Class: Bioroebe::Palindrome2DStructure
Overview
Bioroebe::Palindrome2DStructure
Constant Summary
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- DEFAULT_SEARCH_STRING =
#
DEFAULT_SEARCH_STRING
#
'CGCGAATTCGCG'
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Instance Method Summary
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#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?, #was_or_were, #without_extname, #write_what_into
#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
#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #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, #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, #write_what_into
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
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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
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#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 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
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#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
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#reset ⇒ Object
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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 44
def reset
super()
end
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#run ⇒ Object
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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 102
def run
determine_the_main_sequence
_ = sequence?
if is_palindrome? _
size = _.size
half = size / 2
e
half.times {|n_time|
a = _[half-(n_time+1)] b = _[half+n_time] 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
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#sequence? ⇒ Boolean
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# File 'lib/bioroebe/palindromes/palindrome_2D_structure.rb', line 69
def sequence?
@sequence
end
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#set_sequence(i = first?)
) ⇒ Object
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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
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