Class: Bioroebe::ShowNucleotideSequence

Inherits:
Sequence show all
Includes:
ColoursForBase, CommandlineArguments, InferTheNamespaceModule, InternalHashModule
Defined in:
lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb

Overview

Bioroebe::ShowNucleotideSequence

Constant Summary collapse

USE_THIS_COLOUR =
#

Bioroebe::ShowNucleotideSequence::USE_THIS_COLOUR

This colour is usually “steelblue”.

#
USE_THIS_COLOUR_FOR_DNA

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Sequence

Bioroebe::Sequence::REMOVE_INVALID_CHARACTERS, Bioroebe::Sequence::SHALL_WE_UPCASE

Class Method Summary collapse

Instance Method Summary collapse

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods inherited from Sequence

#automatic_support_for_nucleotides, #description?, #index, #infer_type, #is_DNA?, #is_RNA?, #is_a_protein?, #is_a_protein_now, #map, #n_uracil?, #randomize, #remove_invalid_entries_from_the_dna_sequence, #remove_invalid_entries_from_the_dna_sequence!, #return_string_nucleotides_or_aminoacids, #sanitize_dataset, #sanitize_rna, #save_sequence_to_this_file, sequence_from_file, #set_description, #set_dna, #set_protein, #set_rna, #set_save_file, #set_sequence, #set_type, #shall_we_upcase?, #size?, #to_genbank, #to_regexp, #type?

Methods inherited from RawSequence

#+, #<<, #[]=, #calculate_levensthein_distance, #chars?, #complement, #composition?, #count, #delete, #delete!, #downcase, #each_char, #empty?, #find_substring_indices, #first_position=, #freeze, #gsub, #gsub!, #include?, #insert_at_this_position, #prepend, #remove_n_characters_from_the_left_side, #reverse, #reverse!, #reverse_complement, #scan, #set_raw_sequence, #shuffle, #size?, #split, #start_with?, #strip, #subseq, #to_s, #to_str, #tr!, #upcase!

Constructor Details

#initialize(commandline_arguments = nil, run_already = true) ⇒ ShowNucleotideSequence

#

initialize

The first argument to this class will become the sequence that is to be displayed, such as ‘ATCG’.

#


55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 55

def initialize(
    commandline_arguments = nil,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # === Handle Symbols next
    # ===================================================================== #
    if yielded.is_a? Symbol
      case yielded
      # =================================================================== #
      # === :colourize_start_codon
      # =================================================================== #
      when :colourize_start_codon
        do_colourize_the_start_codon
      end
    # ===================================================================== #
    # === Handle Hashes next
    # ===================================================================== #
    elsif yielded.is_a? Hash
      # =================================================================== #
      # === :colourize_this_subsequence
      #
      # This entry point can be used to supply any other subsequence
      # that the user wants to colourize.
      #
      # Usage example:
      #
      #   {{ colourize_this_subsequence: 'ATG' }}
      #
      # =================================================================== #
      if yielded.has_key? :colourize_this_subsequence
        search_for_this_substring(
          yielded[:colourize_this_subsequence]
        )
      end
    end
  end
  case run_already
  # ======================================================================= #
  # === :do_not_run_yet
  # ======================================================================= #
  when :do_not_run_yet,
       :do_not_run
    run_already = false
  # ======================================================================= #
  # === :do_not_report_anything
  # ======================================================================= #
  when :do_not_report_anything
    do_not_report_anything
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::ShowNucleotideSequence[]

#


651
652
653
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 651

def self.[](i = ARGV)
  new(i)
end

Instance Method Details

#array_colourize_these_substrings? ⇒ Boolean

#

array_colourize_these_substrings?

#

Returns:

  • (Boolean) 


310
311
312
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 310

def array_colourize_these_substrings?
  @internal_hash[:array_colourize_these_substrings]
end

#clear_padding ⇒ Object

#

clear_padding

#


264
265
266
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 264

def clear_padding
  set_padding_to_use('')
end

#colourize_dna_sequence(i = '') ⇒ Object Also known as: colour_for_nucleotides, colourize_rna_sequence

#

colourize_dna_sequence

This method should be used to colourize the primary DNA/RNA sequence.

