bioroebe 0.12.24 → 0.13.31

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

@@ -1,206 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::Tk::AminoacidComposition
-#
-# Usage example:
-#
-#   Bioroebe::GUI::Tk::AminoacidComposition.new(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb'
-# Bioroebe::GUI::Tk::AminoacidComposition.new(ARGV)
-# =========================================================================== #
-require 'tk_paradise/tk_paradise.rb'
-
-module Bioroebe
-
-module GUI
-
-module Tk
-
-class AminoacidComposition # < Base # === Bioroebe::GUI::Tk::AminoacidComposition
-
-  include ::Tk
-
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/count/count_amount_of_aminoacids.rb'
-
-  require 'colours'
-  include Colours
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Aminoacids Composition'
-
-  # ========================================================================= #
-  # === MAIN_FONT
-  # ========================================================================= #
-  MAIN_FONT = TkFont.new(family: 'Helvetica', size: 20, weight: 'bold')
-
-  # ========================================================================= #
-  # === PADDING_TO_USE
-  # ========================================================================= #
-  PADDING_TO_USE = {
-    padx: 10,
-    pady: 10
-  }
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      commandline_arguments = nil,
-      run_already           = true
-    )
-    reset
-    set_commandline_arguments(
-      commandline_arguments
-    )
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-  end
-
-  # ========================================================================= #
-  # === set_commandline_arguments
-  # ========================================================================= #
-  def set_commandline_arguments(i = '')
-    i = [i].flatten.compact
-    @commandline_arguments = i
-  end
-
-  # ========================================================================= #
-  # === commandline_arguments?
-  # ========================================================================= #
-  def commandline_arguments?
-    @commandline_arguments
-  end
-
-  # ========================================================================= #
-  # === first_argument?
-  # ========================================================================= #
-  def first_argument?
-    @commandline_arguments.first
-  end; alias first? first_argument? # === first?
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    root = TkRoot.new { title TITLE }
-    root.geometry('800x500+0+0')
-
-    # ======================================================================= #
-    # Add a frame for the whole application.
-    # ======================================================================= #
-    outermost_frame = TkFrame.new(root)
-
-    label = ::TkLabel.new(outermost_frame) {
-      font(MAIN_FONT)
-      text 'Aminoacid composition:'
-      pack(side: 'top', padx: 10, pady: 10)
-    }
-
-    @text1 = TkVariable.new
-    @entry1 = TkEntry.new(outermost_frame, textvariable: @text1) {
-      font(MAIN_FONT)
-      background 'moccasin'
-    }
-    @entry1.bind('Key', proc {|this_key|
-      case this_key
-      when 'Return','KP_Enter'
-        do_analyse_the_aminoacid_sequence
-      end
-    }, '%K')
-
-    @entry1.pack(outermost_frame)
-
-    callback_do_analyse_the_aminoacid_sequence = proc {
-      do_analyse_the_aminoacid_sequence
-    }
-
-    # ======================================================================= #
-    # === The main button
-    # ======================================================================= #
-    frame_for_the_convert_button = TkFrame.new(
-      outermost_frame,
-      highlightbackground: 'black', 
-      highlightthickness: 2,
-      bd: 0,
-      borderwidth: 2
-    )
-    frame_for_the_convert_button.pack
-    button_convert = TkButton.new(frame_for_the_convert_button) {
-      text 'Analyse the aminoacid composition'
-      font(MAIN_FONT)
-      relief :flat
-      command callback_do_analyse_the_aminoacid_sequence
-      pack
-      borderwidth 5
-    }
-
-    # ======================================================================= #
-    # === The quit-button and its special frame
-    # ======================================================================= #
-    frame_for_the_quit_button = TkFrame.new(
-      outermost_frame,
-      highlightbackground: 'black', 
-      highlightthickness: 2,
-      bd: 0,
-      borderwidth: 2
-    )
-    frame_for_the_quit_button.pack
-    button_quit = ::TkButton.new(frame_for_the_quit_button, text: 'Quit') {
-      font(MAIN_FONT)
-      relief :flat
-      command proc {
-        exit
-      }
-      pack
-      borderwidth 5
-    }
-    ::Tk.run
-  end
-
-  # ========================================================================= #
-  # === do_analyse_the_aminoacid_sequence
-  # ========================================================================= #
-  def do_analyse_the_aminoacid_sequence(
-      i = @entry1.value
-    )
-    i = i.dup if i.frozen?
-    i.upcase!
-    e 'Der input ist: '+i
-    @entry1.value = i
-    hash = Bioroebe.return_composition_from_this_aminoacid_sequence(i)
-    array = hash.to_a.map {|inner_array| inner_array.map {|entry| entry.to_s }}
-pp hash
-pp array
-pp i.encoding.to_s
-e 'Unfinished: we must put this into a widget that displays this properly.'
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::Tk::AminoacidComposition[]
-  # ========================================================================= #
-  def self.[](i = '')
-    new(i)
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Tk::AminoacidComposition.new(ARGV)
-end # tk_aminoacid_composition.rb

