Class: Bioroebe::PalindromeGenerator

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/palindromes/palindrome_generator.rb

Overview

Bioroebe::PalindromeGenerator

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opne, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #set_be_verbose, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

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 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_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Constructor Details

#initialize(length_of_the_palindrome = nil, run_already = true) ⇒ PalindromeGenerator

#

initialize

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 33

def initialize(
    length_of_the_palindrome = nil,
    run_already              = true
  )
  reset
  set_length_of_the_palindrome(
    length_of_the_palindrome
  )
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      set_be_quiet
    end
  end
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::PalindromeGenerator[]

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 228

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

.return_as_string(i = ARGV) ⇒ Object

#

Bioroebe::PalindromeGenerator.return_as_string

This method has been added particularly to embed the information yielded by this class into a webpage (e. g. for sinatra). That way we can make available the functionality for people who visit a website making use of Bioroebe.

Invocation example:

Bioroebe::PalindromeGenerator.return_as_string(6) # => "GTGCAC\nCACGTG\n"
#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 245

def self.return_as_string(i = ARGV)
  _ = ::Bioroebe::PalindromeGenerator.new(i) { :be_quiet }
  result = ''.dup
  result << _.forward_strand? << "\n" <<
            _.reverse_strand? << "\n"
  result
end

Instance Method Details

#find_complementary_nucleotide_to(i) ⇒ Object

#

find_complementary_nucleotide_to

Find the corresponding complementary nucleotide to the given token at hand.

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 204

def find_complementary_nucleotide_to(i)
  return ::Bioroebe.complementary_nucleotide(i)
end

#forward_strand? ⇒ Boolean

#

forward_strand?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 187

def forward_strand?
  @forward_strand
end

#length_of_the_palindrome? ⇒ Boolean

#

length_of_the_palindrome?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 108

def length_of_the_palindrome?
  @length_of_the_palindrome
end

#lpad? ⇒ Boolean

#

lpad?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 115

def lpad?
  '  '
end

#report ⇒ Object

#

report (report tag)

You have to invoke the report method manually, thus, on your own.

We will report first the forward strand and then the reverse strand.

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 126

def report
  e
  if @use_header_with_numbers
    print '       '
    n_times = @reverse_strand.size 
    n_times.times {|n| n += 1 # This begins at 0, hence we add +1.
      if n > 9
        n = n % 10
      end
      print steelblue(n)
    }
    e
  end
  report_forward_strand
  report_reverse_strand
  e
end

#report_forward_strand(i = @forward_strand) ⇒ Object

#

report_forward_strand

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 147

def report_forward_strand(i = @forward_strand)
  e rev+lpad?+"5' - "+simp(i)+rev+" - 3'"
end

#report_reverse_strand(i = @reverse_strand) ⇒ Object

#

report_reverse_strand

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 154

def report_reverse_strand(i = @reverse_strand)
  e rev+lpad?+"3' - "+simp(i)+rev+" - 5'"
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 57

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @use_header_with_numbers
  #
  # If the following variable is set to true then a numbered header will
  # be shown above the sequence.
  # ======================================================================= #
  @use_header_with_numbers = true
  # ======================================================================= #
  # === @forward_strand
  # ======================================================================= #
  @forward_strand = ''.dup
  # ======================================================================= #
  # === @reverse_strand
  # ======================================================================= #
  @reverse_strand = ''.dup
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 194

def result?
  @forward_strand+"\n"+@reverse_strand
end

#return_the_reverse_strand(forward_strand = @forward_strand) ⇒ Object

#

return_the_reverse_strand

This will only return the reverse strand, but not assign to it.

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 163

def return_the_reverse_strand(
    forward_strand = @forward_strand
  )
  reverse_strand = ''.dup
  # ======================================================================= #
  # Ok, the forward strand was built - now we will add the reverse strand.
  # ======================================================================= #
  forward_strand.chars.each {|char|
    complement = find_complementary_nucleotide_to(char)
    reverse_strand << complement
  }
  return reverse_strand
end

#reverse_strand? ⇒ Boolean

#

reverse_strand?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 180

def reverse_strand?
  @reverse_strand
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 211

def run
  first_half = ''.dup # This has the first half of the target.
  (length_of_the_palindrome? / 2).times {
    first_half << ::Bioroebe::DNA_NUCLEOTIDES.sample
  }
  forward_strand = first_half
  first_half.reverse.chars.each {|char|
    complement = find_complementary_nucleotide_to(char)
    forward_strand << complement
  }
  @forward_strand = forward_strand
  @reverse_strand = return_the_reverse_strand
end

#set_length_of_the_palindrome(i = '') ⇒ Object

#

set_length_of_the_palindrome

This setter-method determines the length of the palindrome that is to be generated.

#

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# File 'lib/bioroebe/palindromes/palindrome_generator.rb', line 86

def set_length_of_the_palindrome(
    i = ''
  )
  i = i.first if i.is_a? Array
  i = i.to_i # Must be an Integer.
  if i.odd?
    if be_verbose?
      opnn { :short }
      e
      e
      erev 'The input '+sfancy(i.to_s)+rev+' is odd - we need an '\
           'even number for Palindromes.'
      erev 'Thus, we will deduct 1 from it and use that instead.'
    end
    i -= 1 # Odd numbers will become even here.
  end
  @length_of_the_palindrome = i
end