Class: Bioroebe::Quiz::ThreeLetterToAminoacid

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb

Overview

Bioroebe::Quiz::ThreeLetterToAminoacid

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
ONE_LETTER_TO_FULL_NAME =
#

ONE_LETTER_TO_FULL_NAME

#
FILE_AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER
SLEEP_FOR_THIS_AMOUNT =
#

SLEEP_FOR_THIS_AMOUNT

#
2.2

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

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(i = nil, run_already = true) ⇒ ThreeLetterToAminoacid

#

initialize

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 44

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::Quiz::ThreeLetterToAminoacid[]

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 155

def self.[](i = '')
  new(i)
end

Instance Method Details

#aminoacid_one_letter_to_full_name(i) ⇒ Object

#

aminoacid_one_letter_to_full_name

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 129

def aminoacid_one_letter_to_full_name(i)
  result = @dataset_one_letter_to_full_name[i].dup
  result
end

#ask_the_question ⇒ Object

#

ask_the_question

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 137

def ask_the_question
  e rev+'The three-letter aminoacid `'+sfancy(@key)+rev+
    '` stands for which aminoacid?'
  sleep SLEEP_FOR_THIS_AMOUNT
  reveal_the_answer
end

#determine_keys ⇒ Object

#

determine_keys

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 78

def determine_keys
  @keys = @dataset.keys
end

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 94

def input?
  @input
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 56

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @dataset_one_letter_to_full_name
  # ======================================================================= #
  @dataset_one_letter_to_full_name = YAML.load_file(
    ONE_LETTER_TO_FULL_NAME
  ).invert
  # ======================================================================= #
  # === @dataset
  # ======================================================================= #
  @dataset = YAML.load_file(FILE_AMINOACIDS_THREE_TO_ONE)
  determine_keys
end

#reveal_the_answer ⇒ Object

#

reveal_the_answer (answer tag)

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 112

def reveal_the_answer
  full_name_of_the_aminoacid = aminoacid_one_letter_to_full_name(@answer)
  if full_name_of_the_aminoacid.frozen?
    full_name_of_the_aminoacid = full_name_of_the_aminoacid.dup
  end
  full_name_of_the_aminoacid.capitalize!
  e
  e '     '+slateblue(@answer)+rev+
    ' ('+
      lightblue(full_name_of_the_aminoacid)+rev+
    ')'
  e
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 147

def run
  select_key_and_answer
  ask_the_question
end

#select_key_and_answer ⇒ Object

#

select_key_and_answer

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 101

def select_key_and_answer
  @key = @keys.sample
  if @input and !@input.empty?
    @key = @input
  end
  @answer = @dataset[@key]
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb', line 85

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.to_s.dup
  @input = i
end