bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb

@@ -0,0 +1,643 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::UniversalWidgets::FastaTableWidget
+#
+# This widget is loosely inspired by:
+#
+#   https://raw.githubusercontent.com/labsquare/fastQt/master/screenshot.gif
+#
+# The widget supports loading .fasta files from the commandline - simply
+# pass the file location (local path) to the widget as argument.
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::FastaTableWidget.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb'
+# =========================================================================== #
+require 'universal_widgets/base/base.rb'
+
+module Bioroebe
+
+module GUI
+
+module UniversalWidgets
+
+class FastaTableWidget < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::FastaTableWidget
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  #
+  # Specify which title to use for this widget.
+  # ========================================================================= #
+  TITLE = 'Fasta Table Widget'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '75% or 2000px minimum'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55% or 500px minimum'
+
+  # ========================================================================= #
+  # === FONT_LARGE
+  # ========================================================================= #
+  FONT_LARGE = 'Calibri 32'
+
+  # ========================================================================= #
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
+  # ========================================================================= #
+  MONOSPACED_FONT = :hack_22
+    USE_THIS_FONT = MONOSPACED_FONT
+    USE_THIS_MONOFONT = MONOSPACED_FONT
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === HEADER_TO_USE_FOR_THE_TREE_VIEW
+  # ========================================================================= #
+  HEADER_TO_USE_FOR_THE_TREE_VIEW = [
+    'Local Path',
+    'File size',
+    'n nucleotides',
+    '%GC'
+  ]
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    determine_the_GUI_to_be_used(commandline_arguments)
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super() if respond_to?(:super)
+    reset_the_internal_variables
+    reset_the_base_module # This must come after reset_the_internal_variables().
+    infer_the_namespace
+    # ======================================================================= #
+    # === @configuration
+    # ======================================================================= #
+    @configuration = [true, __dir__, namespace?]
+    # ======================================================================= #
+    # === Set the title, width, height and the font in use.
+    # ======================================================================= #
+    title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
+    handle_CSS if use_gtk3?
+    # ======================================================================= #
+    # === @use_this_directory
+    # ======================================================================= #
+    @use_this_directory = ::Bioroebe.log_directory?+'fasta/'
+    # ======================================================================= #
+    # === @all_fasta_files
+    # ======================================================================= #
+    @all_fasta_files = Dir[@use_this_directory+'*.fasta']
+  end
+
+  # ========================================================================= #
+  # === create_the_entries                                        (entry tag)
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = entry
+    @entry_input_sequence.default_values
+    @entry_input_sequence.hint = 'The sequence will be evaluated '\
+      'whenever it is changed, as-is. Hit the <b>enter</b> key '\
+      'to change it, for convenience.'
+    @entry_input_sequence.on_changed {
+      update_the_main_sequence_variable
+      update_this_sequence_contains_n_nucleotides
+      update_the_table_dataset
+      update_the_labels
+    }
+    # ======================================================================= #
+    # Act on when the user hits the enter-key.
+    # ======================================================================= #
+    @entry_input_sequence.on_enter_key {
+      sanitize_the_sequence
+      do_analyse_the_sequence
+      update_this_sequence_contains_n_nucleotides(
+        return_how_many_nucleotides_this_sequence_contains
+      )
+    }
+  end
+
+  # ========================================================================= #
+  # === entry_input_sequence?
+  # ========================================================================= #
+  def entry_input_sequence?
+    @entry_input_sequence
+  end; alias main_entry? entry_input_sequence? # === main_entry?
+
+  # ========================================================================= #
+  # === dna_sequence?
+  # ========================================================================= #
+  def dna_sequence?
+    @entry_input_sequence.text?
