Class: Bioroebe::ShowCodonTables

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/codons/show_codon_tables.rb

Overview

Bioroebe::ShowCodonTables

Constant Summary

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Instance Method Summary collapse

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(show_what = ARGV) ⇒ ShowCodonTables

#

initialize

#


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# File 'lib/bioroebe/codons/show_codon_tables.rb', line 26

def initialize(
    show_what = ARGV
  )
  reset
  if show_what.is_a? Array
    if show_what.empty?
      show_what << :default
    end
  end
  if show_what.is_a? Array
    first = show_what.first
  else
    first = show_what
  end
  first = first.to_s.delete('-')
  case first.to_sym
  # ======================================================================= #
  # === :human
  # ======================================================================= #
  when :human
    Bioroebe::ShowThisCodonTable.new
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default,
       :everything
    do_display_all_available_codon_tables
  # ======================================================================= #
  # === Show the headers
  # ======================================================================= #
  when :only_names,
       :headers,
       '--headers'
    ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
      e turquoise(number.to_s.rjust(3))
        +') '+
        long_name.ljust(70)
    }
  end
end

Instance Method Details

#do_display_all_available_codon_tables ⇒ Object

#

do_display_all_available_codon_tables

#


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# File 'lib/bioroebe/codons/show_codon_tables.rb', line 84

def do_display_all_available_codon_tables
  # ======================================================================= #
  # Display the human CodonTable first.
  # ======================================================================= #
  Bioroebe::ShowThisCodonTable.new(ARGV)
  e
  erev 'The above is the human CodonTable. We will next show all'
  erev 'available codon tables.'
  e
  ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
    e long_name
    e '=' * 42
    # ===================================================================== #
    # Obtain the very important dataset for that particular codon next:
    # ===================================================================== #
    dataset = ::Bioroebe::CodonTable[number]
    sliced  = dataset.to_a.each_slice(5)
    sliced.each {|array|
      array.each {|codon, aminoacid|
        print_this_line_of_a_codon_table(codon, aminoacid)
      }; e
    }
    e
  }
end

#print_this_line_of_a_codon_table(codon, aminoacid) ⇒ Object

#

print_this_line_of_a_codon_table

#


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# File 'lib/bioroebe/codons/show_codon_tables.rb', line 77

def print_this_line_of_a_codon_table(codon, aminoacid)
  print "#{codon}: #{simp(aminoacid)}   #{rev}"
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/codons/show_codon_tables.rb', line 70

def reset
  super()
end