bioroebe 0.10.80

data/lib/bioroebe/www/sinatra/sinatra.rb

@@ -0,0 +1,1013 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/www/sinatra/sinatra.rb'
+# =========================================================================== #
+begin
+  require 'cyberweb/and_sinatra_base.rb'
+  require 'sinatra'
+rescue LoadError; end
+
+module Bioroebe
+
+class Sinatra < ::Sinatra::Base
+
+  require 'bioroebe/www/embeddable_interface.rb'
+
+  set :port, ::Bioroebe::EmbeddableInterface::USE_THIS_PORT
+
+  # ========================================================================= #
+  # === @embeddable_interface
+  # ========================================================================= #
+  @embeddable_interface = Bioroebe.embeddable_interface
+
+  # ========================================================================= #
+  # === Bioroebe::Sinatra.embeddable_interface?
+  # ========================================================================= #
+  def self.embeddable_interface?
+    @embeddable_interface
+  end
+
+  # ========================================================================= #
+  # === embeddable_interface?
+  # ========================================================================= #
+  def embeddable_interface?
+    ::Bioroebe::Sinatra.embeddable_interface?
+  end
+
+  # ========================================================================= #
+  # === 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 }
+  end
+
+  # ========================================================================= #
+  # === Convert into DNA                    (2 tag, second entry, reverse_complement tag)
+  #
+  # This method will convert RNA into DNA.
+  #
+  #   http://localhost:4567/reverse_complement
+  #
+  # Example:
+  #
+  #   http://localhost:4567/reverse_complement/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  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
+    the_result = ::Bioroebe.reverse_complement(the_params)
+    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>'
+      )+
+      return_paragraph_of_hyperlinks
+    else
+      the_result = embeddable_interface?.return_intro_for_reverse_complement_conversion+
+      p('The reverse complement 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_reverse_complement_action
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+
+  # ========================================================================= #
+  # http://localhost:4567/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: '
+        )+
+        '<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:4567/shuffleseq
+  #
+  # =========================================================================== #
+  get('/shuffleseq'){
+    embeddable_interface?.method_shuffleseq
+  }
+
+  # ========================================================================= #
+  # === /shuffleseq
+  #
+  # http://localhost:4567/shuffleseq
+  # ========================================================================= #
+  ['/shuffleseq'].each {|target|
+    get(target) {
+      Cyberweb::HtmlTemplate[
+        title: 'Shuffleseq - Shuffle a sequence',
+        body:  '<pre>'+
+               ::Bioroebe.shuffleseq(method(:method_reverse_complement))+
+               '</pre>'+
+               footer
+      ].to_s
+    }
+  }
+
+  # ========================================================================= #
+  # === 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
+  }
+
+  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
+
+  # ========================================================================= #
+  # === /random_aminoacids
+  #
+  # http://localhost:4567/random_aminoacids
+  # ========================================================================= #
+  ['/random_aminoacids'].each {|target|
+    get(target) {
+      embeddable_interface?.method_random_aminoacids
+    }
+  }
+
+  # ========================================================================= #
+  # http://localhost:4567/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(:method_reverse_complement))+
+             '</pre>'+
+             footer
+      Cyberweb::HtmlTemplate[
+      title: 'Bioroebe Web-API',
+      body:  body
+    ].to_s
+    }
+  }
+
+  # =========================================================================== #
+  # Example:
+  #
+  #   http://localhost:4567/reverse_complement
+  #
+  # =========================================================================== #
+  get('/reverse_complement'){
+    method_reverse_complement
+  }
+
+  # =========================================================================== #
+  # Example:
+  #
+  #   http://localhost:4567/n_stop_codons_in_this_sequence
+  #   http://localhost:4567/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>'
+      )+
+      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:4567/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
+    }
+  }
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+  end
+
+  # ========================================================================= #
+  # === view
+  #
+  # http://localhost:4567/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:4567/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(:method_random_aminoacids))+
+             '</pre>'+
+             footer
+      Cyberweb::HtmlTemplate[
+      title: 'Source code to random_aminoacids()',
+      body:  body
+    ].to_s
+    }
+  }
+
+  # ========================================================================= #
+  # http://localhost:4567/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
+    }
+  }
+
+  # ========================================================================= #
+  # === Handle palindromes
+  #
+  # This method will try to discover palindromes.
