bioroebe 0.10.80

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

@@ -0,0 +1,510 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::AminoacidComposition
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
+# Bioroebe::GUI::Gtk::AminoacidComposition.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class AminoacidComposition < ::Gtk::Box # === Bioroebe::GUI::Gtk::AminoacidComposition
+
+  require 'bioroebe/count/count_amount_of_aminoacids.rb'
+  require 'bioroebe/toplevel_methods/log_directory.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Aminoacid Composition'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '60%'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '40%'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_18
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :dejavu_condensed_16
+
+  # ========================================================================= #
+  # === FILE_MOLECULAR_WEIGHT
+  # ========================================================================= #
+  FILE_MOLECULAR_WEIGHT = Bioroebe.file_molecular_weight
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    super(:vertical)
+    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)
+    handle_CSS_rules
+    infer_the_size_automatically
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    6
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_user_input
+  end
+
+  # ========================================================================= #
+  # === create_user_input
+  # ========================================================================= #
+  def create_user_input
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = gtk_entry
+    @entry_input_sequence.hint =
+      "Input your aminoacid sequence here, then hit the enter-key to "\
+      "evaluate the given input. Invalid entries (aka <b>non-aminoacids</b>) "\
+      "will be filtered away, so do not be surprised if the sequence may "\
+      "be modified (== <b>sanitized</b>).\n\n"\
+      "The cursor-position will indicate at which aminoacid "\
+      "position we are at.\n"
+    @entry_input_sequence.yellow_background
+    @entry_input_sequence.css_class('pad4px')
+    @entry_input_sequence.signal_connect(:event) {|widget, event|
+      if is_mouse_button_release_event?(event)
+        update_information_deduced_from_the_aminoacid_sequence
+      end
+    }
+  end
+
+  # ========================================================================= #
+  # === set_parent_widget
+  # ========================================================================= #
+  def set_parent_widget(i)
+    @parent_widget = i
+  end
+
+  # ========================================================================= #
+  # === fill_the_table_data_with_this_sequence
+  # ========================================================================= #
+  def fill_the_table_data_with_this_sequence(
+      i = @entry_input_sequence.text?
+    )
+    @list_store.clear
+    hash = Bioroebe.return_composition_from_this_aminoacid_sequence(i)
+    array = hash.to_a.map {|inner_array| inner_array.map {|entry| entry.to_s }}
+    ::Gtk.populate_this_liststore(@list_store, array)
+  end; alias fill_with_this fill_the_table_data_with_this_sequence # === fill_with_this
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = commandline_arguments?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i
+      # ===================================================================== #
+      # === gtk_aminoacid_composition --ubi
+      # ===================================================================== #
+      when /^-?-?ubiquitin$/i,
+           /^-?-?ubi$/i
+        set_main_entry(
+          Bioroebe.return_ubiquitin_sequence
+        )
+        simulate_enter_click
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === main_font?
+  # ========================================================================= #
+  def main_font?
+    USE_THIS_FONT
+  end
+
+  # ========================================================================= #
+  # === slightly_smaller_font?
+  # ========================================================================= #
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  end; alias set_main_input_sequence set_main_entry # === set_main_input_sequence
+
+  # ========================================================================= #
+  # === set_main_input_sequence_and_evaluate_it
+  # ========================================================================= #
+  def set_main_input_sequence_and_evaluate_it(i)
+    simulate_enter_click(i)
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules                                   (CSS tag, css tag)
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_css_file
+    add_these_custom_CSS_rules '
+
+#custom_treeview.view header button {
+  background-color: white;
+  color: royalblue;
+  font-weight: bold;
+  font-size: larger;
+  padding: 8px;
+}'
+    apply_the_CSS
+  end
+
+  # ========================================================================= #
+  # === create_then_add_the_header_bar
+  # ========================================================================= #
+  def create_then_add_the_header_bar
+    require 'bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb'
+    header = return_default_header_bar
+    label_description = text(TITLE)
+    label_description.make_bold
+    header.set_custom_title(label_description)
+
+    header.spacing = 10
+    header.bblack1
+
+    button = button_themed_icon('edit-paste-symbolic.symbolic')
+    button.hint = 'Click this button to show more information '\
+                  'about this application.'
+    content = <<-EOF
+This widget will operate via the following <b>aminoacid weights</b>,
+in Dalton, without the weight of a H₂O water molecule (18g/mol):
+
+EOF
+    content = content.dup
+    YAML.load_file(Bioroebe.file_molecular_weight).each_pair {|key, value|
+      content << "   <b>#{key}</b>: "\
+                 "<span color=\"steelblue\">#{value.to_s.rjust(6)}</span>\n"
+    }
+    content << "
+   Compare with this URL:\n
+     <a href=\"https://www.selleckchem.com/peptide-calculator.html\" title=\"Another useful resource\">https://www.selleckchem.com/peptide-calculator.html</a>
+    "
+    text_widget = gtk_left_aligned_text(content)
+    text_widget.use_this_font = :hack_18
+    button.on_clicked {
+      ::Bioroebe::GUI::Gtk::CustomizedDialog.new(
+        text_widget
+      )
+    }
+    header.pack_start(button)
+    minimal(header, 2)
+  end
+
+  # ========================================================================= #
+  # === calculated_weight?
+  #
+  # This method will calculate the weight.
+  # ========================================================================= #
+  def calculated_weight?(i)
+    dataset = YAML.load_file(FILE_MOLECULAR_WEIGHT)
+    weight = 0
+    if i.is_a?(String) and !i.empty?
+      chars = i.chars.sort
+      chars.each {|this_char|
+        value = dataset[this_char]
+        weight += value if value
+      }
+    end
+    # ======================================================================= #
+    # Must deduct water too.
+    # ======================================================================= #
+    weight -= (18.0 * (i.size - 1))
+    return weight.round(2)
+  end
+
+  # ========================================================================= #
+  # === update_label_cursor_position
+  # ========================================================================= #
+  def update_label_cursor_position
+    cursor_position = @entry_input_sequence.cursor_position
+    character = @entry_input_sequence.text?[cursor_position, 1].to_s
+    unless character.empty?
+      _ = 'The aminoacid at position <b>'+
