bioroebe 0.10.80

data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb

@@ -0,0 +1,284 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::DnaToReverseComplementWidgetModule
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb'
+# include Bioroebe::GUI::DnaToReverseComplementWidgetModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module DnaToReverseComplementWidgetModule # === Bioroebe::GUI::DnaToReverseComplementWidgetModule
+
+  require 'bioroebe/requires/require_sequence.rb'
+  require 'bioroebe/sequence/dna.rb'
+  require 'bioroebe/toplevel_methods/complement.rb'
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'DNA to Reverse Complement'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH  = '70%'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '20% or minimum 200px'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_22
+
+  # ========================================================================= #
+  # === reset_shared_module
+  # ========================================================================= #
+  def reset_shared_module
+    title_width_height(TITLE, WIDTH, HEIGHT)
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    2
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    0
+  end
+
+  # ========================================================================= #
+  # === favicon?
+  # ========================================================================= #
+  def favicon?
+    :tabble
+  end
+
+  # ========================================================================= #
+  # === set_reverse_complement
+  # ========================================================================= #
+  def set_reverse_complement(i)
+    @right_input_field_aa.set_text(i)
+  end
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_left_input_field_for_dna
+  # ========================================================================= #
+  def consider_sanitizing_the_left_input_field_for_dna
+    _ = @left_input_field_dna.text?.dup
+    if _.include? 'U'
+      _.tr!('U','T')
+    end
+    _.upcase!
+    set_dna_sequence(_)
+  end
+
+  # ========================================================================= #
+  # === set_dna_sequence
+  #
+  # This method will set to the input-field on the left hand side.
+  # ========================================================================= #
+  def set_dna_sequence(
+      i = input?
+    )
+    if i.is_a? Array
+      i = i.join(' ').strip
+    end
+    unless i.include?('--') # Reject commandline-arguments, though.
+      @left_input_field_dna.set_text(i)
+    end
+  end
+
+  # ========================================================================= #
+  # === set_input
+  # ========================================================================= #
+  def set_input(i = '')
+    i = i.first if i.is_a? Array
+    i = i.to_s.dup
+    case i # Perform some sanitizing here. (case tag)
+    # ======================================================================= #
+    # === ubiquitin
+    # ======================================================================= #
+    when 'ubiquitin',
+         'ubi'
+      i = ''
+      set_these_aminoacids(::Bioroebe.return_ubiquitin_sequence)
+    end
+    @input = i
+  end
+
+  # ========================================================================= #
+  # === input?
+  # ========================================================================= #
+  def input?
+    @input
+  end
+
+  # ========================================================================= #
+  # === handle_commandline_arguments
+  # ========================================================================= #
+  def handle_commandline_arguments
+    input = input?
+    if input and !input.empty? and !input.include?('--') # Reject commandline-arguments, though.
+      set_dna_sequence(input)
+    end
+  end
+
+  # ========================================================================= #
+  # === create_hbox_containing_the_two_input_fields
+  #
+  # This method will combine the two widgets.
+  # ========================================================================= #
+  def create_hbox_containing_the_two_input_fields
+    
+    # ========================================================================= #
+    # In the middle will be a small arrow, though.
+    # ========================================================================= #
+    @hbox_containing_the_two_input_fields.maximal(@left_input_field_dna)
+    if use_gtk3?
+      @hbox_containing_the_two_input_fields.minimal(@event_box_containing_the_right_arrow)
+    end
+    @hbox_containing_the_two_input_fields.maximal(@right_input_field_aa)
+  end
+
+  # ========================================================================= #
+  # === do_sync_fields
+  #
+  # This method will sync between the two main widgets - the DNA input
+  # field on the left, and the reverse complement on the right side.
+  # ========================================================================= #
+  def do_sync_fields
+    consider_sanitizing_the_left_input_field_for_dna
+    _ = @left_input_field_dna.text?
+    if ::Bioroebe.const_defined? :Controller
+      # ===================================================================== #
+      # Ok, in this case we can store the dataset via a class-method.
