bioroebe 0.10.80 → 0.11.25

data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb

@@ -128,7 +128,7 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   # ========================================================================= #
   def create_skeleton
     create_buttons
-    create_labels
+    create_the_labels
     create_entry
   end
 
@@ -163,46 +163,6 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     @list_store.clear
   end
 
-  # ========================================================================= #
-  # === create_entry                                              (entry tag)
-  # ========================================================================= #
-  def create_entry
-    # ======================================================================= #
-    # === @entry_input_sequence
-    # ======================================================================= #
-    @entry_input_sequence = gtk_entry
-    @entry_input_sequence.yellow_background
-    @entry_input_sequence.hint = 'The sequence will be evaluated '\
-      'whenever it is changed, as-is. Hit the <b>enter</b> key '\
-      'to change it, for convenience.'
-    @entry_input_sequence.on_changed {
-      update_this_sequence_contains_n_nucleotides
-      update_the_table_dataset
-      update_the_GC_content_label
-    }
-    # ======================================================================= #
-    # Act on when the user hits the enter-key.
-    # ======================================================================= #
-    @entry_input_sequence.on_enter_key {
-      sanitize_the_sequence
-      do_analyse_the_sequence
-      update_this_sequence_contains_n_nucleotides(
-        return_how_many_nucleotides_this_sequence_contains
-      )
-    }
-  end
-
-  # ========================================================================= #
-  # === update_the_GC_content_label
-  # ========================================================================= #
-  def update_the_GC_content_label
-    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
-    @label_gc_content.set_text(
-      'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
-    )
-    @label_gc_content.do_markify
-  end; alias update_the_labels update_the_GC_content_label # === update_the_labels
-
   # ========================================================================= #
   # === open_local_file
   # ========================================================================= #
@@ -217,13 +177,6 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     return this_file
   end
 
-  # ========================================================================= #
-  # === set_main_entry
-  # ========================================================================= #
-  def set_main_entry(i)
-    @entry_input_sequence.set_text(i.to_s)
-  end
-
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
   # ========================================================================= #
   # === do_open_a_local_file
@@ -283,26 +236,13 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   # === update_this_sequence_contains_n_nucleotides
   # ========================================================================= #
   def update_this_sequence_contains_n_nucleotides(
-      i = return_how_many_nucleotides_this_sequence_contains
+      i = 
+        return_how_many_nucleotides_this_sequence_contains
     )
     @text_this_sequence_contains.set_text(i.to_s)
     @text_this_sequence_contains.do_markify
   end
 
-  # ========================================================================= #
-  # === create_labels
-  # ========================================================================= #
-  def create_labels
-    # ======================================================================= #
-    # === @label_gc_content
-    # ======================================================================= #
-    @label_gc_content = gtk_left_aligned_label
-    # ======================================================================= #
-    # === @text_this_sequence_contains
-    # ======================================================================= #
-    @text_this_sequence_contains = gtk_left_aligned_label
-  end
-
   # ========================================================================= #
   # === return_dataset_based_on_this_sequence
   # ========================================================================= #
@@ -350,6 +290,13 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     end
   end
 
+  # ========================================================================= #
+  # === update_the_main_sequence_variable
+  # ========================================================================= #
+  def update_the_main_sequence_variable
+    @sequence = @entry_input_sequence.text?.delete('-')
+  end
+
   # ========================================================================= #
   # === connect_skeleton                                        (connect tag)
   # ========================================================================= #
@@ -365,15 +312,9 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     scrolled_window.set_size_request(420, 260)
     minimal(scrolled_window, 5)
     minimal(gtk_horizontal_spacer)
-    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
     update_the_labels
-    minimal(@label_gc_content)
-    minimal(
-      gtk_left_aligned_label(
-        'The <b>AT content</b> (A+T) is: <b>'+
-        (100.0 - _.to_f).round(1).to_s+'%</b>'
-      )
-    )
+    minimal(@label_GC_content)
+    minimal(@label_AT_content)
     hbox = gtk_hbox
     hbox.maximal(@button_reset,                    1)
     hbox.maximal(@button_reset_the_input_sequence, 1)
@@ -399,6 +340,113 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     apply_the_CSS_rules
   end
 
