bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/www/embeddable_interface.rb

@@ -11,7 +11,6 @@ module Bioroebe
 
 module EmbeddableInterface
 
-  require 'bioroebe/sequence/reverse_complement.rb'
   require 'bioroebe/toplevel_methods/chunked_display.rb'
   require 'bioroebe/toplevel_methods/is_on_roebe.rb'
   require 'bioroebe/toplevel_methods/nucleotides.rb'
@@ -29,8 +28,8 @@ module EmbeddableInterface
   require 'bioroebe/parsers/blosum_parser.rb'
 
   require 'bioroebe/colours/colours.rb'
-  include Colours
-  include Colours::E
+  include ::Colours
+  include ::Colours::E
 
   # ========================================================================= #
   # === USE_THIS_PORT
@@ -41,6 +40,11 @@ module EmbeddableInterface
     USE_THIS_PORT = '4567'
   end
 
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'The Bioroebe sinatra-interface'
+
   # ========================================================================= #
   # Bioroebe.disable_colours
   # ^^^ Unsure why were were using this. As of 21.06.2021 this is
@@ -72,6 +76,11 @@ module EmbeddableInterface
   CSS_STYLE_FOR_THE_FORMS =
     'style="margin-left:2em; margin-top:2px"'
 
+  # ========================================================================= #
+  # === BODY_CSS_STYLE
+  # ========================================================================= #
+  BODY_CSS_STYLE = 'margin: 0.8em;'
+
   # ========================================================================= #
   # === ARRAY_FOR_PALINDROMES 
   # ========================================================================= #
@@ -126,7 +135,9 @@ module EmbeddableInterface
   ARRAY_AVAILABLE_TOPLEVEL_ACTIONS_FOR_THE_SINATRA_INTERFACE = %w(
     /blosum
     /compseq
+    /codon_frequency_of_this_string
     /is_palindrome
+    /frequency_per_thousand
     /n_stop_codons_in_this_sequence
     /to_aa
     /to_chunked
@@ -186,22 +197,6 @@ module EmbeddableInterface
     )
   end
 
-  # ========================================================================= #
-  # === method_reverse_complement
-  # ========================================================================= #
-  def method_reverse_complement
-    return_intro_for_reverse_complement_conversion+
-    HtmlTags.p(
-      'You can reverse complement a DNA sequence through this API.'
-    )+
-    HtmlTags.p(
-      'Simply input the nucleotide String, such as "ATGCT", '\
-      'without the "" quotes.'
-    )+
-    return_form_for_reverse_complement_action+
-    hyperlink_paragraph
-  end
-
   # ========================================================================= #
   # === Bioroebe::EmbeddableInterface.localhost_to_use?
   # ========================================================================= #
@@ -209,18 +204,6 @@ module EmbeddableInterface
     "http://localhost:#{USE_THIS_PORT}/"
   end
 
-  # ========================================================================= #
-  # === return_form_for_reverse_complement_action
-  # ========================================================================= #
-  def return_form_for_reverse_complement_action(
-      route_to_this_action = '/reverse_complement/'
-    )
-    '<form id="reverse_complement" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
-     INPUT_TYPE_TEXT_AND_BR_TAG+
-     return_default_submit_button+'
-     </form>'
-  end
-
   # ========================================================================= #
   # === return_sinatra_to_dna
   #
@@ -467,29 +450,6 @@ module EmbeddableInterface
      </form>'
   end
 
-  # ========================================================================= #
-  # === method_random_aminoacids
-  # ========================================================================= #
-  def method_random_aminoacids
-    Cyberweb::HtmlTemplate[
-      title: 'Random Aminoacids',
-      body:  return_header_random_aminoacids+
-        HtmlTags.p(
-          'This entry point can be used to "create" a random sequence '\
-          'of amino acids. Simply input how many aminoacids to '\
-          'create, as a <b>number</b>.')+
-        footer
-    ].to_s
-  end
-
-  # ========================================================================= #
-  # === return_header_random_aminoacids
-  # ========================================================================= #
-  def return_header_random_aminoacids
-    HtmlTags.h1('Random aminoacids',
-      css_style: 'margin-left:0.25em;')
-  end
-
   # ========================================================================= #
   # === return_form_for_is_a_palindrome_action
   # ========================================================================= #
@@ -622,18 +582,20 @@ module EmbeddableInterface
   # ========================================================================= #
   def return_view_string
     body = HtmlTags.h1(
-      'Bioroebe sinatra-interface!',
-       css_style: 'margin-left:0.25em;'
+      HtmlTags.image('https://i.imgur.com/Ufb3XW3.png')+'<br>'+
+      TITLE,
+      css_style: 'margin-left: 0.40em;'
     )+
     HtmlTags.p(
       "The <b>following actions</b>, as links, can be used to make use "\
       "of the Bioroebe project's www interface (through <b>sinatra</b>)."
     )+
     return_index_of_hyperlinks
-    Cyberweb::HtmlTemplate[
+    Cyberweb.template(
       title: title?,
+      body_css_style: BODY_CSS_STYLE,
       body: body
-    ].to_s
+    ).to_s
   end; alias return_root_string return_view_string # === return_root_string
 