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

@@ -1,140 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::Tk::BlosumMatrixViewer
-#
-# Usage example:
-#
-#   Bioroebe::GUI::Tk::BlosumMatrixViewer.new(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb'
-# Bioroebe::GUI::Tk::BlosumMatrixViewer.new(ARGV)
-# =========================================================================== #
-require 'tk_paradise/tk_paradise.rb'
-
-module Bioroebe
-
-module GUI
-
-module Tk
-
-class BlosumMatrixViewer # < Base # === Bioroebe::GUI::Tk::BlosumMatrixViewer
-
-  include ::Tk
-
-  require 'colours'
-  include Colours
-
-  require 'bioroebe/blosum/blosum.rb'
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Blosum Matrix Viewer'
-
-  # ========================================================================= #
-  # === MAIN_FONT
-  # ========================================================================= #
-  MAIN_FONT = TkFont.new(family: 'Helvetica', size: 20, weight: 'bold')
-
-  # ========================================================================= #
-  # === PADDING_TO_USE
-  # ========================================================================= #
-  PADDING_TO_USE = {
-    padx: 10,
-    pady: 10
-  }
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      commandline_arguments = nil,
-      run_already           = true
-    )
-    reset
-    set_commandline_arguments(
-      commandline_arguments
-    )
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-  end
-
-  # ========================================================================= #
-  # === set_commandline_arguments
-  # ========================================================================= #
-  def set_commandline_arguments(i = '')
-    i = [i].flatten.compact
-    @commandline_arguments = i
-  end
-
-  # ========================================================================= #
-  # === commandline_arguments?
-  # ========================================================================= #
-  def commandline_arguments?
-    @commandline_arguments
-  end
-
-  # ========================================================================= #
-  # === first_argument?
-  # ========================================================================= #
-  def first_argument?
-    @commandline_arguments.first
-  end; alias first? first_argument? # === first?
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    root = TkRoot.new { title TITLE }
-    root.geometry('800x500+0+0')
-
-    label = ::TkLabel.new(root) {
-      font(MAIN_FONT)
-      justify :left
-      text 'Blosum Matrix Viewer:'
-      pack(side: 'top', padx: 10, pady: 10)
-    }
-
-    @variable1 = TkVariable.new
-    combo_box = TkCombobox.new(
-      root,
-      width: 30,
-      font:  MAIN_FONT,
-      justify: :left,
-      textvariable: @variable1,
-      background: 'moccasin'
-    )
-    combo_box.values(
-      ::Bioroebe.available_blosum_matrices?
-    )
-    combo_box.pack
-    combo_box.current = 0 # Set the first entry as our default entry for now.
-
-    ::Tk.run
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::Tk::BlosumMatrixViewer[]
-  # ========================================================================= #
-  def self.[](i = '')
-    new(i)
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Tk::BlosumMatrixViewer.new(ARGV)
-end # tk_blosum_matrix_viewer.rb

