse_complement))+
-             '</pre>'+
-             footer
-      Cyberweb::HtmlTemplate[
-      title: 'Bioroebe Web-API',
-      body:  body
-    ].to_s
-    }
-  }
-
-  # =========================================================================== #
-  # Example:
-  #
-  #   http://localhost:4568/reverse_complement
-  #
-  # =========================================================================== #
-  get('/reverse_complement'){
-    embeddable_interface?.method_reverse_complement
-  }
-
-  # =========================================================================== #
-  # Example:
-  #
-  #   http://localhost:4568/n_stop_codons_in_this_sequence
-  #   http://localhost:4568/n_stop
-  #
-  # =========================================================================== #
-  %w( 
-    /n_stop_codons_in_this_sequence
-    /n_stop
-    /nstop
-  ).each {|entry|
-    get(entry){
-      embeddable_interface?.return_intro_for_n_stop_codons_in_this_sequence+
-      p(
-        'This API will return how many stop codons can be '\
-        'found in a given sequence.<br>'
-      )+
+  get('/mirror_source'){
+    file, line_number = ::Bioroebe.method(:mirror_repeat).source_location
+    if File.exist? file
+      readlines = File.readlines(file)
+      source_code = readlines[(line_number - 1) .. -1].join
+      embeddable_interface?.return_intro_for_mirror_repeat_conversion+
       p(
-        'Simply input the nucleotide String, such as "ATGCTTTAG", '\
-        'without the "" quotes.<br><br>'
-      )+
-      embeddable_interface?.return_form_for_n_stop_codons_in_this_sequence(entry)+
-      embeddable_interface?.hyperlink_paragraph
-    }
-  }
-
-  # ========================================================================= #
-  # === /palindromes
-  #
-  # http://localhost:4568/palindromes
-  # ========================================================================= #
-  Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.each {|target|
-    get(target) {
-      embeddable_interface?.return_header_for_palindromes+
-      HtmlTags.p(
-        'Input how many nucleotides shall be part of '\
-        'a palindrome (input an even number)'
+        'The source code for the <b>/mirror</b> functionality is: '
       )+
-      embeddable_interface?.return_form_for_palindromes_action+
-      embeddable_interface?.footer
-    }
-  }
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-  end
-
-  # ========================================================================= #
-  # === view
-  #
-  # http://localhost:4568/view
-  # ========================================================================= #
-  get('/view') { # view tag
-    embeddable_interface?.return_view_string
-  }
-
-  # ========================================================================= #
-  # === not_found
-  # ========================================================================= #
-  not_found {
-    Cyberweb::HtmlTemplate[
-      title: 'API was not found',
-      body:  HtmlTags.p('This particular <b>API</b> was not found.')+
-      HtmlTags.p('You may try any of the following variants instead:')+
-      embeddable_interface?.return_index_of_hyperlinks
-    ].to_s
-  }
-  # ========================================================================= #
-  # http://localhost:4568/random_aminoacids_source
-  # ========================================================================= #
-  ['/random_aminoacids_source'].each {|target|
-    get(target) {
-      body = HtmlTags.p('The source is:')+
-             '<pre>'+
-             ::Bioroebe.return_source_code_of_this_method(method(:random_aminoacids))+
-             '</pre>'+
-             footer
-      Cyberweb::HtmlTemplate[
-      title: 'Source code to random_aminoacids()',
-      body:  body
-    ].to_s
-    }
-  }
-
-  # ========================================================================= #
-  # http://localhost:4568/random_aminoacids/33
-  # ========================================================================= #
-  ['/random_aminoacids/*'].each {|target|
-    get(target) {
-      the_params = params[:splat].join(' ').strip.upcase
-      if the_params.empty?
-        return_header_random_aminoacids+
-        HtmlTags.p(
-          '<b>Please provide some argument to this API.</b>'
-        )+
-        footer
-      else
-        # =================================================================== #
-        # We need to chop the display up a bit if the result is too long.
-        # =================================================================== #
-        the_result = ::Bioroebe.random_aminoacids(the_params)
-        if the_result.size > 80
-          array = the_result.scan(/[A-Z]{80}/)
-          the_result = array.join("<br>\n")
-        end
-        require 'bioroebe/count/count_amount_of_aminoacids.rb'
-        hash_composition = Bioroebe.return_composition_from_this_aminoacid_sequence('HSLOEVCKWUCKFLVNUYWYGPNRAQMDCITKM')
-        result = '<b>'+the_result+'</b>'+'<br><br>'\
-          '(constituting <b>'+the_result.size.to_s+
-          '</b> amino acids.)'+"<br>\n"
-        result2 = "The aminoacid-composition is as follows:<br>\n".dup
-        hash_composition.each_pair {|aminoacid_one_letter, n_times|
-          result2 << "<span style=\"padding-left:2em\"><b>#{aminoacid_one_letter}</b></span>: #{n_times}<br>\n"
-        }
-        # Build the result next.
-        return_header_random_aminoacids+
-        HtmlTags.p(result,'','','margin: 1em')+
-        HtmlTags.p(result2,'','','font-size: 1.6em; float:left; margin: 1em; font-family: monospace;')+
-        footer
-      end
-    }
+      '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
+      source_code+
+      '</pre>'+
+      hyperlink_paragraph
+    else
+      "Can not read the file's content."
+    end
   }
 