+      # ===================================================================== #
+      ::Bioroebe::GUI::Controller.set_dna_sequence(_)
+    end
+    # ======================================================================= #
+    # Next, we must translate from DNA to the reverse complement sequence.
+    # ======================================================================= #
+    _ = ::Bioroebe.complement(_)
+    set_reverse_complement(_.reverse)
+    n_nucleotides = _.size
+    @label_n_nucleotides.set_text(
+      'This DNA sequence contains <b>'+n_nucleotides.to_s+'</b> nucleotides.'
+    )
+    @label_n_nucleotides.do_markify
+  end
+
+  # ========================================================================= #
+  # === return_dna_sequence_label
+  # ========================================================================= #
+  def return_dna_sequence_label
+    bold_label('DNA sequence')
+  end
+
+  # ========================================================================= #
+  # === let_the_left_entry_react_to_enter_events
+  # ========================================================================= #
+  def let_the_left_entry_react_to_enter_events
+    @left_input_field_dna.on_enter {
+      do_sync_fields unless @left_input_field_dna.text?.empty?
+    }
+  end
+
+  # ========================================================================= #
+  # === create_the_top_labels
+  #
+  # The two top labels denote which widget is the one for the DNA
+  # sequence, and which one is for the aminoacid sequence.
+  # ========================================================================= #
+  def create_the_top_labels
+    @dna_sequence_label = return_dna_sequence_label
+    @reverse_complement_sequence_label = return_reverse_complement_to_that_dna_sequence
+  end
+
+  # ========================================================================= #
+  # === return_reverse_complement_to_that_dna_sequence
+  # ========================================================================= #
+  def return_reverse_complement_to_that_dna_sequence
+    bold_label('Reverse complement to that DNA sequence')
+  end
+
+  # ========================================================================= #
+  # === create_button_trigger_conversion
+  # ========================================================================= #
+  def create_button_trigger_conversion
+    # ======================================================================= #
+    # === @button_trigger_conversion
+    # ======================================================================= #
+    @button_trigger_conversion = bold_button('_Trigger Conversion')
+    @button_trigger_conversion.clear_background
+    @button_trigger_conversion.lightgreen
+    @button_trigger_conversion.bblack1
+    @button_trigger_conversion.set_background_colour :whitesmoke
+    @button_trigger_conversion.on_hover(:lightblue)
+    @button_trigger_conversion.on_clicked {
+      do_sync_fields
+    }
+    # ======================================================================= #
+    # Use a tooltip as well for our button:
+    # ======================================================================= #
+    @button_trigger_conversion.hint = 
+      "Clicking on this button will convert from a <b>DNA</b>\n"\
+      "<b>sequence</b> to the <b>corresponding reverse "\
+      "complement sequence</b>.\n\nMake sure you input the DNA sequence "\
+      "on the left hand side."
+  end
+
+  # ========================================================================= #
+  # === create_input_fields
+  #
+  # These are the two input fields, also known as "gtk-entries".
+  # ========================================================================= #
+  def create_input_fields
+    # ======================================================================= #
+    # The DNA widget, a gtk-entry widget.
+    # ======================================================================= #
+    @left_input_field_dna = input_field
+    @left_input_field_dna.width_height(600, 20)
+    @left_input_field_dna.very_light_yellowish_background
+    @left_input_field_dna.hint = 'Input your DNA sequence here. Upon '\
+      'clicking on the arrow or hitting the <b>enter</b> key, the sequence is '\
+      'first converted to DNA, and then the reverse complement is '\
+      'calculated. Afterwards the result is shown on the right input '\
+      'field.'
+    # ======================================================================= #
+    # === The right widget.
+    # ======================================================================= #
+    @right_input_field_aa = input_field
+    @right_input_field_aa.very_light_yellowish_background
+    # ======================================================================= #
+    # The AA widget. Will be highlighted on a click event.
+    # ======================================================================= #
+    if @right_input_field_aa.respond_to? :on_click_event
+      @right_input_field_aa.on_click_event { :highlight_text }
+    end
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    super()
+    handle_commandline_arguments # This must come after the GUI skeleton was created.
