bioroebe 0.10.80 → 0.11.25

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

@@ -94,6 +94,7 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
   # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
+    batch_require_all_relevant_gtk3_files
     reset_the_internal_variables
     # ======================================================================= #
     # === @configuration
@@ -105,6 +106,10 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
     do_handle_all_CSS_related_aspects 
     infer_the_size_automatically
+    # ======================================================================= #
+    # === @nucleotide_analyser
+    # ======================================================================= #
+    @nucleotide_analyser = NucleotideAnalyser.new
   end
 
   # ========================================================================= #
@@ -160,7 +165,7 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
   end
 
   # ========================================================================= #
-  # === create_the_header_bar
+  # === create_the_header_bar                           (header tag, top tag)
   # ========================================================================= #
   def create_the_header_bar
     # ======================================================================= #
@@ -168,7 +173,8 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     # ======================================================================= #
     @header_bar = default_header_bar
     @header_bar.pad8px
-    @header_bar.text(' 🐟  Controller  🐠 ')
+    _ = selectable_text(' 🐟  Controller  🐟 ')
+    @header_bar.central_element(_)
   end
 
   # ========================================================================= #
@@ -200,6 +206,7 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
   # ========================================================================= #
   def batch_require_all_relevant_gtk3_files
     require 'bioroebe/gui/gtk3/alignment/alignment.rb'
+    require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
     require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
     require 'bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb'
     require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
@@ -209,7 +216,6 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     require 'bioroebe/gui/gtk3/gene/gene.rb'
     require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
     require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
-    require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
     require 'bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb'
     require 'bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb'
     require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
@@ -225,33 +231,36 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
   # === connect_skeleton                                        (connect tag)
   # ========================================================================= #
   def connect_skeleton
-    batch_require_all_relevant_gtk3_files
     abort_on_exception
     # ========================================================================= #
     # === DnaToAminoacidWidget
     # ========================================================================= #
     @dna_to_aminoacid_widget = DnaToAminoacidWidget.new
     @dna_to_aminoacid_widget.set_parent_widget(self)
-    @notebook.add_page('dna-to-aminoacid-widget', gtk_vbox(@dna_to_aminoacid_widget))
+    @notebook.add_page('dna-to-aminoacid-widget', vbox(@dna_to_aminoacid_widget))
+    # ======================================================================= #
+    # === nucleotide-analyser
+    # ======================================================================= #
+    @notebook.add_page('nucleotide-analyser', vbox(@nucleotide_analyser))
     # ======================================================================= #
     # === aminoacid-composition
     # ======================================================================= #
     @aminoacid_composition = AminoacidComposition.new
     @aminoacid_composition.set_parent_widget(self)
-    @notebook.add_page('aminoacid-composition', gtk_vbox(@aminoacid_composition))
+    @notebook.add_page('aminoacid-composition', vbox(@aminoacid_composition))
     # ======================================================================= #
     # === protein-to-DNA
     # ======================================================================= #
     @protein_to_DNA = ProteinToDNA.new
-    @notebook.add_page('protein-to-DNA', gtk_vbox(@protein_to_DNA))
+    @notebook.add_page('protein-to-DNA', vbox(@protein_to_DNA))
     # ======================================================================= #
     # === dna-to-reverse-complement
     # ======================================================================= #
-    @notebook.add_page('dna-to-reverse-complement', gtk_vbox(DnaToReverseComplementWidget.new))
+    @notebook.add_page('dna-to-reverse-complement', vbox(DnaToReverseComplementWidget.new))
     # ======================================================================= #
     # === alignment
     # ======================================================================= #
-    @notebook.add_page('alignment', gtk_vbox(Alignment.new))
+    @notebook.add_page('alignment', vbox(Alignment.new))
     # ======================================================================= #
     # === anti-sense-strand
     #
@@ -260,7 +269,7 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     # ======================================================================= #
     # === blosum-matrix-viewer
     # ======================================================================= #
-    @notebook.add_page('blosum-matrix-viewer', gtk_vbox(BlosumMatrixViewer.new))
+    @notebook.add_page('blosum-matrix-viewer', vbox(BlosumMatrixViewer.new))
     # ======================================================================= #
     # === calculate_cell_numbers_of_bacteria
     #
@@ -269,59 +278,55 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     # ======================================================================= #
     # === fasta-table-widget
     # ======================================================================= #
-    @notebook.add_page('fasta-table-widget', gtk_vbox(FastaTableWidget.new))
+    @notebook.add_page('fasta-table-widget', vbox(FastaTableWidget.new))
     # ======================================================================= #
