bioroebe 0.10.80

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

@@ -0,0 +1,566 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::RandomSequence
+#
+# This small widget can be used to "generate" random aminoacids, or
+# random DNA sequence or random RNA sequences quickly.
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/random_sequence/random_sequence.rb'
+# Bioroebe::GUI::Gtk::RandomSequence.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence 
+
+  require 'bioroebe/aminoacids/create_random_aminoacids.rb'
+  require 'bioroebe/toplevel_methods/misc.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  require 'bioroebe/constants/GUIs.rb'
+  include ::Bioroebe::GUI::Gtk
+  include Bioroebe::GUI
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Random Sequence - for DNA, RNA and aminoacids'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH  = 900
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 720
+
+  # ========================================================================= #
+  # === USE_THIS_HEADER
+  # ========================================================================= #
+  USE_THIS_HEADER = ['one-letter abbreviation', 'n times']
+
+  # ========================================================================= #
+  # === GENERATE_N_AMINOACIDS_BY_DEFAULT
+  # ========================================================================= #
+  GENERATE_N_AMINOACIDS_BY_DEFAULT = 15
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_22
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    super(:vertical)
+    register_sigint
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    reset_the_internal_variables
+    # ======================================================================= #
+    # === @configuration
+    # ======================================================================= #
+    @configuration = [true, __dir__, NAMESPACE]
+    title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
+    # ======================================================================= #
+    # === @list_store
+    # ======================================================================= #
+    @list_store = nil
+    handle_CSS
+    infer_the_size_automatically
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    8
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    4
+  end
+
+  # ========================================================================= #
+  # === aminoacid_sequence?
+  # ========================================================================= #
+  def aminoacid_sequence?
+    @entry_containing_the_sequence.text?.to_s
+  end; alias sequence?      aminoacid_sequence? # === sequence?
+       alias main_sequence? aminoacid_sequence? # === main_sequence?
+
+  # ========================================================================= #
+  # === do_open_a_file_and_then_set_the_correct_values
+  # ========================================================================= #
+  def do_open_a_file_and_then_set_the_correct_values
+    filename = ::Gtk.select_file(self) {{ # @parent_widget should be of Gtk::Window class or subclass.
+      show_hidden:                true,
+      add_these_shortcut_folders: ::Bioroebe.log_dir?,
+      current_folder:             ::Bioroebe.log_dir?
+    }}
+    if File.exist? filename
+      _ = filename
+      if _.end_with? '.fasta'
+        require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+        sequence = Bioroebe.parse_fasta_file(_).sequence?
+        set_main_input(sequence)
+        do_evaluate_the_sequence
+      else
+        set_main_input(File.read(_).strip)
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === enable_proper_sorting_for_the_list_store
+  # ========================================================================= #
+  def enable_proper_sorting_for_the_list_store
+    # ======================================================================= #
+    # Sort the number-of-entries found entry a bit differently. This
+    # will sort by putting the most frequently occurring aminoacids
+    # or DNA/RNA nucleotides on top.
+    # ======================================================================= #
+    @list_store.set_sort_func(1) { |_model, iter1, iter2|
+      iter2[1].to_i <=> iter1[1].to_i
+    }
+  end
+
+  # ========================================================================= #
+  # === on_right_click_in_the_tree_view_deselect_the_selection
+  # ========================================================================= #
+  def on_right_click_in_the_tree_view_deselect_the_selection
+    @tree_view.on_right_mouse_button_clicked {|widget, event|
+      @tree_view.deselect_everything
+    }
+  end
+
+  # ========================================================================= #
+  # === create_the_buttons                                          (buttons tag)
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @clear_button
+    # ======================================================================= #
+    @clear_button = bold_button('_Clear the table above')
+    @clear_button.hint = 'Clear the above dataset / table'
+    @clear_button.on_clicked {
+      do_clear_the_list_store
+    }
+    @clear_button.set_name('button1')
+    # ======================================================================= #
+    # === @button_for_generating_a_new_random_sequence
+    # ======================================================================= #
+    @button_for_generating_a_new_random_sequence = bold_button(
+      '_Generate a random aminoacid sequence'
+    ) {{ # Add a tooltip.
+      tooltip: 'Clicking on this button will <b>generate a random '\
+               'aminoacid sequence</b>. Do not set a too high value '\
+               'as that may take a long time, and consume a '\
+               'lot of memory/RAM.'
