Class: Bioroebe::CreateRandomAminoacids

Inherits:
CommandlineApplication show all
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.

#
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Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::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, #opne, #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, #set_be_verbose, #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 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_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?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #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

Constructor Details

#initialize(how_many_aminoacids = CREATE_N_AMINOACIDS, split_at = nil, be_verbose = false, run_already = true, &block) ⇒ CreateRandomAminoacids

#

initialize

#

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# 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
    when :do_report
      @shall_we_report = true
      @be_verbose = true
    end
  end
  run if run_already
end

Instance Method Details

#amino_acid_sequence?Boolean Also known as: amino_acid_sequence, sequence?

#

amino_acid_sequence?

#

Returns:

  • (Boolean)

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 119

def amino_acid_sequence?
  @amino_acid_sequence
end

#determine_the_amino_acid_sequenceObject

#

determine_the_amino_acid_sequence

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 95

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 (menu tag)

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 149

def menu(
    i = return_commandline_arguments_starting_with_hyphens
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === randomAA 35 --disable-colours
    # ===================================================================== #
    when /^-?-?disable(-|_)?colours/i,
         /^-?-?no(-|_)?colours/i
      disable_colours
    end
  end
end

#reportObject

#

report

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 127

def report
  if @shall_we_report
    if use_colours?
      erev @amino_acid_sequence
    else
      e @amino_acid_sequence
    end
  end
end

#resetObject

#

reset

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 71

def reset
  super()
  # ======================================================================= #
  # === @shall_we_report
  # ======================================================================= #
  @shall_we_report = false
end

#runObject

#
=== run                                                       (run tag)
#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 169

def run
  menu
  run_everything
end

#run_everythingObject

#

run_everything

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 140

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

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 112

def set_amino_acid_sequence(i)
  @amino_acid_sequence = i
end

#set_how_many_aminoacids(i = CREATE_N_AMINOACIDS) ⇒ Object

#

set_how_many_aminoacids

#

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# File 'lib/bioroebe/aminoacids/create_random_aminoacids.rb', line 82

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