   # ========================================================================= #
@@ -418,7 +335,7 @@ class Sinatra < ::Sinatra::Base
       the_params = the_params.to_s.strip.upcase if the_params
       the_result = ::Bioroebe::PalindromeGenerator.return_as_string(the_params)
       if the_params.empty?
-        the_result = HtmlTags.p(
+        the_result = p(
           '<b> Please input a DNA sequence</b>'
         )+
         return_paragraph_of_hyperlinks
@@ -429,7 +346,7 @@ class Sinatra < ::Sinatra::Base
         # =================================================================== #
         # Overwrite the_result variable next:
         # =================================================================== #
-        the_result = HtmlTags.p(
+        the_result = p(
           'Generated the following palindrome of '\
           'size <b>'+the_params.to_s+'</b>:'
         )+
@@ -438,62 +355,252 @@ class Sinatra < ::Sinatra::Base
           css_style: 'color: darkblue; margin: 1em; font-size: larger;'
         )+
         return_paragraph_of_hyperlinks
-      end
-      the_result << return_form_for_palindromes_action
-      the_result
-    }
+      end
+      the_result << return_form_for_palindromes_action
+      the_result
+    }
+  }
+
+  # ========================================================================= #
+  # === /codon_frequency_of_this_string
+  #
+  # http://localhost:4568/codon_frequency_of_this_string
+  # ========================================================================= #
+  ['/codon_frequency_of_this_string'].each {|target|
+    get(target) {
+      embeddable_interface?.method_codon_frequency_of_this_string
+    }
+  }
+
+  # ========================================================================= #
+  # === /blosum_source
+  #
+  # http://localhost:4568/blosum_source
+  # ========================================================================= #
+  get('/blosum_source'){
+    file, line_number = ::Bioroebe.method(:blosum).source_location
+    if File.exist? file
+      readlines = File.readlines(file)
+      source_code = readlines[(line_number - 1) .. -1].join
+      embeddable_interface?.return_intro_for_blosum+
+      p(
+        'The source code for the <b>/blosum</b> functionality is: '
+      )+
+      '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
+      source_code+
+      '</pre>'+
+      hyperlink_paragraph
+    else
+      "Can not read the file's content."
+    end
+  }
+
+  # =========================================================================== #
+  # === /mirror
+  #
+  # Example:
+  #
+  #   http://localhost:4568/mirror
+  # =========================================================================== #
+  get('/mirror'){
+    body = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
+           p(
+             'You can "create" a mirror-repeat of DNA/RNA here.'
+           )+
+           p(
+             'Simply input the nucleotide String, such as "ATGCT", '\
+             'without the "" quotes.'
+           )+
+           embeddable_interface?.return_form_for_mirror_repeat_action+
+           embeddable_interface?.hyperlink_paragraph
+    Cyberweb.html_template(
+      title: 'Mirror repeats-API',
+      body:  body
+    )
+  }
+
+  # ========================================================================= #
+  # === Convert into DNA                    (2 tag, second entry, to_dna tag)
+  #
+  # This method will convert RNA into DNA.
+  #
+  #   http://localhost:4568/to_dna
+  #
+  # Example:
+  #
+  #   http://localhost:4568/to_dna/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/to_dna/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    if params.has_key? 'user_input'
+      the_params = params['user_input']
+    end
+    the_params = the_params.strip.upcase if the_params
+    if the_params.include? '&'
+      the_params = the_params[0 .. (the_params.index('&') - 1)]
+    end
+    the_result = ::Bioroebe.to_dna(the_params)
+    if the_params.empty?
+      the_result = embeddable_interface?.return_intro_for_to_dna_conversion+
+      p(
+        '<b> Please input a RNA sequence which will be '\
+        'converted into DNA.</b>'
+      )+
+      return_paragraph_of_hyperlinks
+    else
+      the_result = embeddable_interface?.return_intro_for_to_dna_conversion+
+                   p('Converted into DNA, <b>'+the_params+'</b> '\
+                   'is equivalent to:')+
+                   p(
+                     '<b>'+the_result+'</b>',
+                     css_style: 'margin:1em; font-size: larger; color: blueviolet'
+                   )
+    end
+    the_result << embeddable_interface?.return_form_for_to_dna_action
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+
+  # ========================================================================= #
+  # === view
+  #
+  # http://localhost:4568/view
+  # ========================================================================= #
+  get('/view') { # view tag
+    embeddable_interface?.return_view_string
+  }
+
+  # ========================================================================= #
+  # === Codon Frequencies
+  #
+  # Example:
+  #
+  #   http://localhost:4568/codon_frequency_of_this_string/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/codon_frequency_of_this_string/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    if params.has_key? 'user_input'
+      the_params = params['user_input']
+    end
+    the_params = the_params.strip.upcase if the_params
+    if the_params.is_a? Array
+      the_params = the_params.flatten.first
+    end
+    the_result = ''.dup
+    if the_params.empty?
+      the_result << return_intro_for_reverse_complement_conversion+
+        p(
+          '<b> Please input a DNA sequence.'
+        )+
+        return_paragraph_of_hyperlinks
+    else
+      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
+      the_result << p(
+        Bioroebe.codon_frequency_of_this_string(the_params)
+      )
+    end
+    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
   }
 