+    }}
+    @button_for_generating_a_new_random_sequence.on_click_event {
+      do_generate_a_random_sequence(n_aminoacids?)
+    }
+    @button_for_generating_a_new_random_sequence.set_name('button1')
+    # ======================================================================= #
+    # Next, create, then add the clipboard button:
+    # ======================================================================= #
+    create_the_copy_to_clipboard_button
+  end
+
+  # ========================================================================= #
+  # === create_statistical_top_panel
+  # ========================================================================= #
+  def create_statistical_top_panel
+    # ======================================================================= #
+    # This here has to be added separately from the scrolled-window.
+    # ======================================================================= #
+    @statistical_widget_top_panel = bold_label(
+      'Showing statistical information about the '\
+      'assigned aminoacid sequence next'
+    )
+  end
+
+  # ========================================================================= #
+  # === do_clear_the_list_store
+  # ========================================================================= #
+  def do_clear_the_list_store
+    @list_store.clear
+  end
+
+  # ========================================================================= #
+  # === set_main_input
+  # ========================================================================= #
+  def set_main_input(i)
+    @entry_containing_the_sequence.set_text(i.to_s)
+  end
+
+  # ========================================================================= #
+  # === mode?
+  # ========================================================================= #
+  def mode?
+    @combo_box_for_the_sequence_type.text?
+  end
+
+  # ========================================================================= #
+  # === create_the_top_bar
+  # ========================================================================= #
+  def create_the_top_bar
+    @top_bar = gtk_top_bar
+    button_open_file = gtk_button('_Open File')
+    button_open_file.hint = 'Click on this button to open a local FASTA '\
+                            'file.'
+    button_open_file.on_clicked {
+      do_open_a_file_and_then_set_the_correct_values
+    }
+    button_open_file.bblack1
+    @top_bar.add(button_open_file)
+    # ======================================================================= #
+    # === @combo_box_for_the_sequence_type
+    # ======================================================================= #
+    @combo_box_for_the_sequence_type = gtk_combo_box_entry(
+      %w( aminoacid DNA RNA )
+    )
+    @combo_box_for_the_sequence_type.first_is_active
+    # ======================================================================= #
+    # Respond to the event when the combo-box value changes:
+    # ======================================================================= #
+    @combo_box_for_the_sequence_type.on_changed {
+      _ = @combo_box_for_the_sequence_type.text?
+      @button_for_generating_a_new_random_sequence.set_text(
+        "Generate a random #{_} sequence"
+      )
+      @button_for_generating_a_new_random_sequence.make_bold
+      @statistical_widget_top_panel.set_text(
+        "Showing statistical information about the "\
+        "assigned #{_} sequence next"
+      )
+      @statistical_widget_top_panel.make_bold
+      @tree_view.model = nil
+      @list_store = nil
+      @list_store = gtk_list_store(String, String)
+      case mode?
+      when 'DNA','RNA'
+        if mode? == 'DNA'
+          array1 = %w( A T C G )
+        else
+          array1 = %w( A U C G )
+        end
+        array2 = Array.new(array1.size, '0')
+        zipped = array1.zip(array2) # Zip it up with 0-values here.
+        zipped.each {|a, b|
+          iter = @list_store.append
+          iter.set_value(0, a)
+          iter.set_value(1, b)
+        }
+      else # else we assume a protein.
+      end
+      @tree_view.model = @list_store
+    }
+    @top_bar.add(@combo_box_for_the_sequence_type)
+  end
+
+  # ========================================================================= #
+  # === do_evaluate_the_sequence
+  # ========================================================================= #
+  def do_evaluate_the_sequence(
+      use_this_sequence = main_sequence?
+    )
+    do_clear_the_list_store
+    case mode?
+    # ======================================================================= #
+    # === DNA
+    # ======================================================================= #
+    when 'DNA','RNA'
+      @tree_view.remove_the_columns
+      column1 = ::Gtk::TreeViewColumn.new('DNA-Nucleotide', gtk_cell_renderer_text, { text: 0 })
+      column2 = ::Gtk::TreeViewColumn.new('n times',        gtk_cell_renderer_text, { text: 1 })
+      # ======================================================================= #
+      # Add the two columns to the tree-view next.
