bioroebe 0.10.80 → 0.12.24

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

@@ -8,6 +8,8 @@
 #
 #  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.
 # =========================================================================== #
 # require 'bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb'
 # Bioroebe::GUI::Gtk::FastaTableWidget.run
@@ -27,11 +29,6 @@ class FastaTableWidget < ::Gtk::Frame # === Bioroebe::GUI::Gtk::FastaTableWidget
   require 'gtk_paradise/requires/require_the_base_module.rb'
   include ::Gtk::BaseModule
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === TITLE
   # ========================================================================= #
@@ -81,16 +78,21 @@ class FastaTableWidget < ::Gtk::Frame # === Bioroebe::GUI::Gtk::FastaTableWidget
   # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
+    infer_the_namespace
     reset_the_internal_variables
     # ======================================================================= #
     # === @configuration
     # ======================================================================= #
-    @configuration = [true, __dir__, NAMESPACE]
+    @configuration = [true, __dir__, namespace?]
     title_width_height_font(TITLE, WIDTH, HEIGHT, main_font?)
     # ======================================================================= #
     # === @use_this_directory
     # ======================================================================= #
     @use_this_directory = ::Bioroebe.log_directory?+'fasta/'
+    # ======================================================================= #
+    # === @all_fasta_files
+    # ======================================================================= #
+    @all_fasta_files = Dir[@use_this_directory+'*.fasta']
     handle_CSS_rules
     infer_the_size_automatically
   end
@@ -109,6 +111,13 @@ class FastaTableWidget < ::Gtk::Frame # === Bioroebe::GUI::Gtk::FastaTableWidget
     0
   end
 
+  # ========================================================================= #
+  # === list_store?
+  # ========================================================================= #
+  def list_store?
+    @list_store
+  end; alias liststore? list_store? # === liststore?
+
   # ========================================================================= #
   # === create_view
   # ========================================================================= #
@@ -122,6 +131,7 @@ class FastaTableWidget < ::Gtk::Frame # === Bioroebe::GUI::Gtk::FastaTableWidget
     @view.make_sortable
     @view.the_headers_can_be_moved
     @view.enable_search
+    @view.deselect_on_right_click_event
     deselect_the_main_treeview
   end
 
@@ -154,7 +164,7 @@ class FastaTableWidget < ::Gtk::Frame # === Bioroebe::GUI::Gtk::FastaTableWidget
   end
 
   # ========================================================================= #
-  # === handle_CSS_rules
+  # === handle_CSS_rules                                            (CSS tag)
   # ========================================================================= #
   def handle_CSS_rules
     use_gtk_paradise_project_css_file
@@ -170,21 +180,10 @@ treeview.view header button {
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === populate_the_list_store_with_the_default_dataset
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    set_border_width(15)
-    _ = label_widget
-    _.set_text('FASTA files')
-    _.left_align
-    _.fonty(main_font?)
-    _.make_bold
-    _.css_class('darkblue')
-    _.pad4px
-    all_fasta_files = Dir[@use_this_directory+'*.fasta']
-    
-    array = all_fasta_files.map {|path|
+  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
@@ -210,20 +209,98 @@ treeview.view header button {
     }
 
     populate_this_list_store_with_that_array4(@list_store, array)
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    set_border_width(15)
+    populate_the_list_store_with_the_default_dataset
     scrolled_window = gtk_scrolled_window(@view) { :always }
     scrolled_window.width_height(540, 500)
     vbox = gtk_vbox
     vbox.minimal(scrolled_window, 14)
     add(vbox)
+    style_the_label_widget
   end
 
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
+    menu # Must come before the super() call.
     super()
   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
+
+  # ========================================================================= #
+  # === 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
+    }
+    _.minimal event_box, 10
+    self.label_widget = _
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::Gtk::FastaTableWidget.run
   # ========================================================================= #
@@ -233,9 +310,9 @@ treeview.view header button {
     require 'gtk_paradise/run'
     _ = ::Bioroebe::GUI::Gtk::FastaTableWidget.new(i)
     r = ::Gtk.run
+    _.set_parent_widget(_)
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
 end; end; end; end

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

@@ -335,8 +335,7 @@ pp result
     _ = ::Bioroebe::GUI::Gtk::FormatConverter.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
 end; end; end; end

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

@@ -171,8 +171,7 @@ class Gene < ::Gtk::Box # === Bioroebe::GUI::Gtk::Gene
     _ = ::Bioroebe::GUI::Gtk::Gene.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
 end; end; end; end

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

@@ -152,30 +152,6 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     @entry_on_top
   end
 