   # ========================================================================= #
-  # === Query how many stop codons are in a given DNA sequence
+  # === Convert into DNA                    (2 tag, second entry, reverse_complement tag)
   #
-  # This method will determine how many stop codons are in the given
-  # sequence.
+  # This method will convert RNA into DNA.
   #
-  #   http://localhost:4568/n_stop_codons_in_this_sequence
+  #   http://localhost:4568/reverse_complement
   #
   # Example:
   #
-  #   http://localhost:4568/n_stop_codons_in_this_sequence/ATGCUUUUUUUUUTAG
+  #   http://localhost:4568/reverse_complement/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
-  %w(
-    /n_stop_codons_in_this_sequence/*
-    /n_stop/*
-    /nstop/*
-  ).each {|entry|
-    get(entry) {
-      the_params = params[:splat]
-      if the_params.is_a? Array
-        the_params = the_params.join(' ')
-      end
-      if params.has_key? 'user_input'
-        the_params = params['user_input']
-      end
-      the_params = the_params.strip.upcase if the_params
-      the_result = ::Bioroebe.return_n_stop_codons_in_this_sequence(the_params)
-      if the_params.empty?
-        the_result = return_intro_for_n_stop_codons_in_this_sequence+
-        HtmlTags.p(
+  get('/reverse_complement/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    if params.has_key? 'user_input'
+      the_params = params['user_input']
+    end
+    the_params = the_params.strip.upcase if the_params
+    if the_params.is_a? Array
+      the_params = the_params.flatten.first
+    end
+    the_reverse_complement = ::Bioroebe.reverse_complement(the_params)
+    if the_reverse_complement.is_a? Array
+      the_reverse_complement = the_reverse_complement.first.to_s
+    end
+    the_result = ''.dup
+    if the_params.empty?
+      the_result << return_intro_for_reverse_complement_conversion+
+        p(
           '<b> Please input a DNA sequence which will be '\
-          'investigated next.</b>'
+          'reverse-complemented into DNA.</b>'
         )+
         return_paragraph_of_hyperlinks
-      else
-        the_result = return_intro_for_n_stop_codons_in_this_sequence+
-        HtmlTags.p('This sequence contains <b style="font-size: larger; color: blueviolet">'+
-          the_result.to_s+'</b> stop '\
-          'codons.'
+    else
+      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
+      the_result << _+p(
+        "The reverse complement of <b>5'-#{the_params.to_s}</b> is:"
+      )
+      the_result << p(
+        "<b>5'-#{the_reverse_complement}</b>",
+        css_style: 'margin:1em; font-size: larger; color: blueviolet'
+      )
+    end
+    the_result << embeddable_interface?.return_form_for_reverse_complement_action
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+
+  # ========================================================================= #
+  # http://localhost:4568/to_dna_source
+  # ========================================================================= #
+  get([
+        '/to_dna_source',
+        '/to_aa_source'
+      ]){
+    sanitized_URL_part = request.path_info.to_s.sub('_source','').
+                         delete('/').to_sym
+    file, line_number = ::Bioroebe.method(sanitized_URL_part).source_location
+    if File.exist? file
+      readlines = File.readlines(file)
+      source_code = readlines[(line_number - 1) .. -1].join
+      Cyberweb::HtmlTemplate[
+        title: sanitized_URL_part.to_s+' source code',
+        body:  embeddable_interface?.return_intro_for_to_dna_conversion+
+        p(
+          'The source code for the <b>/'+sanitized_URL_part.to_s+
+          '</b> functionality is: '
         )+
-        HtmlTags.p(
-          '(The <b>input-sequence</b> was <b style="color: darkgreen">'+
-          the_params.to_s+'</b>)'
-        )
-      end
-      the_result << return_form_for_n_stop_codons_in_this_sequence(entry.delete('*'))
-      the_result << hyperlinks_paragraph
-      the_result
-    }
+        '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
+        source_code+
+        '</pre>'+
+        embeddable_interface?.hyperlink_paragraph
+      ].to_s
+    else
+      "Can not read the file's content."
+    end
+  }
+
+  # =========================================================================== #
+  # Example:
+  #
+  #   http://localhost:4568/shuffleseq
+  #
+  # =========================================================================== #
+  get('/shuffleseq'){
+    embeddable_interface?.method_shuffleseq
   }
 
   # ========================================================================= #
@@ -501,7 +608,7 @@ class Sinatra < ::Sinatra::Base
   # ========================================================================= #
   get('/is_palindrome') {
     return_header_for_palindromes('Is palindrome')+
-    HtmlTags.p(
+    p(
       'Input the target sequence, in order to find out whether '\
       'that sequence is a <b>palindrome</b> or whether it is not.'
     )+
@@ -509,6 +616,23 @@ class Sinatra < ::Sinatra::Base
     footer
   }
 
+  # ========================================================================= #
+  # === /shuffleseq
+  #
+  # http://localhost:4568/shuffleseq
+  # ========================================================================= #
+  ['/shuffleseq'].each {|target|
+    get(target) {
+      Cyberweb.html_template(
+        title: 'Shuffleseq - Shuffle a sequence',
+        body:  '<pre>'+
+               ::Bioroebe.shuffleseq(method(:reverse_complement))+
+               '</pre>'+
+               footer
+      )
+    }
+  }
+
   # ========================================================================= #
   # === Is this sequence a palindrome
   #
@@ -528,7 +652,7 @@ class Sinatra < ::Sinatra::Base
     the_params = the_params.to_s.strip.upcase if the_params
     the_result = ::Bioroebe.is_this_sequence_a_palindrome?(the_params).to_s
     if the_params.empty?
-      the_result = HtmlTags.p(
+      the_result = p(
         '<b> Please input a DNA sequence</b>'
       )+
       return_paragraph_of_hyperlinks
@@ -536,7 +660,7 @@ class Sinatra < ::Sinatra::Base
       # =================================================================== #
       # Overwrite the_result variable next:
       # =================================================================== #
-      the_result = HtmlTags.p(
+      the_result = p(
         'Is the sequence <b>'+the_params.to_s+
         '</b> a palindrome?<br><br><b style="margin-left:2em">'+
         ::Bioroebe::VerboseTruth[the_result.to_s]+'</b>'
@@ -547,41 +671,6 @@ class Sinatra < ::Sinatra::Base
     the_result
   }
 