+    let_the_left_entry_react_to_enter_events
+  end
+
+end; end; end

data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb

@@ -0,0 +1,402 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::LevenstheinDistanceModule
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb'
+# include Bioroebe::GUI::LevenstheinDistanceModule
+# Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module LevenstheinDistanceModule
+
+  alias e puts
+
+  require 'bioroebe/constants/GUIs.rb'
+  require 'bioroebe/string_matching/levensthein.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Levensthein Distance'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = 900
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 440
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_21
+
+  # ========================================================================= #
+  # === USE_THIS_MONOFONT
+  # ========================================================================= #
+  USE_THIS_MONOFONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET
+  #
+  # This constant can be used to designate the background colour to
+  # be used for the widget.
+  # ========================================================================= #
+  USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET = :white # :snow # :lavenderblush
+
+  # ========================================================================= #
+  # === INPUT_HINT
+  # ========================================================================= #
+  INPUT_HINT = 
+    "Hit the enter-key to compare the two sequences. Don't forget to "\
+    "assign two sequences first, e. g. ATG and then ATT, as an example."
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES
+  # ========================================================================= #
+  TEXT_COMPARE_THE_TWO_SEQUENCES = '_Compare the two sequences'
+
+  # ========================================================================= #
+  # === instantiate_a_new_levensthein_object
+  # ========================================================================= #
+  def instantiate_a_new_levensthein_object
+    # ======================================================================= #
+    # === @levensthein_object
+    # ======================================================================= #
+    @levensthein_object = ::Bioroebe::Levensthein.new(:dont_run_yet) {
+      :be_quiet
+    }
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    12
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === levensthein_object?
+  # ========================================================================= #
+  def levensthein_object?
+    @levensthein_object
+  end; alias levensthein levensthein_object? # === levensthein
+
+  # ========================================================================= #
+  # === set_entry2
+  # ========================================================================= #
+  def set_entry2(i)
+    entry2?.set_text(i.to_s) unless i and i.start_with? '--'
+  end
+
+  # ========================================================================= #
+  # === input_field_for_gap_cost?
+  # ========================================================================= #
+  def input_field_for_gap_cost?
+    @input_field_for_gap_cost
+  end
+
+  # ========================================================================= #
+  # === set_edit_distance
+  # ========================================================================= #
+  def set_edit_distance(i)
+    i = i.to_s
+    @label_for_the_edit_distance.set_text(i.rjust(2))
+    @label_for_the_edit_distance.make_bold
+  end
+
+  # ========================================================================= #
+  # === return_the_label_for_the_edit_distance
+  # ========================================================================= #
+  def return_the_label_for_the_edit_distance
+    label_for_the_edit_distance = text('0')
+    label_for_the_edit_distance.use_this_font = USE_THIS_MONOFONT
+    label_for_the_edit_distance.make_bold
+    return label_for_the_edit_distance
+  end
+
+  # ========================================================================= #
+  # === create_the_buttons
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_compare_the_two_strings
+    # ======================================================================= #
+    @button_compare_the_two_strings = bold_button(
+      TEXT_COMPARE_THE_TWO_SEQUENCES
+    )
+    @button_compare_the_two_strings.clear_background
+    @button_compare_the_two_strings.set_size_request(200, 40)
+    @button_compare_the_two_strings.set_border_width(4)
+    @button_compare_the_two_strings.bblack2
+    @button_compare_the_two_strings.hint =
+      'Click to compare the two sequences. Ideally use the '\
+      '<b>same length</b> for the two sequences. Make sure to '\
+      'click it once more after you are done, as the auto-calculation '\
+      'currently does NOT take the second entry into '\
+      'consideration.'
+    @button_compare_the_two_strings.on_hover(:lightcyan) 
+    @button_compare_the_two_strings.on_clicked {
+      do_compare_the_two_strings
+    }
+  end
+
+  # ========================================================================= #
+  # === return_hbox_containing_the_edit_distance
+  # ========================================================================= #
+  def return_hbox_containing_the_edit_distance(
+      small_label,
+      label_for_the_edit_distance
+    )
+    return hbox(
+      small_label, label_for_the_edit_distance
+    )
+  end
+
+  # ========================================================================= #
+  # === check_for_commandline_arguments
+  # ========================================================================= #
+  def check_for_commandline_arguments
+    if @commandline_arguments and @commandline_arguments.is_a?(Array)
+      unless @commandline_arguments.empty?