-  # ========================================================================= #
-  # === compare_the_two_sequences
-  #
-  # This is the method that will compare the two sequences.
-  # ========================================================================= #
-  def compare_the_two_sequences
-    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
-    @entry_n_differences.set_text(
-      hamming_distance_object.n_differences?.to_s
-    )
-  end; alias do_compare                   compare_the_two_sequences # === do_compare
-       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
-
-  # ========================================================================= #
-  # === consider_sanitizing_the_input
-  # ========================================================================= #
-  def consider_sanitizing_the_input
-    # ======================================================================= #
-    # The following two lines were added as of 07.05.2020.
-    # ======================================================================= #
-    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
-    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
-  end
-
   # ========================================================================= #
   # === create_entries                               (entries tag, entry tag)
   # ========================================================================= #
@@ -211,10 +187,10 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
         # This is ok.
       when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
         unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
-          widget.set_text(old_text)
+          widget.set_text(old_text.upcase)
         end
       end
-    }
+    } if false # disabled as of August 2022.
     # ======================================================================= #
     # And keep things upcased here:
     # ======================================================================= #
@@ -269,10 +245,10 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     # ======================================================================= #
     # === The top box
     # ======================================================================= #
-    @top_box = gtk_vbox
+    @top_box = vbox
 
     @label_on_top = bold_label(USE_THIS_TITLE)
-    @label_on_top.fancy_tooltips = 
+    @label_on_top.hint = 
       "Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
       "can be accepted as input."
     # ======================================================================= #
@@ -334,6 +310,44 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     show_all
   end
 
+  # ========================================================================= #
+  # === compare_the_two_sequences
+  #
+  # This is the method that will compare the two sequences.
+  # ========================================================================= #
+  def compare_the_two_sequences
+    do_upcase_all_entries
+    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
+    @entry_n_differences.set_text(
+      hamming_distance_object.n_differences?.to_s
+    )
+  end; alias do_compare                   compare_the_two_sequences # === do_compare
+       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
+
+  # ========================================================================= #
+  # === do_upcase_all_entries
+  # ========================================================================= #
+  def do_upcase_all_entries
+    [
+      @entry_on_top,
+      @entry_on_bottom
+    ].each {|entry|
+      entry.do_upcase
+    }
+  end
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_input
+  # ========================================================================= #
+  def consider_sanitizing_the_input
+    # ======================================================================= #
+    # The following two lines were added as of 07.05.2020.
+    # ======================================================================= #
+    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
+    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
+    do_upcase_all_entries
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
@@ -359,8 +373,7 @@ class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance
     r = ::Gtk.run
     r << _
     r.modify_background(:normal, :mintcream)
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::HammingDistance.run_gtk3_widget
 
 end; end; end; end

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

@@ -163,8 +163,7 @@ class LevenstheinDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::LevenstheinDist
     _ = ::Bioroebe::GUI::Gtk::LevenstheinDistance.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::LevenstheinDistanceModule.start_gui_application
        self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::LevenstheinDistance.run_gtk3_widget
 

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

@@ -128,7 +128,7 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   # ========================================================================= #
   def create_skeleton
     create_buttons
-    create_labels
+    create_the_labels
     create_entry
   end
 
@@ -163,46 +163,6 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     @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
   # ========================================================================= #
@@ -217,13 +177,6 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     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
@@ -283,26 +236,13 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   # === update_this_sequence_contains_n_nucleotides
   # ========================================================================= #
   def update_this_sequence_contains_n_nucleotides(
-      i = return_how_many_nucleotides_this_sequence_contains
+      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
   # ========================================================================= #
@@ -350,6 +290,13 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     end
   end
 
+  # ========================================================================= #
+  # === update_the_main_sequence_variable
+  # ========================================================================= #
+  def update_the_main_sequence_variable
+    @sequence = @entry_input_sequence.text?.delete('-')
+  end
+
   # ========================================================================= #
   # === connect_skeleton                                        (connect tag)
   # ========================================================================= #
@@ -365,15 +312,9 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     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>'
-      )
-    )
+    minimal(@label_GC_content)
+    minimal(@label_AT_content)
     hbox = gtk_hbox
     hbox.maximal(@button_reset,                    1)
     hbox.maximal(@button_reset_the_input_sequence, 1)
@@ -399,6 +340,113 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     apply_the_CSS_rules
   end
 
+  # ========================================================================= #
+  # === create_the_labels
+  # ========================================================================= #
+  def create_the_labels
+    # ======================================================================= #
+    # === @label_GC_content
+    # ======================================================================= #
+    @label_GC_content = left_aligned_label
+    @label_GC_content.make_selectable
+    # ======================================================================= #
+    # === @label_AT_content
+    # ======================================================================= #
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_AT_content = left_aligned_label(
+      'The <b>AT content</b> (A+T) is: <b>'+
+      (100.0 - _.to_f).round(1).to_s+'%</b>'
+    )
+    @label_AT_content.make_selectable
+    # ======================================================================= #
+    # === @text_this_sequence_contains
+    # ======================================================================= #
+    @text_this_sequence_contains = left_aligned_label
+    @text_this_sequence_contains.make_selectable
+  end
+
+  # ========================================================================= #
+  # === create_entry                                              (entry tag)
+  # ========================================================================= #
+  def create_entry
+    # ======================================================================= #
+    # === @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
+
+  # ========================================================================= #
+  # === 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
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
@@ -417,8 +465,7 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     _ = ::Bioroebe::GUI::Gtk::NucleotideAnalyser.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
 end; end; end; end

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

@@ -349,8 +349,7 @@ class PrimerDesignWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::PrimerDesignWidg
     _ = ::Bioroebe::GUI::Gtk::PrimerDesignWidget.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
   # ========================================================================= #