#


187
188
189
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 187

def colourize_dna_sequence(i = '')
  ::Colours.send(USE_THIS_COLOUR, i.dup)
end

#display_with_prior_formatting(i = sequence_for_display?, , &block) ⇒ Object

#

display_with_prior_formatting

#


572
573
574
575
576
577
578
579
580
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 572

def display_with_prior_formatting(
    i = sequence_for_display?,
    &block
  )
  do_show_the_ruler
  clear_padding
  format_this_nucleotide_sequence(i, &block)
  report(i) # Need to invoke the original method. Before May 2020 this was display().
end

#do_colourize_the_start_codon ⇒ Object

#

do_colourize_the_start_codon

#


644
645
646
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 644

def do_colourize_the_start_codon
  add_this_substring('ATG')
end

#do_not_report_anything ⇒ Object

#

do_not_report_anything

#


171
172
173
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 171

def do_not_report_anything
  @internal_hash[:shall_we_report] = false
end

#do_properly_display_this_nucleotide_sequence(i = sequence_for_display?, , padding_to_use = padding_to_use?, , show_ruler = show_ruler?, , show_five_prime_leader = show_five_prime_leader?, , show_three_prime_trailer = show_three_prime_trailer?, , &block) ⇒ Object Also known as: display, report_this_sequence, report, format_this_nucleotide_sequence, format_this_string, format

#

do_properly_display_this_nucleotide_sequence (display tag, report tag)

The first argument to this method is the sequence (DNA or RNA) that should be displayed.

This method will only do the reporting by default - not a new format-operation, unless a block has been given to it.

Usage example for this method:

@show_nucleotide_sequence.report_this_sequence(input) {{ padding_to_use: padding? }}
#


335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 335

def do_properly_display_this_nucleotide_sequence(
    i                        = sequence_for_display?,
    padding_to_use           = padding_to_use?,
    show_ruler               = show_ruler?,
    show_five_prime_leader   = show_five_prime_leader?,
    show_three_prime_trailer = show_three_prime_trailer?,
    &block
  )
  # ======================================================================= #
  # === result
  #
  # The variable called result will contain our modified sequence that
  # is to be displayed on the commandline. It should come first, as
  # other parts in this method may append onto it.
  # ======================================================================= #
  result = ''.dup
  if i.nil? and string?
    i = string?
  end
  
