Class: Bioroebe::CreateRandomAminoacids
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::CreateRandomAminoacids
- Defined in:
- lib/bioroebe/aminoacids/create_random_aminoacids.rb
Overview
Bioroebe::CreateRandomAminoacids
Constant Summary collapse
- CREATE_N_AMINOACIDS =
#
CREATE_N_AMINOACIDS
This is the default length, e. g. we will create 50 random aminoacids by default.
#
150
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
-
#amino_acid_sequence? ⇒ Boolean
(also: #amino_acid_sequence, #sequence?)
# === amino_acid_sequence? ========================================================================= #.
-
#determine_the_amino_acid_sequence ⇒ Object
# === determine_the_amino_acid_sequence ========================================================================= #.
-
#initialize(how_many_aminoacids = CREATE_N_AMINOACIDS, split_at = nil, be_verbose = false, run_already = true, &block) ⇒ CreateRandomAminoacids
constructor
# === initialize ========================================================================= #.
-
#menu(i = return_commandline_arguments_starting_with_hyphens) ⇒ Object
# === menu (menu tag) ========================================================================= #.
-
#report ⇒ Object
# === report ========================================================================= #.
-
#reset ⇒ Object
# === reset ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
-
#run_everything ⇒ Object
# === run_everything ========================================================================= #.
-
#set_amino_acid_sequence(i) ⇒ Object
# === set_amino_acid_sequence ========================================================================= #.
-
#set_how_many_aminoacids(i = CREATE_N_AMINOACIDS) ⇒ Object
# === set_how_many_aminoacids ========================================================================= #.
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(how_many_aminoacids = CREATE_N_AMINOACIDS, split_at = nil, be_verbose = false, run_already = true, &block) ⇒ CreateRandomAminoacids
#
initialize
#
38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 38 def initialize( how_many_aminoacids = CREATE_N_AMINOACIDS, split_at = nil, be_verbose = false, run_already = true, &block ) reset set_commandline_arguments( how_many_aminoacids ) set_how_many_aminoacids( how_many_aminoacids ) @be_verbose = be_verbose @split_at = split_at # ======================================================================= # # === Handle blocks next # ======================================================================= # if block_given? yielded = yield case yielded # ===================================================================== # # === :do_report # ===================================================================== # when :do_report @shall_we_report = true set_be_verbose end end run if run_already end |
Instance Method Details
#amino_acid_sequence? ⇒ Boolean Also known as: amino_acid_sequence, sequence?
#
amino_acid_sequence?
#
122 123 124 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 122 def amino_acid_sequence? @amino_acid_sequence end |
#determine_the_amino_acid_sequence ⇒ Object
#
determine_the_amino_acid_sequence
#
98 99 100 101 102 103 104 105 106 107 108 109 110 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 98 def determine_the_amino_acid_sequence use_these_keys_for_the_aminoacids = TWENTY_CANONICAL_AMINOACIDS.split(//) amino_acid_sequence = ''.dup @how_many_aminoacids.times {|aminoacid| amino_acid_sequence << use_these_keys_for_the_aminoacids.sample # return a random character. unless @split_at.nil? amino_acid_sequence << "\n" if (aminoacid + 1) % split_at == 0 end } set_amino_acid_sequence( amino_acid_sequence ) end |
#menu(i = return_commandline_arguments_starting_with_hyphens) ⇒ Object
#
menu (menu tag)
#
152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 152 def ( i = return_commandline_arguments_starting_with_hyphens ) if i.is_a? Array i.each {|entry| (entry) } else case i # case tag # ===================================================================== # # === randomAA 35 --disable-colours # ===================================================================== # when /^-?-?disable(-|_)?colours/i, /^-?-?no(-|_)?colours/i disable_colours end end end |
#report ⇒ Object
#
report
#
130 131 132 133 134 135 136 137 138 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 130 def report if @shall_we_report if use_colours? erev @amino_acid_sequence else e @amino_acid_sequence end end end |
#reset ⇒ Object
#
reset
#
74 75 76 77 78 79 80 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 74 def reset super() # ======================================================================= # # === @shall_we_report # ======================================================================= # @shall_we_report = false end |
#run ⇒ Object
#
=== run (run tag)
#
172 173 174 175 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 172 def run run_everything end |
#run_everything ⇒ Object
#
run_everything
#
143 144 145 146 147 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 143 def run_everything determine_the_amino_acid_sequence report if @be_verbose return @amino_acid_sequence end |
#set_amino_acid_sequence(i) ⇒ Object
#
set_amino_acid_sequence
#
115 116 117 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 115 def set_amino_acid_sequence(i) @amino_acid_sequence = i end |
#set_how_many_aminoacids(i = CREATE_N_AMINOACIDS) ⇒ Object
#
set_how_many_aminoacids
#
85 86 87 88 89 90 91 92 93 |
# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 85 def set_how_many_aminoacids( i = CREATE_N_AMINOACIDS ) if i.is_a? Array i = i.first end i = CREATE_N_AMINOACIDS if i.nil? @how_many_aminoacids = i.to_i end |