-  # ========================================================================= #
-  # === /mirror_source
-  #
-  # http://localhost:4568/mirror_source
-  # ========================================================================= #
-  get('/mirror_source'){
-    file, line_number = ::Bioroebe.method(:mirror_repeat).source_location
-    if File.exist? file
-      readlines = File.readlines(file)
-      source_code = readlines[(line_number - 1) .. -1].join
-      embeddable_interface?.return_intro_for_mirror_repeat_conversion+
-      HtmlTags.p(
-        'The source code for the <b>/mirror</b> functionality is: '
-      )+
-      '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
-      source_code+
-      '</pre>'+
-      hyperlink_paragraph
-    else
-      "Can not read the file's content."
-    end
-  }
-
-  # ========================================================================= #
-  # http://localhost:4568/chunked_display
-  # http://localhost:4568/chunked
-  # http://localhost:4568/upcase
-  # ========================================================================= #
-  Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
-    get(target) {
-      embeddable_interface?.return_header_to_chunked_display+
-      embeddable_interface?.footer
-    }
-  }
-
   # ========================================================================= #
   # === Compseq                                                     (compseq)
   #
@@ -606,91 +695,60 @@ class Sinatra < ::Sinatra::Base
     the_result = ::Bioroebe.compseq(the_params) { :be_quiet }
     if the_params.empty?
       the_result = return_intro_for_compseq+
-      HtmlTags.p(
-        '<b> Please input a DNA sequence which will be '\
-        'compseq into DNA.</b>'
-      )+
-      return_paragraph_of_hyperlinks
-    else
-      the_result = return_intro_for_compseq+
-      HtmlTags.p('The compseq of <b>'+the_params+'</b> is:')+
-      HtmlTags.pre(
-        the_result,
-        css_style: 'margin:1em; margin-left: 4em; font-size: larger; '\
-                   'font-weight: bold; color: blueviolet'
-      )
-    end
-    the_result << return_form_for_compseq_action
-    the_result << hyperlinks_paragraph
-    the_result
-  }
-
-  # ========================================================================= #
-  # http://localhost:4568/to_aa
-  # http://localhost:4568/to_aminoacids
-  # ========================================================================= #
-  Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.each {|target|
-    get(target) {
-      Cyberweb::HtmlTemplate[
-        title: 'To aminoacid conversion',
-        body:   return_header_to_aminoacid_conversion+
-                return_explanation_of_how_to_use_the_aminoacid_conversion+
-                return_form_for_to_aa_action+
-                footer
-      ].to_s
-    }
-  }
-
-  # =========================================================================== #
-  # === /mirror
-  #
-  # Example:
-  #
-  #   http://localhost:4568/mirror
-  # =========================================================================== #
-  get('/mirror'){
-    body = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
-           HtmlTags.p(
-             'You can "create" a mirror-repeat of DNA/RNA here.'
-           )+
-           HtmlTags.p(
-             'Simply input the nucleotide String, such as "ATGCT", '\
-             'without the "" quotes.'
-           )+
-           embeddable_interface?.return_form_for_mirror_repeat_action+
-           embeddable_interface?.hyperlink_paragraph
-    Cyberweb::HtmlTemplate[
-      title: 'Mirror repeats-API',
-      body:  body
-    ].to_s
+      p(
+        '<b> Please input a DNA sequence which will be '\
+        'compseq into DNA.</b>'
+      )+
+      return_paragraph_of_hyperlinks
+    else
+      the_result = return_intro_for_compseq+
+      p('The compseq of <b>'+the_params+'</b> is:')+
+      HtmlTags.pre(
+        the_result,
+        css_style: 'margin:1em; margin-left: 4em; font-size: larger; '\
+                   'font-weight: bold; color: blueviolet'
+      )
+    end
+    the_result << return_form_for_compseq_action
+    the_result << hyperlinks_paragraph
+    the_result
   }
 
-  # =========================================================================== #
-  # === /to_dna
-  #
-  # Usage Examples:
+  # ========================================================================= #
+  # === /codon_frequency_of_this_string
   #
-  #   http://localhost:4568/to_dna
-  #   http://localhost:4568/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
+  # http://localhost:4568/codon_frequency_of_this_string
+  # ========================================================================= #
+  ['/codon_frequency_of_this_string'].each {|target|
+    get(target) {
+      embeddable_interface?.method_codon_frequency_of_this_string
+    }
+  }
+
+  # ========================================================================= #
+  # === /random_aminoacids
   #
-  # =========================================================================== #
-  get('/to_dna'){
-    embeddable_interface?.return_sinatra_to_dna
+  # http://localhost:4568/random_aminoacids
+  # ========================================================================= #
+  ['/random_aminoacids'].each {|target|
+    get(target) {
+      embeddable_interface?.method_random_aminoacids
+    }
   }
 