  # ======================================================================= #
  # == Handle blocks given next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :use_colours
    # ===================================================================== #
    when :use_colours
      disable_colours { :be_quiet }
    # ===================================================================== #
    # === :colourize_start_codon
    # ===================================================================== #
    when :colourize_start_codon
      do_colourize_the_start_codon
    # ===================================================================== #
    # === :show_ruler
    # ===================================================================== #
    when :show_ruler
      show_ruler = true
    # ===================================================================== #
    # === :without_colours
    # ===================================================================== #
    when :without_colours
      show_ruler = yielded
      do_show_the_ruler
    # ===================================================================== #
    # === :complementary_strand
    #
    # When we use this entry point, specifically, we will also
    # revert leader and trailer.
    # ===================================================================== #
    when :complementary_strand
      result << return_three_prime_leader
      i = complementary_strand(
        i.chars
      )
      show_five_prime_leader = false
      show_three_prime_trailer = :use_five_prime_trailer
    # ===================================================================== #
    # === :to_rna
    # ===================================================================== #
    when :to_rna,
         :rna
      i = to_rna(i)
    else
      # =================================================================== #
      # === Handle Hashes past this point
      # =================================================================== #
      if yielded.is_a? Hash
        # ================================================================= #
        # === :use_colours
        # ================================================================= #
        if yielded.has_key? :use_colours
          set_use_colours(yielded.delete(:use_colours))
        end
        # ================================================================= #
        # === :use_this_as_padding
        # ================================================================= #
        if yielded.has_key? :use_this_as_padding
          padding_to_use = yielded[:use_this_as_padding]
        end
        # ================================================================= #
        # === :colourize_this_subsequence
        # ================================================================= #
        if yielded.has_key? :colourize_this_subsequence
          set_search_for(yielded[:colourize_this_subsequence])
        end
        # ================================================================= #
        # === :ruler
        # ================================================================= #
        if yielded.has_key? :ruler
          _ = yielded.delete(:ruler)
          case _
          when :without_colours
            show_ruler = _
          end
        end
      end
    end
  end
  # ======================================================================= #
  # Support for dashed-form display comes next, after we colourized
  # substrings:
  # ======================================================================= #
  if show_in_dashed_form?
    use_this_token_for_rejoining = '-' # This will be the token used for re-joining.
    group_by_n_tokens = 3
    n_times = '.' * group_by_n_tokens.to_i # This line is important to determine the regexp next.
    use_this_regex = /#{n_times}/ # Our regex to be used for splitting.
    i = i.scan(use_this_regex).
          join(use_this_token_for_rejoining) # And re-join it here.
  end
  result << rev if use_colours?
  result << "#{padding_to_use}"
  # ======================================================================= #
  # Consider showing the ruler next, before determining whether we
  # will show the 5' prime leader, as well as before we colourize the
  # substrings:
  # ======================================================================= #
  if show_ruler
    print "#{rev}#{padding_to_use}"
    if show_five_prime_leader
      ee(' '*"#{leader?}".size)
    end
    e ::Bioroebe::Ruler.new(i, :default) {{
        ruler: show_ruler
      }}.result_as_string?
  end
  # ======================================================================= #
  # === Show the 5' leader next:
  # ======================================================================= #
  if show_five_prime_leader
    result << "#{leader?}"
  end
  # ======================================================================= #
  # === Handle blocks given to the method
  # ======================================================================= #
  if block_given?
    yielded = yield
    if yielded.is_a? Symbol
      case yielded
      # =================================================================== #
      # === :piped
      # =================================================================== #
      when :piped
        i.gsub!(/(...)/, "\\1|") # Add | at every third position.
      # =================================================================== #
      # === :colourize_start_codon
      #
      # When a block is given then we actually have to re-format the main
      # string again.
      # =================================================================== #
      when :colourize_start_codon
        do_colourize_the_start_codon
      # =================================================================== #
      # === :complementary_strand
      # =================================================================== #
      when :complementary_strand
        i = ::Bioroebe.complementary_strand(i)
      end
    elsif yielded.is_a? Hash
      # =================================================================== #
      # === :colourize_this_subsequence
      # =================================================================== #
      if yielded.has_key? :colourize_this_subsequence
        search_for_this_substring(
          yielded[:colourize_this_subsequence]
        )
      end
      # =================================================================== #
      # === :show_piped_output
      # =================================================================== #
      if yielded.has_key?(:show_piped_output) and
        (yielded[:show_piped_output] == true)
        i.gsub!(/(...)/, "\\1|") # Add | at every third position.
      end
      # =================================================================== #
      # === :padding_to_use
      # =================================================================== #
      if yielded.has_key? :padding_to_use
        set_padding(yielded.delete(:padding_to_use))
      end
    end
  end
  # ======================================================================= #
  # === Colourize substrings
  #
  # We will next colourize the nucleotides that we determined should
  # be colourized, in particular ATG start codons.
  # ======================================================================= #
  if use_colours? and !array_colourize_these_substrings?.empty?
    # ===================================================================== #
    # In this case we will try to colourize substrings.
    # ===================================================================== #
    array_colourize_these_substrings?.each {|this_substring|
      if i and i.include?(this_substring) # Only make a change if the substring is part of the main sequence.
        i = i.dup if i.frozen?
        i.prepend(return_colour_for_the_dna_sequence)
        i.gsub!(
          /(#{this_substring})/,
          crimson('\1')+
          remove_trailing_escape_part(colour_for_nucleotides)
        )
      end
    }
  end
  result << colourize_dna_sequence(i)
  # ======================================================================= #
  # Consider showing the 3' trailer next.
  # ======================================================================= #
  if show_three_prime_trailer
    case show_three_prime_trailer
    # ===================================================================== #
    # === :use_five_prime_trailer
    #
    # In this case we'll use a 5' trailer, so the reverse display is
    # used here.
    # ===================================================================== #
    when :use_five_prime_trailer
      result << "#{rev} - 5'"
    else
      result << "#{rev}#{trailer?}"
    end
  end
  e result if may_we_report?
end