+  # ========================================================================= #
+  # === create_the_labels
+  # ========================================================================= #
+  def create_the_labels
+    # ======================================================================= #
+    # === @label_GC_content
+    # ======================================================================= #
+    @label_GC_content = left_aligned_label
+    @label_GC_content.make_selectable
+    # ======================================================================= #
+    # === @label_AT_content
+    # ======================================================================= #
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_AT_content = left_aligned_label(
+      'The <b>AT content</b> (A+T) is: <b>'+
+      (100.0 - _.to_f).round(1).to_s+'%</b>'
+    )
+    @label_AT_content.make_selectable
+    # ======================================================================= #
+    # === @text_this_sequence_contains
+    # ======================================================================= #
+    @text_this_sequence_contains = left_aligned_label
+    @text_this_sequence_contains.make_selectable
+  end
+
+  # ========================================================================= #
+  # === create_entry                                              (entry tag)
+  # ========================================================================= #
+  def create_entry
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = entry
+    @entry_input_sequence.default_values
+    @entry_input_sequence.hint = 'The sequence will be evaluated '\
+      'whenever it is changed, as-is. Hit the <b>enter</b> key '\
+      'to change it, for convenience.'
+    @entry_input_sequence.on_changed {
+      update_the_main_sequence_variable
+      update_this_sequence_contains_n_nucleotides
+      update_the_table_dataset
+      update_the_labels
+    }
+    # ======================================================================= #
+    # Act on when the user hits the enter-key.
+    # ======================================================================= #
+    @entry_input_sequence.on_enter_key {
+      sanitize_the_sequence
+      do_analyse_the_sequence
+      update_this_sequence_contains_n_nucleotides(
+        return_how_many_nucleotides_this_sequence_contains
+      )
+    }
+  end
+
+  # ========================================================================= #
+  # === entry_input_sequence?
+  # ========================================================================= #
+  def entry_input_sequence?
+    @entry_input_sequence
+  end; alias main_entry? entry_input_sequence? # === main_entry?
+
+  # ========================================================================= #
+  # === dna_sequence?
+  # ========================================================================= #
+  def dna_sequence?
+    @entry_input_sequence.text?
+  end
+
+  # ========================================================================= #
+  # === update_the_GC_content_label
+  # ========================================================================= #
+  def update_the_GC_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_GC_content.set_text(
+      'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
+    )
+    @label_GC_content.do_markify
+  end
+
+  # ========================================================================= #
+  # === update_the_labels
+  # ========================================================================= #
+  def update_the_labels
+    update_the_GC_content_label
+    update_the_AT_content_label
+  end
+
+  # ========================================================================= #
+  # === update_the_AT_content_label
+  # ========================================================================= #
+  def update_the_AT_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_AT_content.set_text(
+      "The <b>AT content</b> (A+T) is: <b>"\
+      "#{(100.0 - _.to_f).round(1).to_s}%</b>"
+    )
+    @label_AT_content.do_markify
+  end
+
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  end; alias set_dna_sequence set_main_entry # === set_dna_sequence
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #

data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb

@@ -107,7 +107,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_right.clear_background
     scrolled_window_right.width_height(300, 300)
     scrolled_window_right.bblack1
-    scrolled_window_right.css_class('mar2px')
+    scrolled_window_right.mar2px
     # ======================================================================= #
     # === scrolled_window_left
     # ======================================================================= #
@@ -115,7 +115,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_left.clear_background
     scrolled_window_left.width_height(300, 300)
     scrolled_window_left.bblack1
-    scrolled_window_left.css_class('mar2px')
+    scrolled_window_left.mar2px
     top_hpaned = gtk_hpaned(
       scrolled_window_left,
       scrolled_window_right
@@ -126,22 +126,6 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     @dataset[:top_hbox] = top_hpaned
   end
 