+  end
+
+  # ========================================================================= #
+  # === update_the_GC_content_label
+  # ========================================================================= #
+  def update_the_GC_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_GC_content.set_text(
+      'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
+    )
+    @label_GC_content.do_markify
+  end
+
+  # ========================================================================= #
+  # === update_the_labels
+  # ========================================================================= #
+  def update_the_labels
+    update_the_GC_content_label
+    update_the_AT_content_label
+  end
+
+  # ========================================================================= #
+  # === do_style_all_buttons_in_a_uniform_manner
+  # ========================================================================= #
+  def do_style_all_buttons_in_a_uniform_manner
+    return_all_buttons.each {|this_button|
+      this_button.bblack1
+    }
+  end
+
+  # ========================================================================= #
+  # === do_analyse_the_sequence
+  # ========================================================================= #
+  def do_analyse_the_sequence
+    clear_table
+    _ = return_dataset_based_on_this_sequence.each_slice(3).to_a
+    # ======================================================================= #
+    # The first element contains the header, which is not necessary.
+    # ======================================================================= #
+    _.shift 
+    populate_this_list_store3(
+      @list_store, _.compact
+    )
+  end; alias update_the_table_dataset do_analyse_the_sequence # === update_the_table_dataset
+
+  # ========================================================================= #
+  # === clear_table
+  # ========================================================================= #
+  def clear_table
+    @list_store.clear
+  end
+
+  # ========================================================================= #
+  # === open_local_file
+  # ========================================================================= #
+  def open_local_file
+    # ======================================================================= #
+    # We will actively filter for .mp3 files only.
+    # ======================================================================= #
+    widget = ::Gtk::SelectFile.new(self) {{
+      current_folder: ::Bioroebe.log_dir?
+    }}
+    this_file = widget.do_pick_file.text.to_s
+    return this_file
+  end
+
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+  # ========================================================================= #
+  # === do_open_a_local_file
+  # ========================================================================= #
+  def do_open_a_local_file
+    _ = open_local_file # Find a local file. (open tag)
+    if File.exist?(_) and File.file?(_)
+      # ===================================================================== #
+      # Handle FASTA files a bit differently next:
+      # ===================================================================== #
+      if _.end_with?('.fasta') or _.end_with?('.fa')
+        content_of_the_file = Bioroebe.parse_fasta(_).body?
+      else
+        content_of_the_file = File.read(_).to_s
+      end
+      set_main_entry(content_of_the_file)
+    end
+  end
+
+  # ========================================================================= #
+  # === update_this_sequence_contains_n_nucleotides
+  # ========================================================================= #
+  def update_this_sequence_contains_n_nucleotides(
+      i = 
+        return_how_many_nucleotides_this_sequence_contains
+    )
+    @text_this_sequence_contains.set_text(i.to_s)
+    @text_this_sequence_contains.do_markify
+  end
+
+  # ========================================================================= #
+  # === return_dataset_based_on_this_sequence
+  # ========================================================================= #
+  def return_dataset_based_on_this_sequence(
+      sequence = @entry_input_sequence.text?
+    )
+    total = sequence.size
+    dataset = [ # First three entries are the header.
+      'Nucleotide','amount','Percentage',
+      'A', sequence.count('A').to_s, ((sequence.count('A').to_f * 100) / total).round(1).to_s+'%',
+      'T', sequence.count('T').to_s, ((sequence.count('T').to_f * 100) / total).round(1).to_s+'%',
+      'C', sequence.count('C').to_s, ((sequence.count('C').to_f * 100) / total).round(1).to_s+'%',
+      'G', sequence.count('G').to_s, ((sequence.count('G').to_f * 100) / total).round(1).to_s+'%'
+    ]
+    return dataset
+  end
+
+  # ========================================================================= #
+  # === return_how_many_nucleotides_this_sequence_contains
+  # ========================================================================= #
+  def return_how_many_nucleotides_this_sequence_contains(
+      i = @entry_input_sequence.text?
+    )
+    "This sequence contains <b>#{i.size.to_s}</b> nucleotides."
+  end
+
+  # ========================================================================= #
+  # === do_reset_the_input_sequence
+  # ========================================================================= #
+  def do_reset_the_input_sequence
+    @entry_input_sequence.clear
+  end
+
+  # ========================================================================= #
+  # === sanitize_the_sequence
+  # ========================================================================= #
+  def sanitize_the_sequence
+    if @entry_input_sequence.text?