#do_show_the_ruler ⇒ Object

#

do_show_the_ruler

#


303
304
305
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 303

def do_show_the_ruler
  @internal_hash[:show_ruler] = true
end

#main_sequence_as_string? ⇒ Boolean

#

main_sequence_as_string?

#

Returns:

  • (Boolean) 


317
318
319
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 317

def main_sequence_as_string?
  sequence_for_display?.to_s
end

#menu(i = commandline_arguments?.select {|inner_entry| inner_entry.start_with? '--' }) ⇒ Object

#

menu (menu tag)

#


585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 585

def menu(
    i = commandline_arguments?.select {|inner_entry| inner_entry.start_with? '--' }
  )
  if i and i.is_a?(Array)
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --ruler
    #
    # This can be invoked by doing something like:
    #
    #   shownucleotidesequence ATGAAAAGTCAGTCAGGTCACATTGCACGACACACATAAA --ruler
    #
    # ===================================================================== #
    when /^-?-?ruler$/i
      @internal_hash[:show_ruler] = true
    end
  end
end

#padding_to_use? ⇒ Boolean Also known as: padding?

#

padding_to_use?

#

Returns:

  • (Boolean) 


257
258
259
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 257

def padding_to_use?
  @internal_hash[:padding_to_use]
end

#reset ⇒ Object

#

reset (reset tag)

#


120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 120

def reset
  reset_the_internal_hash # This should come first here.
  infer_the_namespace
  enable_colours # This has to be called, in order to get colours-support.
  # ======================================================================= #
  # === :padding_to_use
  #
  # How much padding to use when displaying something.
  # ======================================================================= #
  set_padding_to_use(7) # 7 * ' '.
  # ======================================================================= #
  # === @internal_hash[:show_in_dashed_form]
  #
  # The dashed form is e. g. "ATG-GGC-CGC". By default this is not
  # enabled.
  # ======================================================================= #
  @internal_hash[:show_in_dashed_form] = false
  # ======================================================================= #
  # === :sequence_for_display
  #
  # Must be nil initially.
  # ======================================================================= #
  @internal_hash[:sequence_for_display] = nil
  # ======================================================================= #
  # === @internal_hash[:show_ruler]
  #
  # The next variable determines whether a ruler will be displayed
  # on top of the nucleotide-sequence.
  # ======================================================================= #
  @internal_hash[:show_ruler] = false
  # ======================================================================= #
  # === :show_five_prime_leader
  # ======================================================================= #
  @internal_hash[:show_five_prime_leader] = true
  # ======================================================================= #
  # === :shall_we_report
  # ======================================================================= #
  @internal_hash[:shall_we_report] = true
  # ======================================================================= #
  # === :show_three_prime_trailer
  # ======================================================================= #
  @internal_hash[:show_three_prime_trailer] = true
  # ======================================================================= #
  # === @internal_hash[:array_colourize_these_substrings]
  # ======================================================================= #
  @internal_hash[:array_colourize_these_substrings] = []
end

#return_colour_for_the_dna_sequence ⇒ Object

#

return_colour_for_the_dna_sequence

#


195
196
197
198
199
200
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 195

def return_colour_for_the_dna_sequence
  result = Colours.remove_trailing_code(
    ::Colours.send(USE_THIS_COLOUR)
  )
  return result
end

#return_five_prime_leader ⇒ Object Also known as: leader?

