Class: Bioroebe::ComplementaryDnaStrand
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::ComplementaryDnaStrand
- Defined in:
- lib/bioroebe/nucleotides/complementary_dna_strand.rb
Overview
Bioroebe::ComplementaryDnaStrand
Constant Summary
Constants inherited from CommandlineApplication
Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Instance Method Summary collapse
-
#initialize(i = ARGV, run_already = true) ⇒ ComplementaryDnaStrand
constructor
# === initialize ========================================================================= #.
-
#menu(i = commandline_arguments? ) ⇒ Object
# === menu (menu tag) ========================================================================= #.
-
#report ⇒ Object
# === report ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#result? ⇒ Boolean
# === result? ========================================================================= #.
-
#run ⇒ Object
# === run ========================================================================= #.
-
#show_help ⇒ Object
# === show_help ========================================================================= #.
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) ⇒ ComplementaryDnaStrand
#
initialize
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 23 def initialize( i = ARGV, run_already = true ) reset set_commandline_arguments(i) run if run_already end |
Instance Method Details
#menu(i = commandline_arguments? ) ⇒ Object
#
menu (menu tag)
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 64 def ( i = commandline_arguments? ) if i and i.is_a?(Array) i.each {|entry| (entry) } else case i # ===================================================================== # # === --trailer # ===================================================================== # when /^-?-?trailer/i, /^-?-?header/i, /^-?-?footer/i @show_leader_and_trailer = true # ===================================================================== # # === --help # ===================================================================== # when /^-?-?help/i show_help @continue = false else @continue = true end end end |
#report ⇒ Object
#
report
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 123 def report if @show_leader_and_trailer e "5'-#{@result}-'3" else e @result end end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 35 def reset super() # ======================================================================= # # === @continue # ======================================================================= # @continue = true # ======================================================================= # # === @result # ======================================================================= # @result = nil # ======================================================================= # # === @show_leader_and_trailer # # If the following variable is true, then this class will show the # leading 5'- and trailing -'3 part. # ======================================================================= # @show_leader_and_trailer = false end |
#result? ⇒ Boolean
#
result?
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 57 def result? @result end |
#run ⇒ Object
#
run
#
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# File 'lib/bioroebe/nucleotides/complementary_dna_strand.rb', line 103 def run if @continue _ = first_commandline_argument? if _.include?("5′-") or _.include?("5'-") or _.include?("-3'") or _.include?("5-") @show_leader_and_trailer = true end hash = ::Bioroebe.partner_nucleotide_hash if _ @result = _.chars.map {|entry| hash[entry] }.join end end end |