+      # ======================================================================= #
+      @tree_view.append_column(column1)
+      @tree_view.append_column(column2)
+      @tree_view.is_sortable
+      if mode? == 'DNA'
+        array1 = %w( A T C G )
+      else
+        array1 = %w( A U C G )
+      end
+      array2 = Array.new(array1.size, '0')
+      array2 = Bioroebe.return_DNA_composition_hash(use_this_sequence).values.map(&:to_s)
+      array = array1.zip(array2)
+    # ======================================================================= #
+    # === aminoacids
+    # ======================================================================= #
+    when 'aminoacids'
+      array1 = ::Bioroebe.return_array_of_common_aminoacids
+      array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_sequence).values.map(&:to_s)
+      array = array1.zip(array2) # Zip it up with 0-values here.
+    end
+    ::Gtk.populate_this_liststore(@list_store, array)
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    minimal(@top_bar,                                      3)
+    minimal(@entry_containing_the_sequence,                3)
+    minimal(@button_for_generating_a_new_random_sequence,  3)
+    minimal(@entry_for_n_entries_in_the_sequence,          3)
+    hbox_for_the_button_copy_to_clipboard = gtk_hbox
+    hbox_for_the_button_copy_to_clipboard.minimal(@button_copy_to_clipboard)
+    hbox_for_the_button_copy_to_clipboard.align_into_the_center
+    minimal(hbox_for_the_button_copy_to_clipboard,         3)
+    minimal(@statistical_widget_top_panel,                 0)
+    maximal(@statistical_widget,                           3)
+    show_all
+  end
+
+  # ========================================================================= #
+  # === do_copy_to_the_clipboard
+  # ========================================================================= #
+  def do_copy_to_the_clipboard
+    begin
+      require 'xorg_buffer'
+    rescue LoadError; end
+    if Object.const_defined? :XorgBuffer
+      XorgBuffer.copy_this_text_to_the_clipboard(aminoacid_sequence?)
+    else
+      e 'The gem xorg_buffer is not installed, or could not be found.'
+    end
+  end
+
+  # ========================================================================= #
+  # === n_aminoacids?
+  # ========================================================================= #
+  def n_aminoacids?
+    @entry_for_n_entries_in_the_sequence.text?.to_s
+  end
+
+  # ========================================================================= #
+  # === create_the_entries
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_containing_the_sequence
+    # ======================================================================= #
+    @entry_containing_the_sequence = gtk_entry
+    @entry_containing_the_sequence.on_click_select_everything
+    @entry_containing_the_sequence.yellow_background
+    @entry_containing_the_sequence.bblack1
+    # ======================================================================= #
+    # Add the entry that allows the user to control how many aminoacids
+    # will be "generated".
+    # ======================================================================= #
+    @entry_for_n_entries_in_the_sequence = gtk_entry { :align_center }
+    @entry_for_n_entries_in_the_sequence.set_text(GENERATE_N_AMINOACIDS_BY_DEFAULT.to_s)
+    @entry_for_n_entries_in_the_sequence.yellow_background
+    @entry_for_n_entries_in_the_sequence.on_click_select_everything
+    @entry_for_n_entries_in_the_sequence.bblack1
+    @entry_for_n_entries_in_the_sequence.on_enter {
+      do_generate_a_random_sequence_using_the_value_from_the_proper_entry
+    }
+    @entry_for_n_entries_in_the_sequence.hint = 'Input here how many random '\
+      'amino acids should be generated.'
+  end
+
+  require 'bioroebe/count/count_amount_of_aminoacids.rb'
+  # ========================================================================= #
+  # === create_statistical_information
+  #
+  # This method will fill up the "table".
+  # ========================================================================= #
+  def create_statistical_information
+    create_statistical_top_panel
+    @statistical_widget = gtk_vbox
+    # ======================================================================= #
+    # Next we must create the widget that can hold the hash. This will
+    # be a list-store that can be dynamically updated.
+    # ======================================================================= #
+    array1 = ::Bioroebe.return_array_of_common_aminoacids
+    array2 = Array.new(array1.size, '0')
+    array = array1.zip(array2) # Zip it up with 0-values here.
