Class: Bioroebe::Palindrome2DStructure

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/palindromes/palindrome_2D_structure.rb

Overview

Bioroebe::Palindrome2DStructure

Constant Summary collapse

DEFAULT_SEARCH_STRING =
#

DEFAULT_SEARCH_STRING

#
'CGCGAATTCGCG'

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

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, #opnerev, #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, #runmode?, #set_be_verbose, #set_runmode, #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 BaseModule

#absolute_path, #default_file_read, #file_readlines

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_will_we_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?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #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

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(i = ARGV, run_already = true) ⇒ Palindrome2DStructure

#

initialize

Can also invoke it via rpalindrome. Currently we can find only palindromes which have odd numbers

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 32

def initialize(
    i           = ARGV,
    run_already = true
  )
  reset
  set_commandline_arguments(i)
  run if run_already
end

Instance Method Details

#determine_the_main_sequence ⇒ Object

#

determine_the_main_sequence

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 51

def determine_the_main_sequence
  set_sequence(first?)
end

#display_these_two_nucleotides(a, b) ⇒ Object

#

display_these_two_nucleotides

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 76

def display_these_two_nucleotides(a, b)
  case a # case tag
  when 'A','T','U'
    use_this_token = '='
    n_hydrogen_bonds = 2
  when 'G','C'
    use_this_token = '≡'
    n_hydrogen_bonds = 3
  end
  unless can_base_pair?(a, b)
    use_this_token = ''
    n_hydrogen_bonds = 0
  end
  e "     #{a}#{use_this_token}#{b}  # #{n_hydrogen_bonds}"
end

#display_trailing_connecters ⇒ Object

#

display_trailing_connecters

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 95

def display_trailing_connecters
  e '    /   \\'
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 44

def reset
  super()
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 102

def run
  determine_the_main_sequence
  _ = sequence?
  if is_palindrome? _
    # ===================================================================== #
    # We only support palindromes for the time being. If the sequence
    # is a palindrome, in the DNA or RNA, then we know that it must
    # have an even amount of nucleotides.
    # ===================================================================== #
    size = _.size
    half = size / 2
    # ===================================================================== #
    # To display it in "2D", we start with the two top nucleotides,
    # that is those that are found first when looking at the structure,
    # then we continue. 
    # ===================================================================== #
    e
    half.times {|n_time|
      a = _[half-(n_time+1)] # The first nucleotide.
      b = _[half+n_time]     # The complementary nucleotide.
      display_these_two_nucleotides(a, b)
    }
    display_trailing_connecters
    e
  else
    erev 'The sequence is not a palindrome. Currently this class can only'
    erev 'display palindromes on the commandline.'
  end
end

#sequence? ⇒ Boolean

#

sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 69

def sequence?
  @sequence
end

#set_sequence(i = first?) ) ⇒ Object

#

set_sequence

#


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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 58

def set_sequence(i = first?)
  if i
    i = i.dup if i.frozen?
    i.delete!('|')
  end
  @sequence = i
end