bioroebe 0.10.80 → 0.12.12

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)
   # ========================================================================= #

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/jruby/alignment/alignment.rb

@@ -0,0 +1,165 @@
+include Java
+
+java_import javax.swing.JButton
+java_import javax.swing.JFrame
+java_import javax.swing.JLabel
+java_import javax.swing.JPanel
+java_import javax.swing.JTextArea
+java_import javax.swing.JScrollBar
+java_import javax.swing.JTextField
+java_import javax.swing.JSpinner
+java_import javax.swing.SpinnerNumberModel
+java_import javax.swing.border.Border;
+java_import java.lang.System
+java_import java.awt.Font
+
+module Bioroebe
+
+module GUI
+
+module Jruby
+
+class Alignment < JFrame
+
+  require 'bioroebe/gui/shared_code/alignment/alignment_module.rb'
+  include Bioroebe::GUI::AlignmentModule
+
+  include ::Colours
+
+  require 'swing_paradise/awt/color.rb'
+  include SwingParadise::AWT
+
+  require 'swing_paradise/toplevel_methods/misc.rb'
+  include SwingParadise
+
+  require 'simple_widgets/simple_widgets.rb'
+  include SimpleWidgets
+  SimpleWidgets.use :jruby
+
+  # ========================================================================= #
+  # === LARGE_FONT
+  # ========================================================================= #
+  LARGE_FONT = Font.new('Sans serif', Font::PLAIN, 28)
+
+  # ========================================================================= #
+  # === MEDIUM_FONT
+  # ========================================================================= #
+  MEDIUM_FONT = Font.new('Sans serif', Font::PLAIN, 25)
+
+  # ========================================================================= #
+  # === MEDIUM_FONT_MONOSPACE
+  # ========================================================================= #
+  MEDIUM_FONT_MONOSPACE = Font.new('Monospace', Font::PLAIN, 25)
+
+  # ========================================================================= #
+  # === SMALL_FONT
+  # ========================================================================= #
+  SMALL_FONT = Font.new('Sans serif', Font::PLAIN, 22)
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    reset_the_internal_variables
+    reset_the_alignment_object
+    # reset_the_shared_module
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    frame = jframe(TITLE)
+    panel = JPanel.new # This is an instance of Java::JavaxSwing::JPanel.
+    panel.set_font(MEDIUM_FONT)
+    frame.getContentPane.add(panel)
+    panel.no_layout
+    panel.hint = 'A Panel container'
+
+    label1 = jlabel(TEXT_INPUT_THE_SEQUENCES)
+    label1.font = MEDIUM_FONT
+    label1.setBounds(5, 20, 820, 25) # x, y, width, height
+    
+    # ======================================================================= #
+    # Add the text-area next.
+    # ======================================================================= #
+    @text_view = JTextArea.new
+    @text_view.font = SMALL_FONT
+    
+    @text_view.setBorder(javax.swing.BorderFactory.createLineBorder(Color.black, 2))
+    @text_view.setBounds(10, 60, 720, 400) # x, y, width, height
+    @text_view.background = WHITE
+
+    # ======================================================================= #
+    # === @entry_consensus_sequence
+    # ======================================================================= #
+    @entry_consensus_sequence = JTextField.new
+    @entry_consensus_sequence.center if @entry_consensus_sequence.respond_to?(:center)
+    @entry_consensus_sequence.setBounds(10, 460, 720, 40) # x, y, width, height
+    @entry_consensus_sequence.font = MEDIUM_FONT_MONOSPACE
+    @entry_numbers = JTextField.new 
+    @entry_numbers.setBounds(10, 500, 720, 40) # x, y, width, height
+    @entry_numbers.font = MEDIUM_FONT_MONOSPACE
+    
+    create_the_buttons
+    panel << label1
+    panel << @text_view
+    panel << @entry_consensus_sequence
+    panel << @entry_numbers
+    panel << @button_do_analyse
+    panel << @button_quit
+
+    frame.exit_on_close
+    frame.width_height = 1200, 900
+    frame.top_left
+    frame.show_all
+  end
+
+  # ========================================================================= #
+  # === create_the_buttons                                      (buttons tag)
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_quit
+    # ======================================================================= #
+    @button_quit = quit_button
+    @button_quit.setBounds(130, 650, 300, 50)
+    @button_quit.hint = 'Click this button to quit the application.'
+    @button_quit.on_clicked {
+      do_quit
+    }
+    @button_do_analyse = button('Do analyse')
+    @button_do_analyse.setBounds(130, 600, 300, 44)
+    @button_do_analyse.on_clicked {
+      do_analyse
+      realign_the_numbers_showing_how_long_the_consensus_sequence_is
+    }
+  end
+
+  # ========================================================================= #
+  # === do_analyse
+  # ========================================================================= #
+  def do_analyse(
+      _ = @text_view.text?
+    )
+    _.strip!
+    @alignment.use_this_as_input(_)
+    consensus_sequence = return_the_consensus_sequence
+    @entry_consensus_sequence.set_text(consensus_sequence)
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Jruby::Alignment.new
+end

data/lib/bioroebe/gui/libui/alignment/alignment.rb

@@ -4,6 +4,8 @@
 # =========================================================================== #
 # === Bioroebe::GUI::LibUI::Alignment
 # =========================================================================== #
+# require 'bioroebe/gui/libui/alignment/alignment.rb'
+# =========================================================================== #
 require 'bioroebe/constants/GUIs.rb'
 
 module Bioroebe
@@ -79,7 +81,6 @@ module Alignment # === Bioroebe::GUI::LibUI::Alignment
     @button_do_analyse.on_clicked {
       do_analyse
     }
-    
     outer_vbox << @button_do_analyse
     outer_vbox << @entry_consensus_sequence
     main_window.child = outer_vbox
@@ -105,6 +106,7 @@ module Alignment # === Bioroebe::GUI::LibUI::Alignment
     object = Object.new
     object.extend(Alignment)
     object.reset_then_run
+    return object
   end
 
 end; end; end; end