   # ========================================================================= #
-  # === Convert into DNA                    (2 tag, second entry, to_dna tag)
+  # === mirror*
   #
   # This method will convert RNA into DNA.
   #
-  #   http://localhost:4568/to_dna
+  #   http://localhost:4568/mirror
   #
   # Example:
   #
-  #   http://localhost:4568/to_dna/ATGCUUUUUUUUUU
+  #   http://localhost:4568/mirror/ATGCUUUUUUUUUU
   #
   # ========================================================================= #
-  get('/to_dna/*') {
+  get('/mirror/*') {
     the_params = params[:splat]
     if the_params.is_a? Array
       the_params = the_params.join(' ')
@@ -699,127 +757,55 @@ class Sinatra < ::Sinatra::Base
       the_params = params['user_input']
     end
     the_params = the_params.strip.upcase if the_params
-    if the_params.include? '&'
-      the_params = the_params[0 .. (the_params.index('&') - 1)]
-    end
-    the_result = ::Bioroebe.to_dna(the_params)
+    the_result = ::Bioroebe.mirror_repeat(
+      the_params, false, false, false
+    ).delete('|')
     if the_params.empty?
-      the_result = embeddable_interface?.return_intro_for_to_dna_conversion+
-      HtmlTags.p(
+      the_result = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
+      p(
         '<b> Please input a RNA sequence which will be '\
         'converted into DNA.</b>'
       )+
       return_paragraph_of_hyperlinks
     else
-      the_result = embeddable_interface?.return_intro_for_to_dna_conversion+
-                   HtmlTags.p('Converted into DNA, <b>'+the_params+'</b> '\
-                   'is equivalent to:')+
-                   HtmlTags.p(
-                     '<b>'+the_result+'</b>',
-                     css_style: 'margin:1em; font-size: larger; color: blueviolet'
-                   )
+      the_result = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
+      p(
+        'The mirror repeat of <b>'+the_params+'</b> is:'
+      )+
+      p(
+        '<b>'+the_result+'</b>',
+        css_style: 'margin:1em; font-size: larger; color: blueviolet'
+      )
     end
-    the_result << embeddable_interface?.return_form_for_to_dna_action
+    the_result << embeddable_interface?.return_form_for_mirror_repeat_action
     the_result << embeddable_interface?.hyperlinks_paragraph
     the_result
   }
 
-  # ========================================================================= #
-  # === Convert into a chunked display
-  #
-  # This method will convert RNA into DNA.
-  #
-  #   http://localhost:4568/chunked
-  #
-  # Example:
-  #
-  #   http://localhost:4568/chunked/ATGCUUUUUUUUUU
-  #
-  # ========================================================================= #
-  Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
-    get(target+'/*') {
-      the_params = params[:splat]
-      if the_params.is_a? Array
-        the_params = the_params.join(' ')
-      end
-      if params.has_key? 'user_input'
-        the_params = params['user_input']
-      end
-      the_params = the_params.strip.upcase if the_params
-      the_result = ::Bioroebe.chunked_display(the_params)
-      if the_params.empty?
-        the_result = HtmlTags.p(
-                       '<b> Please input a DNA sequence</b>'
-                     )+
-                     return_paragraph_of_hyperlinks
-      else
-        the_result = HtmlTags.p('Converted into a chunked display:')+
-                     HtmlTags.pre(
-                       '<b>'+the_result+'</b>',
-                       css_style: 'color: darkblue; margin:1em; font-size: larger;'
-                     )+
-                     return_paragraph_of_hyperlinks
-      end
-      Cyberweb::HtmlTemplate[
-        title: 'To chunked display',
-        body:  the_result
-      ].to_s
-    }
-  }
-
   # =========================================================================== #
-  # === /compseq
+  # === /blosum
   #
   # Example:
   #
-  #   http://localhost:4568/compseq
+  #   http://localhost:4568/blosum
   #
   # =========================================================================== #
-  get('/compseq'){
-    Bioroebe::Sinatra.embeddable_interface?.return_sinatra_method_for_compseq
-  }
-
-  # =========================================================================== #
-  # === return_header_to_aminoacid_conversion
-  # =========================================================================== #
-  def return_header_to_aminoacid_conversion
-    Bioroebe::Sinatra.embeddable_interface?.return_header_to_aminoacid_conversion
-  end
-
-  # =========================================================================== #
-  # === return_explanation_of_how_to_use_the_aminoacid_conversion
-  # =========================================================================== #
-  def return_explanation_of_how_to_use_the_aminoacid_conversion
-    Bioroebe::Sinatra.embeddable_interface?.return_explanation_of_how_to_use_the_aminoacid_conversion
-  end
-
-  # =========================================================================== #
-  # === return_form_for_to_aa_action
-  # =========================================================================== #
-  def return_form_for_to_aa_action
-    Bioroebe::Sinatra.embeddable_interface?.return_form_for_to_aa_action
-  end
-
-  # =========================================================================== #
-  # === return_paragraph_of_hyperlinks
-  # =========================================================================== #
-  def return_paragraph_of_hyperlinks
-    embeddable_interface?.return_paragraph_of_hyperlinks
-  end; alias footer               return_paragraph_of_hyperlinks # === footer (footer tag)
-       alias hyperlink_paragraph  return_paragraph_of_hyperlinks # === hyperlink_paragraph
-       alias hyperlinks_paragraph return_paragraph_of_hyperlinks # === hyperlinks_paragraph
-
-  # ========================================================================= #
-  # === /                                                          (main tag)
-  #
-  # This is the root tag, the root of our web-application.
-  # ========================================================================= #
-  get('/') {
-    body = embeddable_interface?.return_root_string
-    Cyberweb::HtmlTemplate[
-      title: 'Bioroebe Web-API',
-      body:  body
-    ].to_s
+  get('/blosum'){
+    _ = ''.dup
+    _ << embeddable_interface?.return_intro_for_blosum
+    _ << p(
+      "You can view different BLOSUM matrices here.<br><br>Choose from:<br><br>\n"
+    )
+    available_blosum_matrices = Bioroebe.available_blosum_matrices?
+    available_blosum_matrices.each {|entry|
+      _ << '<b style="margin-left: 2em">'+entry+'</b><br>'
+    }
+    _ << p(
+      "<br>Name of the BLOSUM matrix:<br>"
+    )+
+    embeddable_interface?.return_form_for_blosum_action+
+    embeddable_interface?.hyperlink_paragraph
+    return _
   }
 