+  #
+  #   http://localhost:4567/palindromes
+  #
+  # Example:
+  #
+  #   http://localhost:4567/palindromes/30
+  #
+  # ========================================================================= #
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_PALINDROMES.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.to_s.strip.upcase if the_params
+      the_result = ::Bioroebe::PalindromeGenerator.return_as_string(the_params)
+      if the_params.empty?
+        the_result = HtmlTags.p(
+          '<b> Please input a DNA sequence</b>'
+        )+
+        return_paragraph_of_hyperlinks
+      else
+        splitted = the_result.split("\n")
+        first = "  5'-#{splitted.first}-3'\n"
+        last  = "  3'-#{splitted.last}-5'\n"
+        # =================================================================== #
+        # Overwrite the_result variable next:
+        # =================================================================== #
+        the_result = HtmlTags.p(
+          'Generated the following palindrome of '\
+          'size <b>'+the_params.to_s+'</b>:'
+        )+
+        HtmlTags.pre(
+          '<b>'+first+last+'</b>',
+          css_style: 'color: darkblue; margin: 1em; font-size: larger;'
+        )+
+        return_paragraph_of_hyperlinks
+      end
+      the_result << return_form_for_palindromes_action
+      the_result
+    }
+  }
+
+  # ========================================================================= #
+  # === 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:4567/n_stop_codons_in_this_sequence
+  #
+  # Example:
+  #
+  #   http://localhost:4567/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+
+        HtmlTags.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+
+        HtmlTags.p('This sequence contains <b style="font-size: larger; color: blueviolet">'+
+          the_result.to_s+'</b> stop '\
+          'codons.'
+        )+
+        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
+    }
+  }
+
+  # ========================================================================= #
+  # http://localhost:4567/is_palindrome
+  # ========================================================================= #
+  get('/is_palindrome') {
+    return_header_for_palindromes('Is palindrome')+
+    HtmlTags.p(
+      'Input the target sequence, in order to find out whether '\
+      'that sequence is a <b>palindrome</b> or whether it is not.'
+    )+
+    return_form_for_is_a_palindrome_action+
+    footer
+  }
+
+  # ========================================================================= #
+  # === Is this sequence a palindrome
+  #
+  # Example:
+  #
+  #   http://localhost:4567/is_palindromes/ATTA
+  #
+  # ========================================================================= #
+  get('/is_palindrome/*') {
+    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.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(
+        '<b> Please input a DNA sequence</b>'
+      )+
+      return_paragraph_of_hyperlinks
+    else
+      # =================================================================== #
+      # Overwrite the_result variable next:
+      # =================================================================== #
+      the_result = HtmlTags.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>'
+      )+
+      return_paragraph_of_hyperlinks
+    end
+    the_result << return_form_for_is_a_palindrome_action
+    the_result
+  }
+
+  # ========================================================================= #
+  # === /mirror_source
+  #
+  # http://localhost:4567/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:4567/chunked_display
+  # http://localhost:4567/chunked
+  # http://localhost:4567/upcase
+  # ========================================================================= #
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_CHUNKED_DISPLAY.each {|target|
+    get(target) {
+      embeddable_interface?.return_header_to_chunked_display+
+      embeddable_interface?.footer
+    }
+  }
+
+  # ========================================================================= #
+  # === Compseq                                                     (compseq)
+  #
+  # Visit:
+  #
+  #   http://localhost:4567/compseq
+  #
+  # Example:
+  #
+  #   http://localhost:4567/compseq/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  get('/compseq/*') {
+    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.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:4567/to_aa
+  # http://localhost:4567/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:4567/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
+  }
+
+  # =========================================================================== #
+  # === /to_dna
+  #
+  # Usage Examples:
+  #
+  #   http://localhost:4567/to_dna
+  #   http://localhost:4567/to_dna/AGUCGAUCGUAUGCAGUCAGUCA
+  #
+  # =========================================================================== #
+  get('/to_dna'){
+    embeddable_interface?.return_sinatra_to_dna
+  }
+
+  # ========================================================================= #
+  # === Convert into DNA                    (2 tag, second entry, to_dna tag)
+  #
+  # This method will convert RNA into DNA.
+  #
+  #   http://localhost:4567/to_dna
+  #
+  # Example:
+  #
+  #   http://localhost:4567/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+
+      HtmlTags.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'
+                   )
+    end
+    the_result << embeddable_interface?.return_form_for_to_dna_action
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+
+  # ========================================================================= #
+  # === Convert into a chunked display
+  #
+  # This method will convert RNA into DNA.
