bioroebe 0.10.80

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

@@ -0,0 +1,428 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::NucleotideAnalyser
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
+# Bioroebe::GUI::Gtk::NucleotideAnalyser.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalyser 
+
+  require 'bioroebe/calculate/calculate_gc_content.rb'
+  require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Nucleotide Analyser'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65% or minimum 350px'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 580
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :hack_16
+
+  # ========================================================================= #
+  # === 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)
+    infer_the_size_automatically
+    set_border_width(10)
+    # ======================================================================= #
+    # === @sequence
+    # ======================================================================= #
+    @sequence = 'GCTATGCATGCATGCTTTTTTTTTTTAGTCAGTCAGTCGATGCATGC'\
+                'ATGCTAGTCAGTCAGTCGATGTGCATGCTAGTCAGTCAGTCGATGCA'
+    # ^^^ overrule for now.
+    initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
+    handle_CSS_rules
+  end
+
+  # ========================================================================= #
+  # === initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
+  # ========================================================================= #
+  def initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets(
+      i = @sequence
+    )
+    # ======================================================================= #
+    # Specify the dataset that we wish to use for the gtk_table3() call.
+    # ======================================================================= #
+    @dataset = return_dataset_based_on_this_sequence(i)
+    @tree_view, @list_store = gtk_table3(
+      @dataset
+    ) {{
+      cell_renderer_text1: :align_to_the_middle,
+      cell_renderer_text2: :align_to_the_middle
+    }}
+    @tree_view.bblack2
+    @tree_view.pad10px
+    @tree_view.set_name('custom_treeview')
+    @tree_view.first_column?.center
+    @tree_view.second_column?.center
+    @tree_view.the_headers_can_be_moved
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    2
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_buttons
+    create_labels
+    create_entry
+  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
+
+  # ========================================================================= #
+  # === create_entry                                              (entry tag)
+  # ========================================================================= #
+  def create_entry
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = gtk_entry
+    @entry_input_sequence.yellow_background
+    @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_this_sequence_contains_n_nucleotides
+      update_the_table_dataset
+      update_the_GC_content_label
+    }
+    # ======================================================================= #
+    # 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
+
+  # ========================================================================= #
+  # === 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; alias update_the_labels update_the_GC_content_label # === update_the_labels
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  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
+
+  # ========================================================================= #
+  # === create_buttons                              (buttons tag, button tag)
+  # ========================================================================= #
+  def create_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
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === create_labels
+  # ========================================================================= #
+  def create_labels
+    # ======================================================================= #
+    # === @label_gc_content
+    # ======================================================================= #
+    @label_gc_content = gtk_left_aligned_label
+    # ======================================================================= #
+    # === @text_this_sequence_contains
+    # ======================================================================= #
+    @text_this_sequence_contains = gtk_left_aligned_label
+  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
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    _ = first_argument?.to_s
+    minimal(@entry_input_sequence, 2)
+    @entry_input_sequence.set_text(@sequence.to_s)
+    minimal(@text_this_sequence_contains, 2)
+    minimal(gtk_horizontal_spacer)
+    @tree_view.all_are_sortable # Make them all sortable.
+    scrolled_window = gtk_scrolled_window(@tree_view) { :never_always }
+    scrolled_window.set_size_request(420, 260)
+    minimal(scrolled_window, 5)
+    minimal(gtk_horizontal_spacer)
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    update_the_labels
+    minimal(@label_gc_content)
+    minimal(
+      gtk_left_aligned_label(
+        'The <b>AT content</b> (A+T) is: <b>'+
+        (100.0 - _.to_f).round(1).to_s+'%</b>'
+      )
+    )
+    hbox = gtk_hbox
+    hbox.maximal(@button_reset,                    1)
+    hbox.maximal(@button_reset_the_input_sequence, 1)
+    hbox.maximal(@button_open_file,                1)
+    minimal(hbox, 2)
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules                                            (CSS tag)
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_CSS_file
+    append_these_custom_CSS_rules '
+#custom_treeview.view header button {
+  color: royalblue;
+  font-weight: bold;
+  font-size: larger;
+  padding: 8px;
+}
+
+'
+    apply_the_CSS_rules
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    do_style_all_buttons_in_a_uniform_manner
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::NucleotideAnalyser.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::NucleotideAnalyser.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_size_then_automatic_title
+    r.top_left_then_run
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::NucleotideAnalyser.run
+end