   # ========================================================================= #
@@ -839,7 +825,7 @@ class Sinatra < ::Sinatra::Base
       end
       if the_params.empty?
         return_header_to_aminoacid_conversion+
-        HtmlTags.p(
+        p(
           '<b>Please provide some argument to this API.</b>'
         )+
         footer
@@ -857,16 +843,16 @@ class Sinatra < ::Sinatra::Base
         the_params = the_params.to_s.strip.delete(' ')
         the_result = ::Bioroebe.to_aa(the_params)
         return_header_to_aminoacid_conversion+
-        HtmlTags.p(
+        p(
           '<b style="color: darkgreen">The input sequence was:</b> <b>'+the_params+'</b>'
         )+
-        HtmlTags.p(
+        p(
           '<b style="color: darkblue; margin-left: 1em;">Frame 1:</b> <b>'+the_result+'</b> # '+the_result.size.to_s+' aminoacids'
         )+
-        HtmlTags.p(
+        p(
           '<b style="color: darkblue; margin-left: 1em;">Frame 2:</b> <b>'+Bioroebe.to_aa(the_params[1 .. -1])+'</b> # '+the_result.size.to_s+' aminoacids'
         )+
-        HtmlTags.p(
+        p(
           '<b style="color: darkblue; margin-left: 1em;">Frame 3:</b> <b>'+Bioroebe.to_aa(the_params[2 .. -1])+'</b> # '+the_result.size.to_s+' aminoacids'
         )+
         footer
@@ -874,101 +860,151 @@ class Sinatra < ::Sinatra::Base
     }
   }
 
-  # =========================================================================== #
-  # === /blosum
-  #
-  # Example:
-  #
-  #   http://localhost:4568/blosum
-  #
-  # =========================================================================== #
-  get('/blosum'){
-    _ = ''.dup
-    _ << embeddable_interface?.return_intro_for_blosum
-    _ << HtmlTags.p(
-      'You can view different BLOSUM matrices here. Choose from:'
-    )
-    available_blosum_matrices = Bioroebe.available_blosum_matrices?
-    available_blosum_matrices.each {|entry|
-      _ << '<b style="margin-left: 2em">'+entry+'</b><br>'
+  # ========================================================================= #
+  # === shuffleseq
+  # ========================================================================= #
+  get('/shuffleseq/*') {
+    the_params = params[:splat]
+    if the_params.is_a? Array
+      the_params = the_params.join(' ')
+    end
+    the_params = the_params.dup
+    if the_params
+      the_params = the_params.strip.upcase
+    end
+    the_result = ::Bioroebe.shuffleseq(the_params)
+    body = embeddable_interface?.return_intro_for_shuffleseq.dup
+    if the_params.empty?
+      body <<
+        p(
+          '<b> Please input a DNA sequence.</b>'
+        )+
+        return_paragraph_of_hyperlinks
+    else
+      body <<
+        HtmlTags.p(
+          'The shuffled sequence of <b>'+the_params.to_s+'</b> is:'
+        )+
+        HtmlTags.p(
+          '<b>'+the_result.to_s+'</b>',
+          css_style: 'margin:1em; font-size: larger; color: blueviolet'
+        )
+    end
+    body << embeddable_interface?.return_form_for_shuffleseq_action
+    body << embeddable_interface?.hyperlinks_paragraph
+    Cyberweb::HtmlTemplate[
+      title: 'Shuffleseq - Shuffle a sequence',
+      body:  body
+    ].to_s
+  }
+
+  # ========================================================================= #
+  # http://localhost:4568/test
+  # ========================================================================= #
+  get('/test') {
+    return_index_of_hyperlinks
+  }
+
+  # ========================================================================= #
+  # http://localhost:4568/reverse_complement_source
+  # ========================================================================= #
+  ['/reverse_complement_source'].each {|target|
+    get(target) {
+      body = HtmlTags.p('The source is:')+
+             '<pre>'+
+             ::Bioroebe.return_source_code_of_this_method(method(:reverse_complement))+
+             '</pre>'+
+             footer
+      Cyberweb::HtmlTemplate[
+      title: 'Bioroebe Web-API',
+      body:  body
+    ].to_s
     }
-    _ << HtmlTags.p(
-      'Name of the BLOSUM matrix:'
-    )+
-    embeddable_interface?.return_form_for_blosum_action+
-    embeddable_interface?.hyperlink_paragraph
-    return _
   }
 