+  #
+  #   http://localhost:4567/chunked
+  #
+  # Example:
+  #
+  #   http://localhost:4567/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
+  #
+  # Example:
+  #
+  #   http://localhost:4567/compseq
+  #
+  # =========================================================================== #
+  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
+  }
+
+  # ========================================================================= #
+  # === /to_aa
+  #
+  # Examples:
+  #
+  #   http://localhost:4567/to_aa/ATGGGGCCCGCGCCA
+  #   http://localhost:4567/to_aa/GGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTG
+  #
+  # ========================================================================= #
+  Bioroebe::EmbeddableInterface::ARRAY_FOR_TO_AMINOACIDS_CONVERSION.map {|entry| "#{entry}/*" }.each {|target|
+    get(target) {
+      the_params = params[:splat]
+      if the_params.is_a? Array
+        the_params = the_params.join(' ')
+      end
+      if the_params.empty?
+        return_header_to_aminoacid_conversion+
+        HtmlTags.p(
+          '<b>Please provide some argument to this API.</b>'
+        )+
+        footer
+      else
+        if params.has_key? 'user_input'
+          the_params = params['user_input']
+        end
+        #
+        if params.include? '&user_input_submit=Submit'
+          params.sub!(/&user_input_submit=Submit/,'')
+        end
+        if params.include? 'user_input='
+          params.sub!(/user_input=/,'')
+        end
+        the_params = the_params.to_s.strip.delete(' ')
+        the_result = ::Bioroebe.to_aa(the_params)
+        return_header_to_aminoacid_conversion+
+        HtmlTags.p(
+          '<b style="color: darkgreen">The input sequence was:</b> <b>'+the_params+'</b>'
+        )+
+        HtmlTags.p(
+          '<b style="color: darkblue; margin-left: 1em;">Frame 1:</b> <b>'+the_result+'</b> # '+the_result.size.to_s+' aminoacids'
+        )+
+        HtmlTags.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(
+          '<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
+      end
+    }
+  }
+
+  # =========================================================================== #
+  # === /blosum
+  #
+  # Example:
+  #
+  #   http://localhost:4567/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>'
+    }
+    _ << HtmlTags.p(
+      'Name of the BLOSUM matrix:'
+    )+
+    embeddable_interface?.return_form_for_blosum_action+
+    embeddable_interface?.hyperlink_paragraph
+    return _
+  }
+
+  # ========================================================================= #
+  # === mirror*
+  #
+  # This method will convert RNA into DNA.
+  #
+  #   http://localhost:4567/mirror
+  #
+  # Example:
+  #
+  #   http://localhost:4567/mirror/ATGCUUUUUUUUUU
+  #
+  # ========================================================================= #
+  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>'
+      )+
+      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:'
+      )+
+      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
+  }
+
+  # ========================================================================= #
+  # === /blosum_source
+  #
+  # http://localhost:4567/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
+  }
+
+  # ========================================================================= #
+  # === blosum*
+  #
+  # This method will show the blosum matrices.
+  #
+  #   http://localhost:4567/blosum
+  #
+  # Example:
+  #
+  #   http://localhost:4567/blosum/42
+  #
+  # ========================================================================= #
+  get('/blosum/*') {
+    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
+    # 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> '\
+                 '<b style="color: blueviolet">'+the_params.to_s+'</b> is:').dup
+    the_result << HtmlTags.p(
+      '<pre style="font-size:1.5em">'+
+      Bioroebe::BlosumParser.return_as_2D_table(the_params).tr('｜','|').to_s+
+      '</pre>',
+      css_style: 'margin:1em; font-size: larger;'
+    )
+    the_result << embeddable_interface?.return_form_for_blosum_action
+    the_result << embeddable_interface?.hyperlinks_paragraph
+    the_result
+  }
+
+end
+
+# =========================================================================== #
+# === Bioroebe.start_sinatra_interface
+# =========================================================================== #
+def self.start_sinatra_interface
+  ::Bioroebe::Sinatra.start_sinatra_interface
+end; self.instance_eval { alias start_sinatra start_sinatra_interface } # === Bioroebe.start_sinatra
+
+end if Object.const_defined? :Sinatra
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe.start_sinatra_interface
+end # bioroebe --sinatra