     # === format-converter
     # ======================================================================= #
-    @notebook.add_page('format-converter', gtk_vbox(FormatConverter.new))
+    @notebook.add_page('format-converter', vbox(FormatConverter.new))
     # ======================================================================= #
     # === gene
     # ======================================================================= #
-    @notebook.add_page('gene', gtk_vbox(Gene.new))
+    @notebook.add_page('gene', vbox(Gene.new))
     # ======================================================================= #
     # === hamming-distance
     # ======================================================================= #
-    @notebook.add_page('hamming-distance', gtk_vbox(HammingDistance.new))
+    @notebook.add_page('hamming-distance', vbox(HammingDistance.new))
     # ======================================================================= #
     # === levensthein-distance
     # ======================================================================= #
-    @notebook.add_page('levensthein-distance', gtk_vbox(LevenstheinDistance.new))
-    # ======================================================================= #
-    # === nucleotide-analyser
-    # ======================================================================= #
-    @notebook.add_page('nucleotide-analyser', gtk_vbox(NucleotideAnalyser.new))
+    @notebook.add_page('levensthein-distance', vbox(LevenstheinDistance.new))
     # ======================================================================= #
     # === parse-pdb-file
     # ======================================================================= #
-    @notebook.add_page('parse-pdb-file', gtk_vbox(ParsePdbFile.new))
+    @notebook.add_page('parse-pdb-file', vbox(ParsePdbFile.new))
     # ======================================================================= #
     # === primer-design-widget
     # ======================================================================= #
-    @notebook.add_page('primer-design-widget', gtk_vbox(PrimerDesignWidget.new))
+    @notebook.add_page('primer-design-widget', vbox(PrimerDesignWidget.new))
     # ======================================================================= #
     # === random-sequence
     # ======================================================================= #
-    @notebook.add_page('random-sequence', gtk_vbox(RandomSequence.new))
+    @notebook.add_page('random-sequence', vbox(RandomSequence.new))
     # ======================================================================= #
     # === restriction-enzymes
     # ======================================================================= #
-    @notebook.add_page('restriction-enzymes', gtk_vbox(RestrictionEnzymes.new))
+    @notebook.add_page('restriction-enzymes', vbox(RestrictionEnzymes.new))
     # ======================================================================= #
     # === show-codon-table
     # ======================================================================= #
-    @notebook.add_page('show-codon-table', gtk_vbox(ShowCodonTable.new))
+    @notebook.add_page('show-codon-table', vbox(ShowCodonTable.new))
     # ======================================================================= #
     # === show-codon-usage
     # ======================================================================= #
-    @notebook.add_page('show-codon-usage', gtk_vbox(ShowCodonUsage.new))
+    @notebook.add_page('show-codon-usage', vbox(ShowCodonUsage.new))
     # ======================================================================= #
     # === sizeseq
     # ======================================================================= #
-    @notebook.add_page('sizeseq', gtk_vbox(Sizeseq.new))
+    @notebook.add_page('sizeseq', vbox(Sizeseq.new))
     # ======================================================================= #
     # === three-to-one
     # ======================================================================= #
-    @notebook.add_page('three-to-one', gtk_vbox(ThreeToOne.new))
+    @notebook.add_page('three-to-one', vbox(ThreeToOne.new))
     # ======================================================================= #
     # === www-finder
     #
@@ -388,8 +393,21 @@ class Controller < ::Gtk::Box # === Bioroebe::GUI::Gtk::Controller
     if @protein_to_DNA.respond_to? :do_determine_the_DNA_sequence
       @protein_to_DNA.do_determine_the_DNA_sequence
     end
+    # ======================================================================= #
+    # Also update the nucleotide-analyser next:
+    # ======================================================================= #
+    @nucleotide_analyser.set_dna_sequence(
+      main_dna_sequence?.delete(' ')
+    )
   end
 
+  # ========================================================================= #
+  # === main_dna_sequence?
+  # ========================================================================= #
+  def main_dna_sequence?
+    @dna_to_aminoacid_widget.dna_sequence?
+  end; alias main_DNA_sequence? main_dna_sequence? # === main_DNA_sequence?
+
 end; end; end
 
 # =========================================================================== #

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

@@ -157,10 +157,17 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === sync_the_entries_back_onto_the_two_main_strings
   # ========================================================================= #
   def sync_the_entries_back_onto_the_two_main_strings
-    @dna_sequence       = left_entry?.text.to_s
+    @dna_sequence       = return_the_main_DNA_sequence
     @aminoacid_sequence = right_entry?.text.to_s
   end
 
+  # ========================================================================= #
+  # === dna_sequence?
+  # ========================================================================= #
+  def dna_sequence?
+    left_entry?.text.to_s
+  end; alias return_the_main_DNA_sequence dna_sequence? # === return_the_main_DNA_sequence
+
   # ========================================================================= #
   # === create_the_entries                                      (entries tag)
   # ========================================================================= #
@@ -228,7 +235,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === sanitized_half_width
   # ========================================================================= #
   def sanitized_half_width
-    (@width / 2)- 30
+    (@width / 2) - 30
   end
 
