Class: Bioroebe::Ruler

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

Overview

Bioroebe::Ruler

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(for_this_sequence = ARGV, group_together_n_nucleotides = 72, run_already = true) ⇒ Ruler

#

initialize

The second argument determines which grouping is to be applied, that is, how many nucleotides are shown per line.

#


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# File 'lib/bioroebe/misc/ruler.rb', line 43

def initialize(
    for_this_sequence            = ARGV,
    group_together_n_nucleotides = 72,
    run_already                  = true
  )
  reset
  set_use_this_sequence(
    for_this_sequence
  )
  # ======================================================================= #
  # The next method can be used to determine how many nucleotides
  # are to be displayed.
  # ======================================================================= #
  set_group_together_n_nucleotides(
    group_together_n_nucleotides
  )
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # === Handle Hashes next
    # ===================================================================== #
    if yielded.is_a? Hash
      # =================================================================== #
      # === :ruler
      # =================================================================== #
      if yielded.has_key? :ruler
        _ = yielded.delete(:ruler)
        case _
        # ================================================================= #
        # === :no_colours
        # ================================================================= #
        when :no_colours,
             :without_colours
          @internal_hash[:highlight_numbers] = false
        end
      end
    else
      case yielded
      # =================================================================== #
      # === :no_colours
      # =================================================================== #
      when :no_colours,
           :without_colours
        @internal_hash[:highlight_numbers] = false
      end
    end
  end
  run if run_already
end

Instance Method Details

#main_sequence? ⇒ Boolean

#

main_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/misc/ruler.rb', line 145

def main_sequence?
  @use_this_sequence
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/misc/ruler.rb', line 99

def reset
  super()
  # ======================================================================= #
  # === @result
  # ======================================================================= #
  @result = []
  # ======================================================================= #
  # === @group_together_n_nucleotides
  # ======================================================================= #
  @group_together_n_nucleotides = 72
  # ======================================================================= #
  # If the next variable is set to true then we will highlight the
  # positions at 1, 5 and 10. This can be toggled to false by the user.
  # ======================================================================= #
  @internal_hash[:highlight_numbers] = true
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/misc/ruler.rb', line 152

def result?
  @result
end

#result_as_string? ⇒ Boolean Also known as: result_as_string

#

result_as_string?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/misc/ruler.rb', line 159

def result_as_string?
  @result.join.strip
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/misc/ruler.rb', line 166

def run
  chunks = main_sequence?.to_s.split(/(.{#{@group_together_n_nucleotides}})/).reject(&:empty?)
  array = chunks.each_slice(@group_together_n_nucleotides).to_a.flatten
  # ======================================================================= #
  # We now have an array of chunks, such as:
  #
  #   ["TGCGCAGGAGGACGAGGACGGCGACTACGAGGAGCTGGTGCTAGCCTTGCGTTCCGAGGAGGACGGCCTG",
  #    "GCCGAAGCACCCGAGCACGGAACCACAGCCA"]
  #
  # ======================================================================= #
  array.each {|sequence| # Each entry will be a sequence of strings.
    _ = ''.dup
    sequence.chars.each_with_index {|char, index| index += 1
      result = index % 10
      if @internal_hash[:highlight_numbers]
        case result
        when 1
          result = crimson(result)+rev
        when 5, 0
          result = royalblue(result)+rev
        else
          result = result.to_s
        end
      end
      _ << result.to_s
    }
    @result << _
  }
end

#set_group_together_n_nucleotides(i = 72) ⇒ Object

#

set_group_together_n_nucleotides

#


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# File 'lib/bioroebe/misc/ruler.rb', line 119

def set_group_together_n_nucleotides(
    i = 72
  )
  case i
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = 72
  end
  @group_together_n_nucleotides = i
end

#set_use_this_sequence(i) ⇒ Object

#

set_use_this_sequence

#


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# File 'lib/bioroebe/misc/ruler.rb', line 135

def set_use_this_sequence(i)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  @use_this_sequence = i
end