+    array.prepend(USE_THIS_HEADER)
+    # ======================================================================= #
+    # Next the tree view is created:
+    # ======================================================================= #
+    @tree_view, @list_store = tree_widget_with_two_columns_per_row(array)
+    do_properly_setup_the_tree_view
+    scrolled_window = gtk_scrolled_window(@tree_view)
+    scrolled_window.set_border_width(10)
+    scrolled_window.bblack1
+    @statistical_widget.maximal(scrolled_window, 5)
+    hbox1 = gtk_hbox
+    hbox1.minimal(@clear_button)
+    hbox1.align_into_the_center
+    @statistical_widget.minimal(hbox1, 2)
+    enable_proper_sorting_for_the_list_store
+    on_right_click_in_the_tree_view_deselect_the_selection
+  end
+
+  # ========================================================================= #
+  # === do_properly_setup_the_tree_view
+  # ========================================================================= #
+  def do_properly_setup_the_tree_view
+    @tree_view.linear_sorting
+    @tree_view.the_headers_can_be_dragged
+  end
+
+  # ========================================================================= #
+  # === do_generate_a_random_sequence_using_the_value_from_the_proper_entry
+  #
+  # This variant will be guaranteed to use the value determined by the
+  # gtk entry.
+  # ========================================================================= #
+  def do_generate_a_random_sequence_using_the_value_from_the_proper_entry(
+      i = n_aminoacids?
+    )
+    do_generate_a_random_sequence(i)
+  end
+
+  # ========================================================================= #
+  # === create_the_copy_to_clipboard_button
+  # ========================================================================= #
+  def create_the_copy_to_clipboard_button
+    # ======================================================================= #
+    # === @button_copy_to_clipboard
+    # ======================================================================= #
+    @button_copy_to_clipboard = bold_button('_Copy to the xorg-clipboard')
+    @button_copy_to_clipboard.hint = 'This will <b>copy the aminoacid '\
+      'sequence</b> to the <b>xorg-clipboard</b>.'
+    @button_copy_to_clipboard.on_clicked {
+      do_copy_to_the_clipboard
+    }
+    @button_copy_to_clipboard.set_name('button1')
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_buttons # Call this before the top_bar is created.
+    create_statistical_information # Call this before the top-bar is created.
+    create_the_top_bar
+    create_the_entries
+  end
+
+  # ========================================================================= #
+  # === do_generate_a_random_sequence
+  # ========================================================================= #
+  def do_generate_a_random_sequence(
+      n_aminoacids = :default
+    )
+    case n_aminoacids
+    when nil, :default
+      n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
+    end
+    n_aminoacids = n_aminoacids.to_s
+    # ======================================================================= #
+    # We also must update the entry that displays the aminoacids. We have
+    # to check whether we use aminoacids or not, though.
+    # ======================================================================= #
+    case mode?
+    when /RNA/i,
+         /DNA/i
+      use_this_as_the_new_sequence = :: Bioroebe.generate_random_dna_sequence(n_aminoacids).to_s
+      array1 = Bioroebe::DNA_NUCLEOTIDES
+      if mode?.to_s == 'RNA'
+        use_this_as_the_new_sequence = ::Bioroebe.generate_random_rna_sequence(n_aminoacids).to_s
+        array1 = Bioroebe::RNA_NUCLEOTIDES
+      end
+      hash = {}
+      array1.each {|this_key|
+        hash[this_key] = 0
+      }
+      use_this_as_the_new_sequence.chars.each {|this_nucleotide|
+        hash[this_nucleotide.to_s] += 1
+      }
+      array2 = hash.values.map {|entry| entry.to_s }
+    else # else assume protein sequence
+      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)
+    end
+    @entry_containing_the_sequence.set_content(use_this_as_the_new_sequence)
+    # ======================================================================= #
+    # Next we have to build up our array, which is then passed into the
+    # list-store.
+    # ======================================================================= #
+    array = array1.zip(array2) # Zip it up with 0-values here.
+    ::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
+  # ========================================================================= #
+  def run
+    super()
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::RandomSequence.start_gui_application
+  # ========================================================================= #
+  def self.start_gui_application(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    # ======================================================================= #
+    # Instantiate a new GUI next.
+    # ======================================================================= #
+    _ = ::Bioroebe::GUI::Gtk::RandomSequence.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_size_then_automatic_title
+    r.background_colour :white
+    r.easy_exit
+    r.top_left_then_run
+  end; self.instance_eval { alias run start_gui_application } # === RandomSequence.run
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::RandomSequence.run
+end # gtkrandomsequence

data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config

@@ -0,0 +1,6 @@
+width:                                       900
+height:                                      720
+padding:                                       4
+title:                       Restriction Enzymes
+favicon:                                 :tabble
+font_in_use:                             Sans 20