bioroebe 0.10.80 → 0.12.12

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
@@ -126,7 +125,9 @@ 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 +187,6 @@ 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 +194,6 @@ 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 +440,6 @@ 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
   # ========================================================================= #
@@ -672,6 +622,105 @@ 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::HtmlTemplate[
+      title: 'Codon Frequence of this string',
+      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::HtmlTemplate[
+      title: 'Codon Frequence per thousand',
+      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
 
 # =========================================================================== #