-  # ========================================================================= #
-  # === mirror*
+  # =========================================================================== #
+  # === reverse_complement
   #
-  # This method will convert RNA into DNA.
+  # Invocation example:
   #
-  #   http://localhost:4568/mirror
+  #   http://localhost:4568/reverse_complement
   #
-  # Example:
+  # =========================================================================== #
+  get('/reverse_complement'){
+    embeddable_interface?.method_reverse_complement
+  }
+
+  # =========================================================================== #
+  # === n_stop_codons_in_this_sequence
   #
-  #   http://localhost:4568/mirror/ATGCUUUUUUUUUU
+  # Invocation example:
   #
-  # ========================================================================= #
-  get('/mirror/*') {
-    the_params = params[:splat]
-    if the_params.is_a? Array
-      the_params = the_params.join(' ')
-    end
-    if params.has_key? 'user_input'
-      the_params = params['user_input']
-    end
-    the_params = the_params.strip.upcase if the_params
-    the_result = ::Bioroebe.mirror_repeat(
-      the_params, false, false, false
-    ).delete('|')
-    if the_params.empty?
-      the_result = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
-      HtmlTags.p(
-        '<b> Please input a RNA sequence which will be '\
-        'converted into DNA.</b>'
+  #   http://localhost:4568/n_stop_codons_in_this_sequence
+  #   http://localhost:4568/n_stop
+  #
+  # =========================================================================== #
+  %w( 
+    /n_stop_codons_in_this_sequence
+    /n_stop
+    /nstop
+  ).each {|entry|
+    get(entry){
+      embeddable_interface?.return_intro_for_n_stop_codons_in_this_sequence+
+      p(
+        'This API will return how many stop codons can be '\
+        'found in a given sequence.<br>'
       )+
-      return_paragraph_of_hyperlinks
-    else
-      the_result = embeddable_interface?.return_intro_for_mirror_repeat_conversion+
-      HtmlTags.p(
-        'The mirror repeat of <b>'+the_params+'</b> is:'
+      p(
+        'Simply input the nucleotide String, such as "ATGCTTTAG", '\
+        'without the "" quotes.<br><br>'
       )+
-      HtmlTags.p(
-        '<b>'+the_result+'</b>',
-        css_style: 'margin:1em; font-size: larger; color: blueviolet'
-      )
-    end
-    the_result << embeddable_interface?.return_form_for_mirror_repeat_action
-    the_result << embeddable_interface?.hyperlinks_paragraph
-    the_result
+      embeddable_interface?.return_form_for_n_stop_codons_in_this_sequence(entry)+
+      embeddable_interface?.hyperlink_paragraph
+    }
   }
 
-  # ========================================================================= #
-  # === /blosum_source
+  # =========================================================================== #
+  # === /compseq
   #
-  # http://localhost:4568/blosum_source
-  # ========================================================================= #
-  get('/blosum_source'){
-    file, line_number = ::Bioroebe.method(:blosum).source_location
-    if File.exist? file
-      readlines = File.readlines(file)
-      source_code = readlines[(line_number - 1) .. -1].join
-      embeddable_interface?.return_intro_for_blosum+
-      HtmlTags.p(
-        'The source code for the <b>/blosum</b> functionality is: '
-      )+
-      '<pre style="color: darkblue; margin-left:2em; font-weight: bold">'+
-      source_code+
-      '</pre>'+
-      hyperlink_paragraph
-    else
-      "Can not read the file's content."
-    end
+  # Example:
+  #
+  #   http://localhost:4568/compseq
+  #
+  # =========================================================================== #
+  get('/compseq'){
+    Bioroebe::SinatraWrapper.embeddable_interface?.return_sinatra_method_for_compseq
   }
 
+  # =========================================================================== #
+  # === return_header_to_aminoacid_conversion
+  # =========================================================================== #
+  def return_header_to_aminoacid_conversion
+    Bioroebe::SinatraWrapper.embeddable_interface?.return_header_to_aminoacid_conversion
+  end
+
+  # =========================================================================== #
+  # === return_explanation_of_how_to_use_the_aminoacid_conversion
+  # =========================================================================== #
+  def return_explanation_of_how_to_use_the_aminoacid_conversion
+    Bioroebe::SinatraWrapper.embeddable_interface?.return_explanation_of_how_to_use_the_aminoacid_conversion
+  end
+
+  # =========================================================================== #
+  # === return_form_for_to_aa_action
+  # =========================================================================== #
+  def return_form_for_to_aa_action
+    Bioroebe::SinatraWrapper.embeddable_interface?.return_form_for_to_aa_action
+  end
+
+  # =========================================================================== #
+  # === return_paragraph_of_hyperlinks
+  # =========================================================================== #
+  def return_paragraph_of_hyperlinks
+    embeddable_interface?.return_paragraph_of_hyperlinks
+  end; alias footer               return_paragraph_of_hyperlinks # === footer (footer tag)
+       alias hyperlink_paragraph  return_paragraph_of_hyperlinks # === hyperlink_paragraph
+       alias hyperlinks_paragraph return_paragraph_of_hyperlinks # === hyperlinks_paragraph
+
   # ========================================================================= #
   # === blosum*
   #
@@ -991,9 +1027,9 @@ class Sinatra < ::Sinatra::Base
     end
     # No longer upcase since as of August 2021.
     # the_params = the_params.strip.upcase if the_params
-    the_result = HtmlTags.p('The content of the <b>BLOSUM matrix</b> '\
+    the_result = p('The content of the <b>BLOSUM matrix</b> '\
                  '<b style="color: blueviolet">'+the_params.to_s+'</b> is:').dup
-    the_result << HtmlTags.p(
+    the_result << p(
       '<pre style="font-size:1.5em">'+
       Bioroebe::BlosumParser.return_as_2D_table(the_params).tr('｜','|').to_s+
       '</pre>',
@@ -1005,123 +1041,64 @@ class Sinatra < ::Sinatra::Base
   }
 
