Class: Bioroebe::Palindrome2DStructure
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::Palindrome2DStructure
- 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
Instance Method Summary collapse
-
#determine_the_main_sequence ⇒ Object
# === determine_the_main_sequence ========================================================================= #.
-
#display_these_two_nucleotides(a, b) ⇒ Object
# === display_these_two_nucleotides ========================================================================= #.
-
#display_trailing_connecters ⇒ Object
# === display_trailing_connecters ========================================================================= #.
-
#initialize(i = ARGV, run_already = true) ⇒ Palindrome2DStructure
constructor
# === initialize.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run ========================================================================= #.
-
#sequence? ⇒ Boolean
# === sequence? ========================================================================= #.
-
#set_sequence(i = first?) ) ⇒ Object
# === set_sequence ========================================================================= #.
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?
#
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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 |