Class: Bioroebe::FindLongestSubstringViaLCSalgorithm

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb

Overview

Bioroebe::FindLongestSubstring

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

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(this_string = ARGV, run_already = true) ⇒ FindLongestSubstringViaLCSalgorithm

#

initialize

#

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 38

def initialize(
    this_string = ARGV,
    run_already = true
  )
  reset
  set_string1(this_string)
  if block_given?
    yielded = yield
    case yielded
    when :do_also_show_the_two_sequences,
         :also_show_the_sequence
      @also_show_the_two_sequences = true 
    end
  end
  run if run_already
end

Instance Method Details

#determine_whether_diff_lcs_is_available ⇒ Object

#

determine_whether_diff_lcs_is_available

#

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 137

def determine_whether_diff_lcs_is_available
  if diff_lcs_is_available?
    lcs = ::Bioroebe.return_longest_substring_via_LCS_algorithm(seq1, seq2)
    if @also_show_the_two_sequences
      do_show_the_two_sequences
    end
    e
    erev 'The longest substring (including gaps) between '\
         'these two sequences is:'
    e
    e "  #{sfancy(lcs)}#{rev} (#{sfancy(lcs.size)}#{rev} characters)"
    e
  else
    opnn; erev 'The gem '+sfancy('diff-lcs')+rev+' is not installed. '\
               'Please install it if you'
    opnn; erev 'wish to make use of this gem here.'
  end
end

#diff_lcs_is_available? ⇒ Boolean

#

diff_lcs_is_available?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 125

def diff_lcs_is_available?
  unless Object.const_defined? :Diff
    begin
      require 'diff-lcs'
    rescue LoadError; end
  end
  Object.const_defined? :Diff
end

#do_show_the_two_sequences ⇒ Object

#

do_show_the_two_sequences

#

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 159

def do_show_the_two_sequences
  erev 'Sequence 1: '+sfancy(seq1?)
  erev 'Sequence 2: '+sfancy(seq2?)
end

#reset ⇒ Object

#

reset

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 58

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @string1
  # ======================================================================= #
  @string1 = nil
  # ======================================================================= #
  # === @string2
  # ======================================================================= #
  @string2 = nil
  # ======================================================================= #
  # === @also_show_the_two_sequences
  # ======================================================================= #
  @also_show_the_two_sequences = false # if true then also show these two strings.
end

#run ⇒ Object

#

run

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 167

def run
  determine_whether_diff_lcs_is_available
end

#set_string1(i) ⇒ Object

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set_string1

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 81

def set_string1(i)
  if i.is_a? Array
    first = i.first
    if first
      if first.include? '|'
        splitted = first.split('|').map(&:strip)
        set_string2(splitted.last)
        i = splitted.first
      end
    end
  elsif i.is_a?(String) and i.include?('|')
    splitted = i.split('|').map(&:strip)
    set_string2(splitted.last)
    i = splitted.first
  end
  @string1 = i
end

#set_string2(i) ⇒ Object

#

set_string2

#

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 102

def set_string2(i)
  @string2 = i
end

#string1? ⇒ Boolean Also known as: seq1, seq1?

#

string1?

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Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 109

def string1?
  @string1
end

#string2? ⇒ Boolean Also known as: seq2, seq2?

#

string2?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 117

def string2?
  @string2
end