bioroebe 0.10.80 → 0.11.32

data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb

@@ -19,11 +19,6 @@ module Bioroebe
 
 class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::CheckForMismatches
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === COLOUR_TO_BE_USED_FOR_A_MISMATCH
   #
@@ -49,10 +44,7 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace         = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @first_sequence
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/compacter.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -52,10 +47,7 @@ class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @ask_for_user_input
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/compseq/compseq.rb

@@ -47,11 +47,6 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # ========================================================================= #
   COLOURIZE_CpG_ISLANDS = true
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === EXPECTED_FREQUENCY
   # ========================================================================= #
@@ -108,10 +103,7 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @identifier
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb

@@ -44,11 +44,6 @@ https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP007215.2
 https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
 '
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -66,10 +61,7 @@ https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/dot_alignment.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class DotAlignment < ::Bioroebe::CommandlineApplication # === Bioroebe::DotAlignment
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -43,10 +38,7 @@ class DotAlignment < ::Bioroebe::CommandlineApplication # === Bioroebe::DotAlign
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @may_we_continue
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb

@@ -42,10 +42,7 @@ class MoveFileToItsCorrectLocation < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @try_to_relocate_the_file_to_an_appropriate_subdirectory
     #

data/lib/bioroebe/utility_scripts/showorf/constants.rb

@@ -6,11 +6,6 @@ module Bioroebe
 
 class ShowOrf < ::Bioroebe::CommandlineApplication
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === COLOURIZE_VERTICAL_TOKEN
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/showorf/reset.rb

@@ -11,10 +11,7 @@ class ShowOrf < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @show_these_frames
     #

data/lib/bioroebe/version/version.rb

@@ -9,7 +9,7 @@ module Bioroebe
   # ========================================================================= #
   # === VERSION
   # ========================================================================= #
-  VERSION = '0.10.80'
+  VERSION = '0.11.32'
 
   # ========================================================================= #
   # === LAST_UPDATE
@@ -17,7 +17,7 @@ module Bioroebe
   # This variable keeps track as to when the bioroebe project was last
   # updated. The notation is: DD.MM.YYYY
   # ========================================================================= #
-  LAST_UPDATE = '24.06.2022'
+  LAST_UPDATE = '25.09.2022'
 
   # ========================================================================= #
   # === URL_TO_THE_DOCUMENTATION

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'
@@ -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
 
 # =========================================================================== #