bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb

@@ -1,166 +0,0 @@
-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/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb

@@ -1,82 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-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 java.lang.System
-java_import java.awt.Font
-
-module Bioroebe
-
-module GUI
-
-module Jruby
-
-class BlosumMatrixViewer < JFrame
-
-  require 'colours'
-  include Colours
-
-  require 'bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb'
-  include Bioroebe::GUI::BlosumMatrixViewerModule
-
-  require 'simple_widgets/simple_widgets.rb'
-  include SimpleWidgets
-  SimpleWidgets.use :jruby
-
-  # ========================================================================= #
-  # === 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.new(TITLE)
-    panel = new_jpanel # This is an instance of Java::JavaxSwing::JPanel.
-    panel.setFont(Font.new 'Sans serif', Font::PLAIN, 25)
-    frame.getContentPane.add(panel)
-    panel.setLayout(nil)
-    panel.hint = 'A Panel container'
-
-    entry1 = entry('Apple')
-    entry1.setFont(Font.new 'Sans serif', Font::PLAIN, 28)
-    entry1.setBounds(10, 60, 190, 50) # x, y, width, height
-   
-    panel << entry1
-
-    frame.setDefaultCloseOperation JFrame::EXIT_ON_CLOSE
-    frame.width_height(WIDTH, HEIGHT)
-    frame.setLocationRelativeTo(nil)
-
-    frame.show_all
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Jruby::BlosumMatrixViewer.new
-end

data/lib/bioroebe/gui/libui/README.md

@@ -1,4 +0,0 @@
-This directory may contain code for libUI bindings via ruby.
-
-This is very experimental as of 2020 (and 2021). We'll see
-how this proceeds from there.

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

@@ -1,116 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::Alignment
-# =========================================================================== #
-# require 'bioroebe/gui/libui/alignment/alignment.rb'
-# =========================================================================== #
-require 'bioroebe/constants/GUIs.rb'
-
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-module Alignment # === Bioroebe::GUI::LibUI::Alignment
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-  
-  require 'bioroebe/sequence/alignment.rb'
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Alignment'
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize
-    reset
-  end
-
-  # ========================================================================= #
-  # === reset_then_run
-  # ========================================================================= #
-  def reset_then_run
-    reset
-    run
-  end
-
-  # ========================================================================= #
-  # === reset
-  # ========================================================================= #
-  def reset
-    # ======================================================================= #
-    # === @alignment
-    # ======================================================================= #
-    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
-  end
-    
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_entries
-  end
-
-  # ========================================================================= #
-  # === create_the_entries
-  # ========================================================================= #
-  def create_the_entries
-    # ======================================================================= #
-    # === @entry_consensus_sequence
-    # ======================================================================= #
-    @entry_consensus_sequence = ui_entry
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    main_window = ui_margined_window(TITLE, 1200, 200, 15)
-    outer_vbox = ui_vbox
-    @text_buffer = ui_text_view
-    outer_vbox << @text_buffer
-    @button_do_analyse = ui_button('Do Analyse')
-    @button_do_analyse.on_clicked {
-      do_analyse
-    }
-    outer_vbox << @button_do_analyse
-    outer_vbox << @entry_consensus_sequence
-    main_window.child = outer_vbox
-    main_window.complex_finalizer
-  end
-
-  # ========================================================================= #
-  # === do_analyse
-  # ========================================================================= #
-  def do_analyse(
-      _ = @text_buffer.text?
-    )
-    _ = _.to_s
-    @alignment.use_this_as_input(_)
-    consensus_sequence = @alignment.consensus_sequence?
-    @entry_consensus_sequence.set_text(consensus_sequence)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::LibUI::Alignment.run
-  # ========================================================================= #
-  def self.run
-    object = Object.new
-    object.extend(Alignment)
-    object.reset_then_run
-    return object
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::Alignment.run
-end

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

@@ -1,112 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::BlosumMatrixViewer
-# =========================================================================== #
-require 'bioroebe/constants/GUIs.rb'
-
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-module BlosumMatrixViewer # === Bioroebe::GUI::LibUI::BlosumMatrixViewer
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-
-  require 'bioroebe/blosum/blosum.rb'
-  require 'bioroebe/parsers/blosum_parser.rb'
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Blosum Matrix Viewer'
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize
-    reset
-  end
-
-  # ========================================================================= #
-  # === reset_then_run
-  # ========================================================================= #
-  def reset_then_run
-    reset
-    run
-  end
-
-  # ========================================================================= #
-  # === reset
-  # ========================================================================= #
-  def reset
-  end
-    
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    main_window = ui_margined_window(
-      TITLE, 1200, 500, 1
-    )
-    outer_vbox = padded_vbox
-    outer_vbox.minimal(
-      ui_text('Available BLOSUM matrices:')
-    )
-    @combo_box = ui_combobox(
-      Bioroebe.array_available_blosum_matrices?
-    )
-    outer_vbox.minimal(
-      @combo_box
-    )
-    @text_buffer = ui_text_buffer
-    outer_vbox.maximal(@text_buffer)
-    # @combo_box.on_changed {
-    #   do_sync_the_combo_box_text_onto_the_text_buffer
-    # }
-    # ^^ the above currently does not work.
-    # This explains the manual line below for now, to
-    # set up the initial value.
-    do_sync_the_combo_box_text_onto_the_text_buffer('blosum45')
-    main_window.child = outer_vbox
-    main_window.intelligent_exit
-  end
-
-  # ========================================================================= #
-  # === do_sync_the_combo_box_text_onto_the_text_buffer
-  # ========================================================================= #
-  def do_sync_the_combo_box_text_onto_the_text_buffer(
-      _ = @combo_box.text?
-    )
-    @text_buffer.set_text(
-      Bioroebe::BlosumParser.return_as_2D_table(_).tr(
-        '｜','|'
-      )
-    )
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::LibUI::BlosumMatrixViewer.run
-  # ========================================================================= #
-  def self.run
-    object = Object.new
-    object.extend(BlosumMatrixViewer)
-    object.reset_then_run
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::BlosumMatrixViewer.run
-end

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

@@ -1,60 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::CalculateCellNumbersOfBacteria
-# =========================================================================== #
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-class CalculateCellNumbersOfBacteria # === Bioroebe::GUI::LibUI::CalculateCellNumbersOfBacteria
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-
-  require 'bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb'
-  include Bioroebe::GUI::CalculateCellNumbersOfBacteriaModule
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      run_already = true
-    )
-    reset
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-    reset_shared_module
-  end
-
-def connect_skeleton
-  outer_vbox = padded_vbox
-  outer_vbox.minimal(@hbox1, 1)
-  outer_vbox.minimal(@hbox2, 1)
-  outer_vbox.minimal(@hbox3, 1)
-  outer_vbox.maximal(@button_to_calculate_how_many_bacteria_will_exist)
-  button_quit = quit_button
-  outer_vbox.maximal(button_quit)
-  window = ui_padded_main_window(
-    TITLE,
-    WIDTH,
-    HEIGHT,
-    0
-  )
-  window.add(outer_vbox)
-  window.intelligent_exit
-end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::CalculateCellNumbersOfBacteria.new  
-end

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

@@ -1,116 +0,0 @@
-#!/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