bioroebe 0.10.80 → 0.12.24

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/jruby/aminoacid_composition/aminoacid_composition.rb

@@ -0,0 +1,166 @@
+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 AminoacidComposition < JFrame
+
+  require 'bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb'
+  include Bioroebe::GUI::AminoacidCompositionModule
+
+  include ::Colours
+
+  require 'swing_paradise/awt/color.rb'
+  include SwingParadise::AWT
+
+  require 'swing_paradise/toplevel_methods/misc.rb'
+  include SwingParadise
+  extend SwingParadise
+
+  require 'simple_widgets/simple_widgets.rb'
+  include SimpleWidgets
+  SimpleWidgets.use :jruby
+
+  # ========================================================================= #
+  # === LARGE_FONT
+  # ========================================================================= #
+  LARGE_FONT = jruby_font('Sans serif 28')
+
+  # ========================================================================= #
+  # === MEDIUM_FONT
+  # ========================================================================= #
+  MEDIUM_FONT = jruby_font('Sans serif 25')
+
+  # ========================================================================= #
+  # === MEDIUM_FONT_MONOSPACE
+  # ========================================================================= #
+  MEDIUM_FONT_MONOSPACE = jruby_font('Monospace 25')
+
+  # ========================================================================= #
+  # === SMALL_FONT
+  # ========================================================================= #
+  SMALL_FONT = jruby_font('Sans serif 22')
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    reset_the_internal_variables
+  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(TITLE)
+    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, 110, 720, 400) # x, y, width, height
+    @text_view.background = WHITE
+
+    # ======================================================================= #
+    # === @entry_user_input
+    # ======================================================================= #
+    @entry_user_input = JTextField.new
+    @entry_user_input.setBounds(10, 65, 720, 35) # x, y, width, height
+    @entry_user_input.font = MEDIUM_FONT_MONOSPACE
+    @entry_user_input.background = LIGHT_YELLOW
+
+    @entry_user_input.addKeyListener {|event|
+      # char = event.key_char.chr.to_s
+      @entry_user_input.set_text(@entry_user_input.text?.upcase) # Upcase it.
+      update_the_label_n_aminoacids
+    }
+    @label_n_aminoacids = text('ABC')
+    @label_n_aminoacids.font = MEDIUM_FONT_MONOSPACE
+    update_the_label_n_aminoacids
+    @label_n_aminoacids.setBounds(770, 65, 450, 35) # x, y, width, height
+    create_the_buttons
+    panel << label1
+    panel << @text_view
+    panel << @entry_user_input
+    panel << @label_n_aminoacids
+    panel << @button_do_analyse
+    panel << @button_quit
+
+    frame.exit_on_close
+    frame.width_height = 1400, 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_xyz
+      update_the_label_n_aminoacids
+    }
+  end
+
+  # ========================================================================= #
+  # === update_the_label_n_aminoacids
+  # ========================================================================= #
+  def update_the_label_n_aminoacids
+    @label_n_aminoacids.set_text(
+      return_how_many_aminoacids_are_in_the_sequence
+    )
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Jruby::AminoacidComposition.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

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

@@ -0,0 +1,116 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === LibuiParadise::GUI::LibUI::Prototype
+# =========================================================================== #
+module LibuiParadise
+
+module GUI
+
+module LibUI
+
+class Prototype # === LibuiParadise::GUI::LibUI::Prototype
+
+  require 'libui_paradise/extensions/extensions.rb'
+  include LibuiParadise::Extensions
+
+  require 'bioroebe/gui/libui/alignment/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'A prototype for LibUI'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = 680
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 520
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    title_width_height(TITLE, WIDTH, HEIGHT)
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                            (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_skeleton
+    # ======================================================================= #
+    # === @window
+    # ======================================================================= #
+    @window = ui_padded_main_window(title?, width?, height?, 0)
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    outer_vbox = padded_vbox
+    # ======================================================================= #
+    # First add the two buttons on top:
+    # ======================================================================= #
+    hbox_on_top = padded_hbox
+    button_refresh = ui_button('Refresh')
+    button_refresh.on_clicked {
+      e 'TODO: Refresh this ... or add any other functionality.'
+    }
+    hbox_on_top.maximal(button_refresh)
+    hbox_on_top.maximal(quit_button)
+    tab = LibuiParadise.tab
+    outer_vbox.maximal(tab)
+    outer_vbox.minimal(hbox_on_top)
+    outer_vbox.add_hsep
+
+    grid = ui_padded_grid
+    #                         widget, left, top, xspan, yspan, hexpand, halign, vexpand, valign
+    grid.ui_grid_append(text('Left'),  0, 0, 1, 1, 0, 0.5, 1, 0)
+    grid.ui_grid_append(text('Right'), 1, 0, 1, 1, 0, 0.5, 1, 0)
+
+    3.times.each {|index| index += 1
+      # ===================================================================== #
+      # left, top, xspan, yspan, hexpand, halign, vexpand, valign
+      #  0,    0,    2,     1,      0,      0,       1,      0
+      # ===================================================================== #
+      grid.ui_grid_append(text(index.to_s), 0, 1+index, 1, 1, 1, 1, 1, 1)
+      label_exam_topic = text(entry.to_s)
+      grid.ui_grid_append(label_exam_topic, 1, 1+index, 1, 1, 1, 1, 1, 1)
+    }
+    outer_vbox.maximal(grid)
+    
+
+    hbox2 = create_hbox
+
+    #alignment = Object.new
+    #alignment.extend(Bioroebe::GUI::LibUI::Alignment)
+    #alignment.reset_then_run
+    #::LibUI.tab_append(tab, 'Page 1', alignment)
+    ::LibUI.tab_append(tab, 'Page 2', hbox2)
+
+    @window.add(outer_vbox)
+    @window.intelligent_exit
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  LibuiParadise::GUI::LibUI::Prototype.new  
+end