+      if @entry_input_sequence.text?.include? '-'
+        new_sequence = @entry_input_sequence.text?.delete('-')
+        @sequence = new_sequence
+        @entry_input_sequence.set_text(new_sequence)
+        @dataset = return_dataset_based_on_this_sequence(@entry_input_sequence.text?)
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === update_the_main_sequence_variable
+  # ========================================================================= #
+  def update_the_main_sequence_variable
+    @sequence = @entry_input_sequence.text?.delete('-')
+  end
+
+  # ========================================================================= #
+  # === update_the_AT_content_label
+  # ========================================================================= #
+  def update_the_AT_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_AT_content.set_text(
+      "The <b>AT content</b> (A+T) is: <b>"\
+      "#{(100.0 - _.to_f).round(1).to_s}%</b>"
+    )
+    @label_AT_content.do_markify
+  end
+
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  end; alias set_dna_sequence set_main_entry # === set_dna_sequence
+
+  # ========================================================================= #
+  # === create_the_buttons                          (buttons tag, button tag)
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_reset
+    # ======================================================================= #
+    @button_reset = button('_Reset the table')
+    @button_reset.hint = 'This button will clear the table-result '\
+                         'shown above.'
+    @button_reset.on_clicked {
+      clear_table
+    }
+    # ======================================================================= #
+    # === @button_reset_the_input_sequence
+    # ======================================================================= #
+    @button_reset_the_input_sequence = button('Reset the _input sequence')
+    @button_reset_the_input_sequence.enable_markup
+    @button_reset_the_input_sequence.hint = 'This button will '\
+      'reset (aka clear) the input sequence. The input sequence is kept '\
+      'on top of this widget, as a gtk-entry.'
+    @button_reset_the_input_sequence.on_clicked {
+      do_reset_the_input_sequence
+    }
+    # ======================================================================= #
+    # === @button_open_file
+    # ======================================================================= #
+    @button_open_file = button('_Open file')
+    @button_open_file.enable_markup
+    @button_open_file.hint = 'This button can be used to open a local'\
+                             'file, typically a FASTA (.fasta) file.'
+    @button_open_file.on_clicked {
+      do_open_a_local_file
+    }
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    2
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    0
+  end
+
+  # ========================================================================= #
+  # === main_font?
+  # ========================================================================= #
+  def main_font?
+    USE_THIS_FONT
+  end
+
+  # ========================================================================= #
+  # === slightly_smaller_font?
+  # ========================================================================= #
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === deselect_the_main_treeview
+  # ========================================================================= #
+  def deselect_the_main_treeview
+    @view.deselect
+  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 '
+treeview.view header button {
+  color: black;
+  background-color: oldlace;
+  border: 1px solid black;
+  margin: 1px;
+}
+
+'
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === populate_the_list_store_with_the_default_dataset
+  # ========================================================================= #
+  def populate_the_list_store_with_the_default_dataset
+    array = @all_fasta_files.map {|path|
+      parse_fasta_object = ::Bioroebe.parse_fasta(path) { :be_quiet }
+      n_nucleotides = parse_fasta_object.n_nucleotides?
+      gc_content = parse_fasta_object.gc_content # Bioroebe.gc_content
+      # ===================================================================== #
+      # Must round it to two decimal points next:
+      # ===================================================================== #
+      gc_content = gc_content.round(2)
+      [path, File.size(path), n_nucleotides, gc_content]
+    }.sort_by {|path, size, n_nucleotides, gc_content|
+      size
+    }
+    # ======================================================================= #
+    # Sort the "filesize" entry a bit differently.
+    # ======================================================================= #
+    @list_store.set_sort_func(1) { |_model, iter1, iter2|
+      iter2[1].to_s.to_f <=> iter1[1].to_s.to_f
+    }
+    # ======================================================================= #
+    # Sort the "n nucleotides" entry a bit differently.