+          (cursor_position+1).to_s+
+          '</b> is: <b>'+character.to_s+'</b>.'
+      @label_cursor_position.set_text(_)
+      @label_cursor_position.do_markify
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::AminoacidComposition.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::AminoacidComposition.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic
+    r.top_left_then_run
+  end
+
+  # ========================================================================= #
+  # === path_to_the_fasta_file?
+  # ========================================================================= #
+  def path_to_the_fasta_file?
+    ::Bioroebe.log_dir?+
+    'fasta/aminoacid_sequence.fasta'
+  end
+
+  # ========================================================================= #
+  # === return_widget_containing_the_toolbox_images
+  # ========================================================================= #
+  def return_widget_containing_the_toolbox_images
+    hbox = gtk_hbox
+    @event_box1 = gtk_event_box(
+      image_folder_visiting_symbolic
+    )
+    @event_box1.hint = 'Click on this image to create a new local '\
+      '.fasta file with that sequence. The location will be '\
+      'at: <b>'+
+      path_to_the_fasta_file?+
+      '</b>'
+    @event_box1.on_clicked {
+      do_create_a_new_fasta_file
+    }
+    hbox.minimal(@event_box1, 4)
+    return hbox
+  end
+
+  # ========================================================================= #
+  # === do_open_a_local_FASTA_file
+  # ========================================================================= #
+  def do_open_a_local_FASTA_file(
+      this_widget = @parent_widget
+    )
+    require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
+    # ======================================================================= #
+    # We will actively filter for .mp3 files only.
+    # ======================================================================= #
+    widget = ::Gtk::SelectFile.new(this_widget) {{
+      filter_for_these_file_types: '.fasta',
+      current_folder:              ::Bioroebe.log_dir?+'fasta/'
+    }}
+    this_file = widget.do_pick_file.text.to_s
+    if File.exist?(this_file) and File.file?(this_file) # Ensure that it really is a file.
+      require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+      dataset = File.read(this_file)
+      _ = Bioroebe::ParseFasta.new
+      unless dataset.start_with?('--')
+        _.set_data(dataset) # This will use the default file.
+        _.split_into_proper_sections
+        set_main_entry(_.body?)
+        fill_with_this(_.body?)
+        do_update_the_widget_on_the_right_side
+      end
+    end
+    return this_file
+  end
+
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+  # ========================================================================= #
+  # === do_create_a_new_fasta_file
+  # ========================================================================= #
+  def do_create_a_new_fasta_file
+    what = @entry_input_sequence.text?.dup
+    what.prepend(
+      "> Random aminoacid sequence generated via a ruby-gtk3 "\
+      "GUI (#{what.size} aminoacids)\n"
+    )
+    into = path_to_the_fasta_file?
+    ::Bioroebe.write_what_into(what, into)
+    vbox1 = gtk_vbox
+    use_this_as_the_label = text(
+      "Created a new file at:\n"
+    )
+    vbox1.minimal(use_this_as_the_label, 5)
+    vbox1.width_height(600, 400)
+    entry1 = gtk_bold_entry(into)
+    entry1.deselect
+    entry1.width_height(300, 30)
+    entry1.light_yellowish_background
+    vbox1.minimal(entry1, 5)
+    use_this_as_the_label.deselect
+    popup_over_this_widget(
+      @event_box1,
+      vbox1
+    ).popup
+  end
+
+  # ========================================================================= #
+  # === simulate_enter_click
+  # ========================================================================= #
+  def simulate_enter_click(
+      _ = @entry_input_sequence.text?
+    )
+    _.upcase!
+    # ======================================================================= #
+    # First weed out all invalid aminoacids:
+    # ======================================================================= #
+    _ = ::Bioroebe.filter_away_invalid_aminoacids(_)
+    @entry_input_sequence.set_text(_)
+    fill_the_table_data_with_this_sequence(_)
+    @label_n_aminoacids.set_text(
+      "This sequence has <b>#{_.size}</b> aminoacids."
+    )
+    @label_n_aminoacids.do_markify
+    @label_molecular_weight.set_text(
+      'The molecular weight of these aminoacids is: <b>'+
+      calculated_weight?(_).to_s+'</b> Dalton'
+    )
+    @label_molecular_weight.do_markify
+    update_label_cursor_position
+  end; alias update_information_deduced_from_the_aminoacid_sequence simulate_enter_click # === update_information_deduced_from_the_aminoacid_sequence
+       alias do_update_the_widget_on_the_right_side                 simulate_enter_click # === do_update_the_widget_on_the_right_side
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    create_then_add_the_header_bar
+    if first? and !first?.start_with?('--')
+      @entry_input_sequence.set_text(first?.to_s)
+    end
+    # ======================================================================= #
+    # === @list_store
+    # ======================================================================= #
+    @list_store = gtk_liststore(String, String)
+    # ======================================================================= #
+    # Sort the number of aminoacids a bit differently.
+    # ======================================================================= #
+    @list_store.set_sort_func(1) { |_model, iter1, iter2|
+      iter2[1].to_i <=> iter1[1].to_i
+    }
+    create_the_treeview
+    columns = @treeview.columns?
+    columns[0].allow_resizing
+    columns[1].allow_resizing
+    columns[0].sortable_based_on(0)
+    columns[1].sortable_based_on(1)
+    hbox = gtk_hbox
+    hbox.maximal(@entry_input_sequence, 6)
+    event_box = gtk_event_box(image_file_open)
+    event_box.hint = 'Click on this button in order to '\
+      'open a local .FASTA file.'
+    event_box.on_clicked {
+      do_open_a_local_FASTA_file
+    }
+    hbox.minimal(event_box,       1)
+    add(hbox)
+    @entry_input_sequence.on_enter {
+      simulate_enter_click
+    }
+    scrolled_window = gtk_scrolled_window(@treeview) { :always }
+    scrolled_window.width_height(300, 600)
+    scrolled_window.bblack1
+    scrolled_window.css_class('pad2px')
+    @label_n_aminoacids = left_aligned_text
+    small_vbox = gtk_vbox
+    small_vbox.pad4px
+    small_vbox.border_width = 5
+    small_vbox.minimal(@label_n_aminoacids, 4)
+    @label_molecular_weight = left_aligned_text
+    small_vbox.minimal(@label_molecular_weight, 3)
+    @label_cursor_position = left_aligned_text
+    small_vbox.minimal(@label_cursor_position,  3)
+    small_vbox.minimal(return_widget_containing_the_toolbox_images, 5)
+    _ = draggable_from_left_to_right(scrolled_window, small_vbox)
+    _.position = 350
+    minimal(_, 1)
+  end
+
+  # ========================================================================= #
+  # === create_the_treeview
+  # ========================================================================= #
+  def create_the_treeview
+    @treeview = gtk_tree_view(@list_store) { :clickable_headers }
+    @treeview.set_name('custom_treeview')
+    @treeview.headers('Aminoacid','n times')
+    @treeview.clickable_headers
+    @treeview.set_enable_search(true)
+    @treeview.set_reorderable(true)
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    super()
+    menu
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::AminoacidComposition.run
+end # gtkaa --ubi