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

@@ -55,7 +55,7 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
   # ========================================================================= #
   def reset
   end
-    
+
   # ========================================================================= #
   # === create_skeleton                                          (create tag)
   # ========================================================================= #
@@ -125,6 +125,11 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
   def do_generate_a_random_sequence_using_the_value_from_the_proper_entry(
       i = n_aminoacids?
     )
+    i = i.to_i
+    if i > 5_000_000
+      i = 5_000_000
+      set_main_entry(i.to_s)
+    end
     do_generate_a_random_sequence(i)
   end
 
@@ -138,7 +143,11 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
     when nil, :default
       n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
     end
-    n_aminoacids = n_aminoacids.to_s
+    n_aminoacids = n_aminoacids.to_i
+    if n_aminoacids > 5_000_000
+      n_aminoacids = 5_000_000
+      set_main_entry(n_aminoacids.to_s)
+    end
     use_this_as_the_new_sequence = ::Bioroebe.create_random_aminoacids(n_aminoacids).to_s
     array1 = ::Bioroebe.return_array_of_common_aminoacids
     array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_as_the_new_sequence).values.map(&:to_s)
@@ -158,6 +167,13 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
     @entry_use_this_length.text?.to_s
   end
 
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_use_this_length.set_text(i.to_s)
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::LibUI::RandomSequence.run
   # ========================================================================= #

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

@@ -4,6 +4,8 @@
 # =========================================================================== #
 # === Bioroebe::GUI::LibUI::ShowCodonTable
 # =========================================================================== #
+# require 'bioroebe/gui/libui/show_codon_table/show_codon_table.rb'
+# =========================================================================== #
 require 'bioroebe/constants/GUIs.rb'
 
 module Bioroebe

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

@@ -35,11 +35,10 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
   # === create_skeleton                                          (create tag)
   # ========================================================================= #
   def create_skeleton
-    @entry1 = ui_entry
-    @entry2 = ui_entry
-    @checkbox1 = ui_checkbox
-    @checkbox1.is_active
-    @checkbox2 = ui_checkbox
+    @entry1 = entry
+    @entry2 = entry
+    @checkbox1 = checked_checkbox
+    @checkbox2 = checkbox
   end
 
   # ========================================================================= #
@@ -72,7 +71,7 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
     small_hbox2 << ui_text('1-to-3 conversion')
     small_hbox2 << @checkbox2
     vbox_with_checkbuttons << small_hbox2
-
+    vbox_with_checkbuttons << quit_button
     bottom_hbox << vbox_with_checkbuttons
     outer_vbox << bottom_hbox
     main_window.child = outer_vbox
@@ -92,6 +91,9 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
     else
       new_result = Bioroebe.one_to_three(i.delete('-')).to_s
     end
+    if new_result and new_result.empty?
+      error_msg('No result found. Is it a three-letter aminoacid?')
+    end
     @entry2.set_text(new_result) if new_result and !new_result.empty?
   end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
 

data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb

@@ -0,0 +1,102 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::AlignmentModule
+#
+# Usage example:
+#
+#   Alignment.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/alignment/alignment_module.rb'
+# include Bioroebe::GUI::AlignmentModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module AlignmentModule # === Bioroebe::GUI::AlignmentModule
+
+  require 'colours'
+  require 'bioroebe/sequence/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Alignment'
+
+  # ========================================================================= #
+  # === TEXT_INPUT_THE_SEQUENCES
+  # ========================================================================= #
+  TEXT_INPUT_THE_SEQUENCES = 'Input the sequences that you wish '\
+                             'to compare to one another'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '35% or 300px minimum'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '45% or 200px minimum'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_20
+
+  # ========================================================================= #
+  # === FONT_FOR_THE_ENTRIES
+  #
+  # The entries must use a mono-spaced font.
+  # ========================================================================= #
+  FONT_FOR_THE_ENTRIES = :hack_20
+
+  # ========================================================================= #
+  # === reset_the_alignment_object
+  # ========================================================================= #
+  def reset_the_alignment_object
+    # ======================================================================= #
+    # === @alignment
+    # ======================================================================= #
+    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
+  end
+
+  # ========================================================================= #
+  # === return_the_consensus_sequence
+  # ========================================================================= #
+  def return_the_consensus_sequence
+    @alignment.consensus_sequence?
+  end
+
+  # ========================================================================= #
+  # === text_view_widget?
+  # ========================================================================= #
+  def text_view_widget?
+    @text_view
+  end
+
+  # ========================================================================= #
+  # === realign_the_numbers_showing_how_long_the_consensus_sequence_is
+  # ========================================================================= #
+  def realign_the_numbers_showing_how_long_the_consensus_sequence_is
+    @entry_numbers.center if @entry_numbers.respond_to?(:center)
+    n_characters = @entry_consensus_sequence.text?.size
+    @entry_numbers.set_text(return_fill_up_to(n_characters))
+  end
+
+  # ========================================================================= #
+  # === return_fill_up_to
+  # ========================================================================= #
+  def return_fill_up_to(i)
+    _ = ''.dup
+    i.times {|counter|
+      counter = (counter+1) % 10
+      _ << counter.to_s
+    }
+    return _
+  end
+
+end; end; end