   # ========================================================================= #
@@ -238,6 +245,17 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     @left_entry
   end
 
+  # ========================================================================= #
+  # === do_properly_space_the_top_left_entry
+  # ========================================================================= #
+  def do_properly_space_the_top_left_entry
+    old_text = @left_entry.text?.delete(' ')
+    _ = old_text.
+        gsub(/(.{3})/,' \1').
+        lstrip
+    @left_entry.set_text(_)
+  end
+
   # ========================================================================= #
   # === entry_for_the_codon_table?
   # ========================================================================= #
@@ -264,7 +282,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # ========================================================================= #
   def update_the_dna_sequence_then_do_the_conversion
     set_dna_sequence(
-      left_entry?.text
+      left_entry?.text.upcase # Upcasing this is more elegant, in my opinion.
     )
     do_the_conversion
   end
@@ -289,33 +307,6 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # @right_entry.on_click_event { :select_text }
   end
 
-  # ========================================================================= #
-  # === create_button_trigger_conversion
-  # ========================================================================= #
-  def create_button_trigger_conversion
-    # ======================================================================= #
-    # === @button_trigger_conversion
-    # ======================================================================= #
-    @button_trigger_conversion = gtk_bold_button('_Trigger Conversion')
-    @button_trigger_conversion.disallow_resizing
-    @button_trigger_conversion.set_size_request(125, 40)
-    @button_trigger_conversion.lightgreen
-    @button_trigger_conversion.set_background_colour :whitesmoke
-    @button_trigger_conversion.on_clicked {
-      update_the_dna_sequence_then_do_the_conversion
-    }
-    @button_trigger_conversion.bblack2
-    # ======================================================================= #
-    # Use a tooltip as well for our button:
-    # ======================================================================= #
-    @button_trigger_conversion.hint = 
-      "Clicking on this button will convert from a <b>DNA</b> "\
-      "<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
-      "Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
-      "on the left hand side. The space character, aka ' ', will "\
-      "be ignored."
-  end
-
   # ========================================================================= #
   # === connect_skeleton                                        (connect tag)
   # ========================================================================= #
@@ -325,9 +316,9 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # The two top labels denote which widget is the one for the DNA
     # sequence, and which one is for the aminoacid sequence.
     # ======================================================================= #
-    dna_sequence_label       = gtk_bold_label('DNA sequence')
+    dna_sequence_label       = bold_label('DNA sequence')
     dna_sequence_label.set_size_request(sanitized_half_width, 42)
-    aminoacid_sequence_label = gtk_bold_label('Aminoacid sequence')
+    aminoacid_sequence_label = bold_label('Aminoacid sequence')
     aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
     # ======================================================================= #
     # API for .attach() is:
@@ -357,6 +348,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     dropdown_box.use_this_font = SMALLER_FONT
     dropdown_box.first_element_is_active
     dropdown_box.bblack1
+    dropdown_box.pad5px
     dropdown_box.hint = 'When a new codon table is assigned, via the '\
       'drop-down menu, then any assigned DNA sequence will be automatically '\
       'translated to its corresponding amino acid sequence.'
@@ -370,11 +362,16 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     hbox.minimal(dropdown_box,                      3)
     add(hbox)
     vbox = gtk_vbox
-    @label_n_DNA_nucleotides = gtk_bold_label('n DNA nucleotides: ')
+    # ======================================================================= #
+    # === @label_n_DNA_nucleotides
+    # ======================================================================= #
+    @label_n_DNA_nucleotides = bold_label('n DNA nucleotides: ')
     @label_n_DNA_nucleotides.align_left
+    @label_n_DNA_nucleotides.make_selectable
     vbox.add(@label_n_DNA_nucleotides)
-    @label_n_aminoacids = gtk_bold_label('n aminoacids:      ')
+    @label_n_aminoacids = bold_label('n aminoacids:      ')
     @label_n_aminoacids.align_left
+    @label_n_aminoacids.make_selectable
     vbox.add(@label_n_aminoacids)
     minimal(vbox)
   end
@@ -388,7 +385,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     @header_bar.bblack1
     button_open_file = icon_theme(:open_file)
     button_open_file.hint = 'Click on this button to open a '\
-      'local FASTA file.'
+                            'local FASTA file.'
     button_open_file.on_clicked {
       result = do_pick_a_local_file
       if result and File.file?(result) and result.end_with?('.fasta','.fa')
@@ -410,9 +407,9 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
       current_folder:         ::Bioroebe.log_dir?,
       additional_directories: [
         ::Bioroebe.log_dir?,
-        ENV['PC'],
-        ENV['MY_TEMP'],
-        ENV['RSRC']
+        ENV['PC'].to_s,
+        ENV['MY_TEMP'].to_s,
+        ENV['RSRC'].to_s
       ]
     }}
     _ = ::Gtk.main_file?.to_s
@@ -505,17 +502,6 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     set_dna_sequence(i)
   end
 