   # ========================================================================= #
-  # === /random_aminoacids
-  #
-  # http://localhost:4568/random_aminoacids
-  # ========================================================================= #
-  ['/random_aminoacids'].each {|target|
-    get(target) {
-      embeddable_interface?.method_random_aminoacids
-    }
-  }
-
-  # ========================================================================= #
-  # === /codon_frequency_of_this_string
+  # === Random aminoacids
   #
-  # http://localhost:4568/codon_frequency_of_this_string
+  # http://localhost:4568/random_aminoacids/33
   # ========================================================================= #
-  ['/codon_frequency_of_this_string'].each {|target|
+  ['/random_aminoacids/*'].each {|target|
     get(target) {
-      embeddable_interface?.method_codon_frequency_of_this_string
-    }
-  }
-
-  # ========================================================================= #
-  # === Codon Frequencies
-  #
-  # Example:
-  #
-  #   http://localhost:4568/codon_frequency_of_this_string/ATGCUUUUUUUUUU
-  #
-  # ========================================================================= #
-  get('/codon_frequency_of_this_string/*') {
-    the_params = params[:splat]
-    if the_params.is_a? Array
-      the_params = the_params.join(' ')
-    end
-    if params.has_key? 'user_input'
-      the_params = params['user_input']
-    end
-    the_params = the_params.strip.upcase if the_params
-    if the_params.is_a? Array
-      the_params = the_params.flatten.first
-    end
-    the_result = ''.dup
-    if the_params.empty?
-      the_result << return_intro_for_reverse_complement_conversion+
+      the_params = params[:splat].join(' ').strip.upcase
+      if the_params.empty?
+        return_header_random_aminoacids+
         p(
-          '<b> Please input a DNA sequence.'
+          '<b>Please provide some argument to this API.</b>'
         )+
-        return_paragraph_of_hyperlinks
-    else
-      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
-      the_result << p(
-        Bioroebe.codon_frequency_of_this_string(the_params)
-      )
-    end
-    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
-    the_result << embeddable_interface?.hyperlinks_paragraph
-    the_result
-  }
-# ========================================================================= #
-  # === /codon_frequency_of_this_string
-  #
-  # http://localhost:4568/codon_frequency_of_this_string
-  # ========================================================================= #
-  ['/codon_frequency_of_this_string'].each {|target|
-    get(target) {
-      embeddable_interface?.method_codon_frequency_of_this_string
+        footer
+      else
+        # =================================================================== #
+        # We need to chop the display up a bit if the result is too long.
+        # =================================================================== #
+        the_result = ::Bioroebe.random_aminoacids(the_params)
+        if the_result.size > 80
+          array = the_result.scan(/[A-Z]{80}/)
+          the_result = array.join("<br>\n")
+        end
+        require 'bioroebe/count/count_amount_of_aminoacids.rb'
+        hash_composition = Bioroebe.return_composition_from_this_aminoacid_sequence('HSLOEVCKWUCKFLVNUYWYGPNRAQMDCITKM')
+        result = '<b>'+the_result+'</b>'+'<br><br>'\
+          '(constituting <b>'+the_result.size.to_s+
+          '</b> amino acids.)'+"<br>\n"
+        result2 = "The aminoacid-composition is as follows:<br>\n".dup
+        hash_composition.each_pair {|aminoacid_one_letter, n_times|
+          result2 << "<span style=\"padding-left:2em\"><b>#{aminoacid_one_letter}</b></span>: #{n_times}<br>\n"
+        }
+        # Build the result next.
+        return_header_random_aminoacids+
+        p(result,'','','margin: 1em')+
+        p(result2,'','','font-size: 1.6em; float:left; margin: 1em; font-family: monospace;')+
+        footer
+      end
     }
   }
 
-  # ========================================================================= #
-  # === Codon Frequencies
-  #
-  # Example:
-  #
-  #   http://localhost:4568/frequency_per_thousand/ATGCUUUUUUUUUU
-  #
-  # ========================================================================= #
-  get('/frequency_per_thousand/*') {
-    the_params = params[:splat]
-    if the_params.is_a? Array
-      the_params = the_params.join(' ')
-    end
-    if params.has_key? 'user_input'
-      the_params = params['user_input']
-    end
-    the_params = the_params.strip.upcase if the_params
-    if the_params.is_a? Array
-      the_params = the_params.flatten.first
-    end
-    the_result = ''.dup
-    if the_params.empty?
-      the_result << return_intro_for_reverse_complement_conversion+
-        p(
-          '<b>Please input a DNA sequence.</b>'
-        )+
-        return_paragraph_of_hyperlinks
-    else
-      _ = embeddable_interface?.return_intro_for_reverse_complement_conversion
-      the_result << HtmlTags.pre(
-        Bioroebe.frequency_per_thousand(the_params)
-      )
-    end
-    the_result << embeddable_interface?.return_form_for_codon_frequency_of_this_string
-    the_result << embeddable_interface?.hyperlinks_paragraph
-    the_result
-  }
-  
 end
 
-# =========================================================================== #
-# === Bioroebe.start_sinatra_interface
-# =========================================================================== #
+# ========================================================================= #
+# === Bioroebe::SinatraWrapper.start_sinatra_interface
+#
+# This method can be used to start the sinatra interface.
+# ========================================================================= #
 def self.start_sinatra_interface
-  ::Bioroebe::Sinatra.start_sinatra_interface
+  erev 'Trying to start the sinatra-interface of Bioroebe next.'
+  e
+  erev 'This should use the following URL:'
+  e
+  erev "  #{sfancy(Bioroebe::EmbeddableInterface.localhost_to_use?)}"
+  e
+  ::Bioroebe::SinatraWrapper.run!
 end; self.instance_eval { alias start_sinatra start_sinatra_interface } # === Bioroebe.start_sinatra
 
-end if Object.const_defined? :Sinatra
+end
 
 if __FILE__ == $PROGRAM_NAME
   Bioroebe.start_sinatra_interface