Class: Bioroebe::ShowRestrictionEnzymes
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::ShowRestrictionEnzymes
- Defined in:
- lib/bioroebe/enzymes/show_restriction_enzymes.rb
Overview
Bioroebe::ShowRestrictionEnzymes
Constant Summary
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Class Method Summary collapse
-
.[](i = ARGV) ⇒ Object
# === Bioroebe::ShowRestrictionEnzymes[] ========================================================================= #.
Instance Method Summary collapse
-
#colourize_value(i) ⇒ Object
# === colourize_value.
-
#initialize(run_already = true) ⇒ ShowRestrictionEnzymes
constructor
# === initialize ========================================================================= #.
-
#notify_the_user_about_the_available_restriction_enzymes ⇒ Object
# === notify_the_user_about_the_available_restriction_enzymes ========================================================================= #.
-
#report_how_many_restriction_enzymes_were_found ⇒ Object
# === report_how_many_restriction_enzymes_were_found ========================================================================= #.
-
#reset ⇒ Object
# === reset ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
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(run_already = true) ⇒ ShowRestrictionEnzymes
#
initialize
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 29 def initialize( run_already = true ) reset run if run_already end |
Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::ShowRestrictionEnzymes[]
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 100 def self.[](i = ARGV) new(i) end |
Instance Method Details
#colourize_value(i) ⇒ Object
#
colourize_value
We delegate to crimson() for the colour, but only if we actually make use of colours.
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 77 def colourize_value(i) if use_colours? i = slateblue(i) if i.include? ' ' # Here we also assume that this has at least one number. splitted = i.split ' ' splitted[-1] = crimson(splitted[-1]) # Colourize the number red. i = splitted.join ' ' end end i end |
#notify_the_user_about_the_available_restriction_enzymes ⇒ Object
#
notify_the_user_about_the_available_restriction_enzymes
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 50 def notify_the_user_about_the_available_restriction_enzymes erev 'Available Restriction Enzymes (from file '+ sfile(::Bioroebe.restriction_enzymes_file)+'):' # ======================================================================= # # Obtain all restriction enzymes next, in Array form. # ======================================================================= # ::Bioroebe.restriction_enzymes(:array_format).each {|key,value| _ = ('%15s' % key) erev _+seagreen(' → ')+rev+colourize_value(value) } end |
#report_how_many_restriction_enzymes_were_found ⇒ Object
#
report_how_many_restriction_enzymes_were_found
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 65 def report_how_many_restriction_enzymes_were_found n_enzymes = ::Bioroebe.restriction_enzymes.size.to_s erev "A total of #{sfancy(n_enzymes)}#{rev} "\ "registered restrictions-enzymes were found." end |
#reset ⇒ Object
#
reset
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 39 def reset super() # ======================================================================= # # === @use_colours # ======================================================================= # @use_colours = true end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/enzymes/show_restriction_enzymes.rb', line 92 def run notify_the_user_about_the_available_restriction_enzymes report_how_many_restriction_enzymes_were_found end |