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

@@ -1,262 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::Tk::HammingDistance
-#
-# Usage example:
-#
-#   Bioroebe::GUI::Tk::HammingDistance.new(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/gui/tk/three_to_one/three_to_one.rb'
-# Bioroebe::GUI::Tk::HammingDistance.new(ARGV)
-# =========================================================================== #
-require 'tk_paradise/tk_paradise.rb'
-require 'tk_paradise/base/base.rb'
-
-module Bioroebe
-
-module GUI
-
-module Tk
-
-class HammingDistance < ::Tk::Base # === Bioroebe::GUI::Tk::HammingDistance
-
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/string_matching/hamming_distance.rb'
-
-  include ::Tk
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Hamming distance'
-
-  # ========================================================================= #
-  # === MAIN_FONT
-  # ========================================================================= #
-  MAIN_FONT = TkFont.new(family: 'Helvetica', size: 20, weight: 'bold')
-
-  # ========================================================================= #
-  # === SMALLER_FONT
-  # ========================================================================= #
-  SMALLER_FONT = TkFont.new(family: 'Helvetica', size: 16, weight: 'bold')
-
-  # ========================================================================= #
-  # === USE_THIS_BACKGROUND_COLOUR
-  # ========================================================================= #
-  USE_THIS_BACKGROUND_COLOUR = 'mintcream'
-
-  # ========================================================================= #
-  # === MONOSPACED_FONT
-  # ========================================================================= #
-  MONOSPACED_FONT = TkFont.new(family: 'Hack', size: 22, weight: 'bold')
-
-  # ========================================================================= #
-  # === PADDING_TO_USE
-  # ========================================================================= #
-  PADDING_TO_USE = {
-    padx: 10,
-    pady: 10
-  }
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      commandline_arguments = nil,
-      run_already           = true
-    )
-    reset
-    set_commandline_arguments(
-      commandline_arguments
-    )
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-    super()
-  end
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    root = TkRoot.new {
-      title TITLE
-      background USE_THIS_BACKGROUND_COLOUR
-    }
-    root.geometry('700x400+0+0')
-    root.minsize(400, 200)
-    # ======================================================================= #
-    # Add a frame for the whole application.
-    # ======================================================================= #
-    outermost_frame = TkFrame.new(root) {
-      background USE_THIS_BACKGROUND_COLOUR
-    }
-
-    label = ::TkLabel.new(outermost_frame) {
-      font(MAIN_FONT)
-      text TITLE
-      pack(
-        side: 'top', padx: 10, pady: 10
-      )
-      background USE_THIS_BACKGROUND_COLOUR
-    }
-    ::TkLabel.new(outermost_frame) {
-      font SMALLER_FONT
-      text "The Hamming distance - a number - measures "\
-           "the number of\npositions at which two strings "\
-           "of equal length are different."
-      pack(
-        side: 'top', # must be top-aligned to appear on top.
-        padx: 5,
-        pady: 5,
-        fill: 'both'
-      )
-      background USE_THIS_BACKGROUND_COLOUR
-    }
-
-    @text1 = TkVariable.new(
-      'AGUUCGAUGGAAAATAT'
-    )
-
-    # ======================================================================= #
-    # === @entry1 
-    # ======================================================================= #
-    @entry1 = TkEntry.new(outermost_frame, textvariable: @text1) {
-      font(MONOSPACED_FONT)
-      background 'lightsteelblue'
-    }
-    @entry1.pack(outermost_frame)
-    @entry1.configure(width: 35)
-
-    @text2 = TkVariable.new(
-      'AGUCCGGUCGAAAAAAA'
-    )
-    # ======================================================================= #
-    # === @entry2
-    # ======================================================================= #
-    @entry2 = TkEntry.new(outermost_frame, textvariable: @text2) {
-      font(MONOSPACED_FONT)
-      background 'lightsteelblue'
-    }
-    @entry2.pack(outermost_frame)
-    @entry2.configure(width: 35)
-
-    callback_do_compare = proc {
-      do_compare
-    }
-
-    # ======================================================================= #
-    # === The convert-button with its special frame comes next
-    # ======================================================================= #
-    frame_for_the_convert_button = TkFrame.new(
-      outermost_frame,
-      highlightbackground: 'black', 
-      highlightthickness: 2,
-      bd: 0,
-      borderwidth: 2
-    )
-    frame_for_the_convert_button.pack
-    button_convert = TkButton.new(frame_for_the_convert_button) {
-      text 'Compare the two sequences'
-      font(MAIN_FONT)
-      relief :flat
-      command callback_do_compare
-      pack
-      borderwidth 5
-    }
-
-    @text3 = tk_variable
-    # ======================================================================= #
-    # === @entry_n_differences                               (main entry tag)
-    #
-    # This is the third (and last) entry.
-    # ======================================================================= #
-    @entry_n_differences = TkEntry.new(outermost_frame, textvariable: @text3) {
-      font(MAIN_FONT)
-      width 250
-      background 'yellow'
-      borderwidth 5
-      relief 'groove'
-    }
-    @entry_n_differences.configure(width: 25)
-    @entry_n_differences.configure(highlightbackground: 'blue')
-    @entry_n_differences.configure(highlightcolor: 'green')
-    @entry_n_differences.pack(outermost_frame)
-
-    # ======================================================================= #
-    # === The quit-button and its special frame
-    # ======================================================================= #
-    frame_for_the_quit_button = TkFrame.new(
-      outermost_frame,
-      highlightbackground: 'black', 
-      highlightthickness: 2,
-      bd: 0,
-      borderwidth: 2
-    )
-    frame_for_the_quit_button.pack
-    button_quit = ::TkButton.new(frame_for_the_quit_button, text: 'Quit') {
-      font(MAIN_FONT)
-      relief :flat
-      command proc {
-        exit
-      }
-      pack
-      borderwidth 5
-    }
-
-    ::Tk.run
-  end
-
-  # ========================================================================= #
-  # === seq2?
-  # ========================================================================= #
-  def seq2?
-    @text2
-  end
-
-  # ========================================================================= #
-  # === seq1?
-  # ========================================================================= #
-  def seq1?
-    @text1
-  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 }
-    _ = hamming_distance_object.n_differences?.to_s
-    @entry_n_differences.delete(0,'end') # Clear it first.
-    @entry_n_differences.insert(0, _)
-  end; alias do_compare                   compare_the_two_sequences # === do_compare
-       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::Tk::HammingDistance[]
-  # ========================================================================= #
-  def self.[](i = '')
-    new(i)
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Tk::HammingDistance.new(ARGV)
-end # tk_hamming_distance