-  # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
-  # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    @main_vbox.maximal(@dataset[:top_hbox], 4)
-    @main_vbox.maximal(@middle_bar)
-    button_box = button_box(
-      @dataset[:backtrack_button],
-      @dataset[:quit_button]
-    )
-    button_box.vertical_layout
-    @main_vbox.minimal(button_box)
-    add(@main_vbox)
-  end
-
   # ========================================================================= #
   # === create_left_buffer
   # ========================================================================= #
@@ -161,6 +145,22 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     super()
   end
 
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    @main_vbox.maximal(@dataset[:top_hbox], 4)
+    @main_vbox.maximal(@middle_bar)
+    button_box = button_box(
+      @dataset[:backtrack_button],
+      @dataset[:quit_button]
+    )
+    button_box.vertical_layout
+    @main_vbox.minimal(button_box)
+    add(@main_vbox)
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::Gtk::ProteinToDNA.run
   # ========================================================================= #

data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb

@@ -43,12 +43,12 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH  = 900
+  WIDTH = '45% or minimum 1200px'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 720
+  HEIGHT = '45% or minimum 980px'
 
   # ========================================================================= #
   # === USE_THIS_HEADER
@@ -478,8 +478,20 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
     create_the_entries
   end
 
+  # ========================================================================= #
+  # === handle_CSS
+  # ========================================================================= #
+  def handle_CSS
+    use_gtk_paradise_project_css_file
+    use_project_css_file
+    apply_the_CSS
+  end
+
   # ========================================================================= #
   # === do_generate_a_random_sequence
+  #
+  # This is the method that will be run whenever a new random aminoacid
+  # sequence is to be generated.
   # ========================================================================= #
   def do_generate_a_random_sequence(
       n_aminoacids = :default
@@ -521,18 +533,14 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
     # list-store.
     # ======================================================================= #
     array = array1.zip(array2) # Zip it up with 0-values here.
+    # ======================================================================= #
+    # Next, populate the liststore with the new data - since as of July
+    # 2022 we will sort it based on most aminoacids though:
+    # ======================================================================= #
+    array = array.sort_by {|a, b| b }.reverse # This sorts by highest first.
     ::Gtk.populate_this_liststore(@list_store, array)
   end
 
-  # ========================================================================= #
-  # === handle_CSS
-  # ========================================================================= #
-  def handle_CSS
-    use_gtk_paradise_project_css_file
-    use_project_css_file
-    apply_the_CSS
-  end
-
   # ========================================================================= #
   # === run
   # ========================================================================= #

data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb

@@ -143,13 +143,6 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     end
   end
 
-  # ========================================================================= #
-  # === left_buffer?
-  # ========================================================================= #
-  def left_buffer?
-    @dataset[:left_buffer]
-  end; alias left? left_buffer? # === left?
-
   # ========================================================================= #
   # === right_buffer?
   # ========================================================================= #
@@ -164,6 +157,20 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     @dataset[:left_buffer].set_text(i.to_s)
   end
 
+  # ========================================================================= #
+  # === aminoacid_sequence?
+  # ========================================================================= #
+  def aminoacid_sequence?
+    left_buffer?.to_s
+  end
+
+  # ========================================================================= #
+  # === left_buffer?
+  # ========================================================================= #
+  def left_buffer?
+    @dataset[:left_buffer]
+  end; alias left? left_buffer? # === left?
+
   # ========================================================================= #
   # === do_determine_the_backtrack_sequence                           (click tag)
   #
@@ -182,11 +189,4 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     right_buffer?.set_text(text_for_right_hand_side)
   end; alias do_determine_the_DNA_sequence do_determine_the_backtrack_sequence # === do_determine_the_DNA_sequence
 
-  # ========================================================================= #
-  # === aminoacid_sequence?
-  # ========================================================================= #
-  def aminoacid_sequence?
-    left_buffer?.to_s
-  end
-
 end; end; end

data/lib/bioroebe/misc/ruler.rb

@@ -24,6 +24,7 @@
 # variant - that one should work fine.
 # =========================================================================== #
 # require 'bioroebe/misc/ruler.rb'
+# Bioroebe.ruler_return_as_string_without_colours 'ATGCTGACAGGGGGGGEEEEEE'
 # Bioroebe::Ruler.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'