   # ========================================================================= #
@@ -672,6 +634,107 @@ module EmbeddableInterface
      </form>'
   end
 
+  # ========================================================================= #
+  # === method_reverse_complement
+  # ========================================================================= #
+  def method_reverse_complement
+    return_intro_for_reverse_complement_conversion+
+    HtmlTags.p(
+      'You can reverse complement a DNA sequence through this API.'
+    )+
+    HtmlTags.p(
+      'Simply input the nucleotide String, such as "ATGCT", '\
+      'without the "" quotes.'
+    )+
+    return_form_for_reverse_complement_action+
+    hyperlink_paragraph
+  end
+
+  # ========================================================================= #
+  # === method_random_aminoacids
+  # ========================================================================= #
+  def method_random_aminoacids
+    Cyberweb::HtmlTemplate[
+      title: 'Random Aminoacids',
+      body:  return_header_random_aminoacids+
+        HtmlTags.p(
+          'This entry point can be used to "create" a random sequence '\
+          'of amino acids. Simply input how many aminoacids to '\
+          'create, as a <b>number</b>.')+
+        footer
+    ].to_s
+  end
+
+  # ========================================================================= #
+  # === return_header_random_aminoacids
+  # ========================================================================= #
+  def return_header_random_aminoacids
+    HtmlTags.h1('Random aminoacids',
+      css_style: 'margin-left:0.25em;')
+  end
+
+  # ========================================================================= #
+  # === return_header_codon_frequency_of_this_string
+  # ========================================================================= #
+  def return_header_codon_frequency_of_this_string
+    HtmlTags.h1('Codon frequence of this string',
+      css_style: 'margin-left:0.25em;')
+  end
+
+  # ========================================================================= #
+  # === return_form_for_reverse_complement_action
+  # ========================================================================= #
+  def return_form_for_reverse_complement_action(
+      route_to_this_action = '/reverse_complement/'
+    )
+    '<form id="reverse_complement" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === return_form_for_codon_frequency_of_this_string
+  # ========================================================================= #
+  def return_form_for_codon_frequency_of_this_string(
+      route_to_this_action = '/codon_frequency_of_this_string/'
+    )
+    '<form id="codon_frequency_of_this_string" '+CSS_STYLE_FOR_THE_FORMS+' action="'+route_to_this_action+'">'+
+     INPUT_TYPE_TEXT_AND_BR_TAG+
+     return_default_submit_button+'
+     </form>'
+  end
+
+  # ========================================================================= #
+  # === method_codon_frequency_of_this_string
+  # ========================================================================= #
+  def method_codon_frequency_of_this_string
+    Cyberweb.template(
+      title:          'Codon Frequence of this string',
+      body_css_style: BODY_CSS_STYLE,
+      body:           return_header_codon_frequency_of_this_string+
+        HtmlTags.p(
+          'This entry point can be used to show the codon frequency '\
+          'of the given string.')+
+        footer
+    ).to_s
+  end
+
+  # ========================================================================= #
+  # === method_codon_frequency_per_thousand
+  # ========================================================================= #
+  def method_codon_frequency_per_thousand
+    Cyberweb.template(
+      title: 'Codon Frequence per thousand',
+      body_css_style: BODY_CSS_STYLE,
+      body:  return_header_codon_frequency_of_this_string+
+        HtmlTags.p(
+          'This entry point can be used to show the codon frequency '\
+          'of the given string.')+
+        footer
+    ).to_s
+  end
+
 end
 
 # =========================================================================== #