Class: Bioroebe::GUI::Gtk::FastaTableWidget

Inherits:
Gtk::Frame
  • Object
show all
Includes:
Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb

Overview

Bioroebe::GUI::Gtk::FastaTableWidget

Constant Summary collapse

TITLE =
#

TITLE

#
'Fasta Table Widget'
WIDTH =
#

WIDTH

#
'75% or minimum 1000px'
HEIGHT =
#

HEIGHT

#
'50% or minimum 500px'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_20
HEADER_TO_USE_FOR_THE_TREE_VIEW =
#

HEADER_TO_USE_FOR_THE_TREE_VIEW

#
[
  'Local Path',
  'File size',
  'n nucleotides',
  '%GC'
]

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(commandline_arguments = ARGV, run_already = true) ⇒ FastaTableWidget

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 65

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  super(' FASTA files ')
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::FastaTableWidget.run

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 307

def self.run(
    i = ARGV
  )
  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
end

Instance Method Details

#append_this_fasta_file(i) ⇒ Object Also known as: append_this_file

#

append_this_fasta_file

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 259

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

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 110

def border_size?
  0
end

#clear_the_old_dataset ⇒ Object

#

clear_the_old_dataset

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 270

def clear_the_old_dataset
  @all_fasta_files.clear
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 217

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

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 141

def create_skeleton
  create_view
end

#create_view ⇒ Object

#

create_view

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 124

def create_view
  @list_store = gtk_list_store(String, String, String, String)
  # ======================================================================= #
  # === @view
  # ======================================================================= #
  @view = gtk_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

#deselect_the_main_treeview ⇒ Object

#

deselect_the_main_treeview

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 162

def deselect_the_main_treeview
  @view.deselect
end

#handle_CSS_rules ⇒ Object

#

handle_CSS_rules (CSS tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 169

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  more_CSS_then_apply_it '
treeview.view header button {
color: black;
background-color: oldlace;
border: 1px solid black;
margin: 1px;
}
'
end

#list_store? ⇒ Boolean Also known as: liststore?

#

list_store?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 117

def list_store?
  @list_store
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 155

def main_font?
  USE_THIS_FONT
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 240

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

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 103

def padding?
  2
end

#populate_the_list_store_with_the_default_dataset ⇒ Object

#

populate_the_list_store_with_the_default_dataset

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 185

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

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 80

def reset
  infer_the_namespace
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @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

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 232

def run
  menu # Must come before the super() call.
  super()
end

#second_column? ⇒ Boolean

#

second_column?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 148

def second_column?
  @view.columns?[1]
end

#style_the_label_widget ⇒ Object

#

style_the_label_widget

#

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# File 'lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb', line 277

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