+        set_entry1(@commandline_arguments[0])
+        set_entry2(@commandline_arguments[1])
+      end
+    end
+  end; alias parse_the_commandline_arguments check_for_commandline_arguments # === parse_the_commandline_arguments
+
+  # ========================================================================= #
+  # === create_the_entries                           (entries tag, entry tag)
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # Next, add the two input-fields for our two nucleotide sequences.
+    # ======================================================================= #
+    # ======================================================================= #
+    # === @input_for_string1
+    # ======================================================================= #
+    @input_for_string1 = input
+    @input_for_string1.light_green_background
+    @input_for_string1.bblack1
+    @input_for_string1.css_class('pad4px')
+    @input_for_string1.on_enter { do_compare_the_two_strings }
+    @input_for_string1.use_this_font = USE_THIS_MONOFONT
+    @input_for_string1.hint = INPUT_HINT
+    # ======================================================================= #
+    # === @input_for_string2
+    # ======================================================================= #
+    @input_for_string2 = input
+    @input_for_string2.light_green_background
+    @input_for_string2.bblack1
+    @input_for_string2.css_class('pad4px')
+    @input_for_string2.on_enter { do_compare_the_two_strings }
+    @input_for_string2.use_this_font = USE_THIS_MONOFONT
+    @input_for_string2.hint = INPUT_HINT
+  end
+
+  # ========================================================================= #
+  # === create_the_third_row
+  # ========================================================================= #
+  def create_the_third_row
+    # ======================================================================= #
+    # === @text3
+    # ======================================================================= #
+    @text3 = bold_text_left_aligned(
+      'Score for gap (gap cost): '
+    )
+    @input_field_for_gap_cost = spinbutton(-50, 150)
+    @input_field_for_gap_cost.yellow_background
+    @input_field_for_gap_cost.bblack1
+    @input_field_for_gap_cost.set_value(
+      levensthein_object?.score_for_gaps?.to_s.to_i
+    )
+    @input_field_for_gap_cost.align_to_center
+    @input_field_for_gap_cost.on_changed {
+      recalculate_the_score
+    }
+  end
+
+  # ========================================================================= #
+  # === create_the_first_row
+  # ========================================================================= #
+  def create_the_first_row
+    # ======================================================================= #
+    # === @text1
+    # ======================================================================= #
+    @text1 = bold_text_left_aligned('Score for match (match cost): ')
+    # ======================================================================= #
+    # === @input_field_for_matches
+    # ======================================================================= #
+    @input_field_for_matches = spinbutton(-50, 150)
+    @input_field_for_matches.bblack1
+    @input_field_for_matches.center
+    @input_field_for_matches.yellow_background
+    @input_field_for_matches.set_size_request(100, 40)
+    @input_field_for_matches.set_value(
+      levensthein_object?.score_for_match?.to_s.to_i
+    )
+    @input_field_for_matches.align_to_center
+    @input_field_for_matches.on_changed {
+      recalculate_the_score
+    }
+  end
+
+  # ========================================================================= #
+  # === return_hbox4
+  # ========================================================================= #
+  def return_hbox4(
+      label_for_the_total_score = @label_for_the_total_score
+    )
+    # ======================================================================= #
+    # === Total score: label
+    # ======================================================================= #
+    small_label_for_total_score = bold_label('Total score:     ')
+    small_label_for_total_score.make_selectable
+    # ======================================================================= #
+    # === @hbox4
+    # ======================================================================= #
+    hbox4 = hbox(
+      small_label_for_total_score,
+      label_for_the_total_score
+    )
+    return hbox4 
+  end
+
+  # ========================================================================= #
+  # === create_the_labels
+  # ========================================================================= #
+  def create_the_labels
+    # ======================================================================= #
+    # === @label_for_the_total_score
+    # ======================================================================= #
+    @label_for_the_total_score = text('0')
+    @label_for_the_total_score.use_this_font = USE_THIS_MONOFONT
+    @label_for_the_total_score.make_bold
+    @label_for_the_total_score.make_selectable
+    # ======================================================================= #
+    # === @label_for_the_edit_distance
+    # ======================================================================= #
+    @label_for_the_edit_distance = return_the_label_for_the_edit_distance
+  end
+
+  # ========================================================================= #
+  # === set_entry1
+  # ========================================================================= #
+  def set_entry1(i)
+    entry1?.set_text(i.to_s) unless i and i.start_with? '--'
+  end
+
+  # ========================================================================= #
+  # === entry1?