#

return_five_prime_leader

#


230
231
232
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 230

def return_five_prime_leader
  "5' - "
end

#return_three_prime_leader ⇒ Object

#

return_three_prime_leader

#


223
224
225
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 223

def return_three_prime_leader
  "3' - "
end

#return_three_prime_trailer ⇒ Object Also known as: trailer?

#

return_three_prime_trailer

#


237
238
239
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 237

def return_three_prime_trailer
  " - 3'"
end

#run ⇒ Object

#

run (run tag)

#


626
627
628
629
630
631
632
633
634
635
636
637
638
639
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 626

def run
  menu(
    commandline_arguments?
  )
  _ = first_argument?
  if _.nil? or _.empty?
    erev 'Nothing to display.'
  else
    set_sequence_for_display(_) # Always set the sequence in this case.
    if shall_we_report?
      do_properly_display_this_nucleotide_sequence(_)
    end
  end
end

#search_for_this_substring(i) ⇒ Object Also known as: set_search_for, add_this_substring

#

search_for_this_substring

This method can be used to search for substrings, aka matches.

#


611
612
613
614
615
616
617
618
619
620
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 611

def search_for_this_substring(i)
  if i.is_a? Array
    i.each {|entry| search_for_this_substring(entry) }
  else
    unless @internal_hash[:array_colourize_these_substrings].include? i
      @internal_hash[:array_colourize_these_substrings] << i
      @internal_hash[:array_colourize_these_substrings].compact! # Added in 2021, to remove possible nil-values.
    end
  end
end

#sequence_for_display? ⇒ Boolean Also known as: formatted_sequence?, sequence_for_display

#

sequence_for_display?

This method will return the sequence that will be displayed on the commandline, for instance.

#

Returns:

  • (Boolean) 


215
216
217
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 215

def sequence_for_display?
  @internal_hash[:sequence_for_display]
end

#set_padding_to_use(i = '') ⇒ Object Also known as: set_padding

#

set_padding_to_use

#


244
245
246
247
248
249
250
251
252
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 244

def set_padding_to_use(
    i = ''
  )
  if i and i.to_s =~ /^\d+$/i # And "if it is a number, and a number only".
    i = ' ' * i.to_i
  end
  i = i.dup if i and i.frozen?
  @internal_hash[:padding_to_use] = i
end

#set_sequence_for_display(i) ⇒ Object Also known as: set_this_sequence

#

set_sequence_for_display

This is the raw sequence that will be displayed. Only store the nucleotides, NOT 5’ and 3’ primer/trailer.

#


289
290
291
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 289

def set_sequence_for_display(i)
  @internal_hash[:sequence_for_display] = i
end

#shall_we_report? ⇒ Boolean Also known as: may_we_report?, shall_we_report

#

shall_we_report?

#

Returns:

  • (Boolean) 


278
279
280
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 278

def shall_we_report?
  @internal_hash[:shall_we_report]
end

#show_five_prime_leader? ⇒ Boolean

#

show_five_prime_leader?

#

Returns:

  • (Boolean) 


178
179
180
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 178

def show_five_prime_leader?
  @internal_hash[:show_five_prime_leader]
end

#show_in_dashed_form? ⇒ Boolean

#

show_in_dashed_form?

#

Returns:

  • (Boolean) 


205
206
207
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 205

def show_in_dashed_form?
  @internal_hash[:show_in_dashed_form]
end

#show_ruler? ⇒ Boolean

#

show_ruler?

#

Returns:

  • (Boolean) 


296
297
298
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 296

def show_ruler?
  @internal_hash[:show_ruler]
end

#show_three_prime_trailer? ⇒ Boolean

#

show_three_prime_trailer?

#

Returns:

  • (Boolean) 


271
272
273
 
# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence/show_nucleotide_sequence.rb', line 271

def show_three_prime_trailer?
  @internal_hash[:show_three_prime_trailer]
end