+    # ======================================================================= #
+    @list_store.set_sort_func(2) { |_model, iter1, iter2|
+      iter2[2].to_s.to_f <=> iter1[2].to_s.to_f
+    }
+    populate_this_list_store_with_that_array4(@list_store, array)
+  end
+
+  # ========================================================================= #
+  # === list_store?
+  # ========================================================================= #
+  def list_store?
+    @list_store
+  end; alias liststore? list_store? # === liststore?
+
+  # ========================================================================= #
+  # === create_the_view
+  # ========================================================================= #
+  def create_the_view
+    @list_store = ::Gtk::ListStore.new(
+      String,
+      String,
+      String,
+      String
+    )
+    # ======================================================================= #
+    # === @view
+    # ======================================================================= #
+    @view = create_tree_view(@list_store)
+    @view.headers = HEADER_TO_USE_FOR_THE_TREE_VIEW
+    @view.make_sortable
+    @view.the_headers_can_be_moved
+    @view.enable_search
+    @view.deselect_on_right_click_event
+    deselect_the_main_treeview
+  end
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_view
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    menu # Must come before the run_super() invocation.
+    run_super
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === second_column?
+  # ========================================================================= #
+  def second_column?
+    @view.columns?[1]
+  end
+
+  # ========================================================================= #
+  # === append_this_fasta_file
+  # ========================================================================= #
+  def append_this_fasta_file(i)
+    unless @all_fasta_files.include?(i)
+      if i.end_with?('.fa','.fasta','.txt','.md')
+        @all_fasta_files << i
+      end
+    end
+  end; alias append_this_file append_this_fasta_file # === append_this_file
+
+  # ========================================================================= #
+  # === clear_the_old_dataset
+  # ========================================================================= #
+  def clear_the_old_dataset
+    @all_fasta_files.clear
+  end
+
+  # ========================================================================= #
+  # === style_the_label_widget
+  # ========================================================================= #
+  def style_the_label_widget
+    _ = hbox
+    label = text('FASTA files')
+    label.left_align
+    label.fonty(main_font?)
+    label.make_bold
+    label.css_class('darkblue')
+    label.pad4px
+    _.minimal(label,  10)
+    event_box = event_box(image_document_open)
+    event_box.on_clicked {
+      filename = ::Gtk.select_file(@parent_widget) {{ # @parent_widget should be of Gtk::Window class or subclass.
+        current_folder:             return_pwd,
+        show_hidden:                true,
+        add_these_shortcut_folders: Bioroebe.fasta_dir?
+      }}
+      if filename and File.exist?(filename)
+        append_this_file(filename)
+        # @view.clear
+        liststore?.clear
+        populate_the_list_store_with_the_default_dataset
+      end
+    }
+    @outer_vbox.minimal event_box, 10
+    #self.label_widget = _
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = commandline_arguments?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      # ===================================================================== #
+      # Load existing files:
+      # ===================================================================== #
+      if i and File.exist?(i)
+        clear_the_old_dataset
+        append_this_fasta_file(i)
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+
+    populate_the_list_store_with_the_default_dataset
+    scrolled_window = create_scrolled_window(@view) { :always }
+    scrolled_window.width_height(540, 500)
+    @outer_vbox = create_vbox
+    @outer_vbox.minimal(scrolled_window, 14)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << @outer_vbox
+
+    ::UniversalWidgets.set_main_window(window)
+    upon_delete_event_quit_the_application
+    window.use_this_font = font?
+    window.show_all
+    window.set_padding(padding?)
+    window.set_border_size(border_size?)
+    window.set_size_request(width?, height?)
+    window.set_default_size(width?, height?)
+    style_the_label_widget
+    window.top_left
+    run_main
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::FastaTableWidget[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::FastaTableWidget.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::FastaTableWidget.new(i)
+    )
+    r.background_colour(:white)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::FastaTableWidget.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::FastaTableWidget.start_gui_application
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::UniversalWidgets::FastaTableWidget.new(ARGV)
+end # gtkfastatablewidget