+  # ========================================================================= #
+  def entry1?
+    @input_for_string1
+  end
+
+  # ========================================================================= #
+  # === entry2?
+  # ========================================================================= #
+  def entry2?
+    @input_for_string2
+  end
+
+  # ========================================================================= #
+  # === let_the_fist_entry_respond_to_on_changed_events
+  # ========================================================================= #
+  def let_the_fist_entry_respond_to_on_changed_events(
+      widget_to_use = @input_for_string1
+    )
+    if use_gtk?
+      widget_to_use.on_changed {
+        do_compare_the_two_sequences
+      }
+    else # else assume libui
+      # widget_to_use.on_changed {
+      #   do_compare_the_two_sequences
+      # }
+      # Does not work right now.
+    end
+  end
+
+  # ========================================================================= #
+  # === create_the_second_row
+  # ========================================================================= #
+  def create_the_second_row
+    # ======================================================================= #
+    # === Score for mismatch
+    # ======================================================================= #
+    @text2 = bold_text_left_aligned('Score for mismatch (mismatch cost): ')
+    # ======================================================================= #
+    # === @input_field_for_mismatches
+    # ======================================================================= #
+    @input_field_for_mismatches = spinbutton(-50, 150)
+    @input_field_for_mismatches.center
+    @input_field_for_mismatches.yellow_background
+    @input_field_for_mismatches.bblack1
+    @input_field_for_mismatches.set_size_request(100, 40)
+    @input_field_for_mismatches.set_value(
+      levensthein_object?.score_for_mismatch?.to_s.to_i
+    )
+    @input_field_for_mismatches.align_to_center
+    @input_field_for_mismatches.on_changed {
+      recalculate_the_score
+    }
+  end
+
+  # ========================================================================= #
+  # === do_compare_the_two_strings                                (click tag)
+  #
+  # This is the main action of the widget.
+  # ========================================================================= #
+  def do_compare_the_two_strings(
+      text1 = entry1?.text?,
+      text2 = entry2?.text?
+    )
+    # ======================================================================= #
+    # First capitalize the two entries:
+    # ======================================================================= #
+    entry1?.set_text(text1.upcase)
+    entry2?.set_text(text2.upcase)
+    @levensthein_object.reset_the_score
+    @levensthein_object.set_match_score(@input_field_for_matches.text?)
+    @levensthein_object.set_mismatch_score(@input_field_for_mismatches.text?)
+    @levensthein_object.set_gap_score(input_field_for_gap_cost?.text?)
+    @levensthein_object.set_string1(text1)
+    @levensthein_object.set_string2(text2)
+    @levensthein_object.run
+    set_edit_distance(
+      @levensthein_object.edit_distance?
+    )
+    total_score = @levensthein_object.total_score?.to_s
+    @label_for_the_total_score.set_text(total_score)
+    @label_for_the_total_score.make_bold
+  end; alias do_compare_the_two_sequences do_compare_the_two_strings # === do_compare_the_two_sequences
+       alias recalculate_the_score        do_compare_the_two_strings # === recalculate_the_score
+
+  # ========================================================================= #
+  # === return_the_edit_distance_label
+  # ========================================================================= #
+  def return_the_edit_distance_label
+    small_label = bold_label('Edit distance: ')
+    small_label.make_selectable
+    small_label.hint = 'This number tells us how many differences '\
+                       'exist between the two sequences at hand.'
+    return small_label
+  end
+
+end; end; end