data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb

@@ -0,0 +1,55 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb'
+# =========================================================================== #
+require 'gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class CustomizedDialog < ::Gtk::Dialog # === Bioroebe::GUI::Gtk::CustomizedDialog
+
+  alias e puts
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(*optional_widgets_to_add)
+    super()
+    set_title('Amino Acid Composition')
+    set_default_size(800, 550)
+    add_close_button
+    set_border_width(15)
+    set_default_response(::Gtk::ResponseType::CLOSE)
+    signal_connect(:response) { |widget, response|
+      case response
+      when :close, -7
+        destroy
+      end
+    }
+    optional_widgets_to_add.flatten.each {|this_widget_is_to_be_added|
+      add_this_widget(this_widget_is_to_be_added)
+    }
+    show_all
+  end
+
+  # ========================================================================= #
+  # === add_this_widget
+  # ========================================================================= #
+  def add_this_widget(i = nil)
+    child.add(i) if i
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk3::CustomizedDialog.new
+end # rb 029_gtk_dialog_sample.rb

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

@@ -0,0 +1,6 @@
+width:                                       840
+height:                                      600
+padding:                                       4
+title:                         Anti Sense Strand
+favicon:                                 :tabble
+font_in_use:                             Sans 20

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

@@ -0,0 +1,29 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb'
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class AntiSenseStrand < ::Gtk::Box # === Bioroebe::GUI::Gtk::AntiSenseStrand 
+
+  require 'bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb'
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::AntiSenseStrand.run
+  # ========================================================================= #
+  def self.run
+    Bioroebe::GUI::AntiSenseStrand.new('gtk3') { :use_vbox_on_the_toplevel }
+  end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::AntiSenseStrandModule.start_gui_application
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::AntiSenseStrand.run
+end # gtkantisensestrand