Module: Bioroebe::GUI::ShowCodonUsageModule

Included in:
Gtk::ShowCodonUsage, LibUI::ShowCodonUsage
Defined in:
lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb

Constant Summary collapse

TITLE =
#

TITLE

#
'Show Codon Usage'
WIDTH =
#

WIDTH

#
'65% or minimum 600px'
HEIGHT =
#

HEIGHT

#
'50%'
TEST_SEQUENCE =
#

TEST_SEQUENCE

#
'AGACGTACGTACGTCAGTCAGTACGTACTGATCGTAGCTAGCTACGTGACC'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_20

Instance Method Summary collapse

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 69

def border_size?
  4
end

#create_box_top_five_codons ⇒ Object

#

create_box_top_five_codons

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 162

def create_box_top_five_codons
  if use_gtk3?
    @box_top_five_codons = gtk_box # This is a Gtk::Box. It will contain @label_top_five_codons.
  else
    @box_top_five_codons = padded_vbox
  end
  @box_top_five_codons.set_font(:hack_20)
end

#create_the_label_showing_n_nucleotides ⇒ Object

#

create_the_label_showing_n_nucleotides

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 188

def create_the_label_showing_n_nucleotides
  @label_showing_n_nucleotides = label
  @label_showing_n_nucleotides.set_font('Bitstream Vera Sans 22')
end

#create_the_label_top_five_codons ⇒ Object

#

create_the_label_top_five_codons

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 174

def create_the_label_top_five_codons
  @label_top_five_codons = label
end

#create_the_main_entry ⇒ Object

#

create_the_main_entry (entry tag)

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 196

def create_the_main_entry
  # ======================================================================= #
  # === @entry1
  # ======================================================================= #
  @entry1 = entry
  @entry1.set_text(@use_this_as_the_input_sequence)
  @entry1.set_font(:hack_20)
  @entry1.hint =
    "This entry should contain the nucleotide sequence that "\
    "the user wants to analyse. \n\nAs soon as the user has "\
    "finished the sequence, the '<b>enter</b>' key can be used "\
    "to analyse the sequence."
  @entry1.on_enter {
    do_the_conversion_then_update_the_label_as_well
  } if @entry1.respond_to? :on_enter
end

#create_the_text_view ⇒ Object

#

create_the_text_view

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 181

def create_the_text_view
  @text_view = text_view
end

#do_the_conversion(i = @entry1.text?) ⇒ Object

#

do_the_conversion

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 112

def do_the_conversion(
    i = @entry1.text?
  )
  # ======================================================================= #
  # First, we remove any numbers from the given input at hand:
  # ======================================================================= #
  shortened_sequence = ::Bioroebe.remove_numbers_from(i)
  unless i == shortened_sequence
    i = shortened_sequence
    @entry1.set_text(i)
  end
  hash = Bioroebe::ShowCodonUsage.new(i) { :be_quiet }.result?
  _ = ''.dup     
  hash.each_pair {|key, value|
    _ << "#{key}: #{value}\n"
  }
  text_for_the_label = "The <b>top 5 codons</b> are:\n\n".dup
  keys = hash.keys[0 .. 4] # Grab the first 5 entries.
  hash.each_pair {|key, value|
    if keys.include? key
      if use_gtk3?
        text_for_the_label << '<b>'+key.to_s+'</b>: '+value.to_s+"\n"
      else
        text_for_the_label << key.to_s+': '+value.to_s+"\n"
      end
    end
  }
  @label_top_five_codons.set_text(
    text_for_the_label
  )
  @label_top_five_codons.do_markify # Apply any markup rules here.
  @text_view.set_text(_.strip)
end

#do_the_conversion_then_update_the_label_as_well ⇒ Object

#

do_the_conversion_then_update_the_label_as_well

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 104

def do_the_conversion_then_update_the_label_as_well
  do_the_conversion
  update_the_label_as_well
end

#handle_the_commandline_arguments(i = @commandline_arguments) ⇒ Object

#

handle_the_commandline_arguments

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 149

def handle_the_commandline_arguments(i = @commandline_arguments)
  i.each {|entry|
    if File.file? entry
      @use_this_as_the_input_sequence = File.read(entry).
                                        strip.delete("\n").delete(' ')
      sync_the_input_sequence_onto_the_main_entry
    end
  }
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 62

def padding?
  8
end

#reset_the_shared_module ⇒ Object

#

reset_the_shared_module

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 49

def reset_the_shared_module
  # ======================================================================= #
  # === @use_this_as_the_input_sequence
  #
  # Assign a dummy-sequence for startup. This can be changed via the
  # commandline-input.
  # ======================================================================= #
  @use_this_as_the_input_sequence = TEST_SEQUENCE
end

#sync_the_input_sequence_onto_the_main_entry(i = @use_this_as_the_input_sequence) ⇒ Object

#

sync_the_input_sequence_onto_the_main_entry

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 91

def sync_the_input_sequence_onto_the_main_entry(
    i = @use_this_as_the_input_sequence
  )
  if i
    @entry1.set_text(i)
    update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(i)
    do_the_conversion_then_update_the_label_as_well unless i.empty?
  end
end

#update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(i = @entry1.text?.size.to_s) ⇒ Object Also known as: update_the_label_as_well

#

update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence

#

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# File 'lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb', line 76

def update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(
    i = @entry1.text?.size.to_s
  )
  if use_gtk3?
    _ = "n nucleotides: <b>#{i}</b>"
  else
    _ = "n nucleotides: #{i}"
  end
  @label_showing_n_nucleotides.set_text(_)
  @label_showing_n_nucleotides.do_markify
end