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_header_bar
-    create_grid
-    create_button_trigger_conversion
-    create_the_entries
-    create_the_event_box
-  end
-
   # ========================================================================= #
   # === set_aminoacid_sequence
   # ========================================================================= #
@@ -573,6 +559,46 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
        alias do_trigger_the_conversion           do_the_conversion # === do_trigger_the_conversion
        alias do_determine_the_aminoacid_sequence do_the_conversion # === do_determine_the_aminoacid_sequence
 
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_header_bar
+    create_grid
+    create_button_trigger_conversion
+    create_the_entries
+    create_the_event_box
+  end
+
+  # ========================================================================= #
+  # === create_button_trigger_conversion
+  # ========================================================================= #
+  def create_button_trigger_conversion
+    # ======================================================================= #
+    # === @button_trigger_conversion
+    # ======================================================================= #
+    @button_trigger_conversion = bold_button('_Trigger Conversion')
+    @button_trigger_conversion.clear_background
+    @button_trigger_conversion.disallow_resizing
+    @button_trigger_conversion.set_size_request(125, 40)
+    @button_trigger_conversion.set_background_colour :whitesmoke
+    @button_trigger_conversion.on_hover(:lightgreen)
+    @button_trigger_conversion.on_clicked {
+      update_the_dna_sequence_then_do_the_conversion
+      do_properly_space_the_top_left_entry
+    }
+    @button_trigger_conversion.bblack2
+    # ======================================================================= #
+    # Use a tooltip as well for our button:
+    # ======================================================================= #
+    @button_trigger_conversion.hint = 
+      "Clicking on this button will convert from a <b>DNA</b> "\
+      "<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
+      "Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
+      "on the left hand side. The space character, aka ' ', will "\
+      "be ignored."
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
@@ -584,7 +610,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # ========================================================================= #
   # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

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

@@ -152,30 +152,6 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     @entry_on_top
   end
 
-  # ========================================================================= #
-  # === compare_the_two_sequences
-  #
-  # This is the method that will compare the two sequences.
-  # ========================================================================= #
-  def compare_the_two_sequences
-    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
-    @entry_n_differences.set_text(
-      hamming_distance_object.n_differences?.to_s
-    )
-  end; alias do_compare                   compare_the_two_sequences # === do_compare
-       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
-
-  # ========================================================================= #
-  # === consider_sanitizing_the_input
-  # ========================================================================= #
-  def consider_sanitizing_the_input
-    # ======================================================================= #
-    # The following two lines were added as of 07.05.2020.
-    # ======================================================================= #
-    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
-    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
-  end
-
   # ========================================================================= #
   # === create_entries                               (entries tag, entry tag)
   # ========================================================================= #
@@ -211,10 +187,10 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
         # This is ok.
       when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
         unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
-          widget.set_text(old_text)
+          widget.set_text(old_text.upcase)
         end
       end
-    }
+    } if false # disabled as of August 2022.
     # ======================================================================= #
     # And keep things upcased here:
     # ======================================================================= #
@@ -269,10 +245,10 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     # ======================================================================= #
     # === The top box
     # ======================================================================= #
-    @top_box = gtk_vbox
+    @top_box = vbox
 
     @label_on_top = bold_label(USE_THIS_TITLE)
-    @label_on_top.fancy_tooltips = 
+    @label_on_top.hint = 
       "Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
       "can be accepted as input."
     # ======================================================================= #
@@ -334,6 +310,44 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     show_all
   end
 
+  # ========================================================================= #
+  # === compare_the_two_sequences
+  #
+  # This is the method that will compare the two sequences.
+  # ========================================================================= #
+  def compare_the_two_sequences
+    do_upcase_all_entries
+    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
+    @entry_n_differences.set_text(
+      hamming_distance_object.n_differences?.to_s
+    )
+  end; alias do_compare                   compare_the_two_sequences # === do_compare
+       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
+
+  # ========================================================================= #
+  # === do_upcase_all_entries
+  # ========================================================================= #
+  def do_upcase_all_entries
+    [
+      @entry_on_top,
+      @entry_on_bottom
+    ].each {|entry|
+      entry.do_upcase
+    }
+  end
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_input
+  # ========================================================================= #
+  def consider_sanitizing_the_input
+    # ======================================================================= #
+    # The following two lines were added as of 07.05.2020.
+    # ======================================================================= #
+    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
+    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
+    do_upcase_all_entries
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #