Class: Bioroebe::FindLongestSubstring

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

Overview

Bioroebe::FindLongestSubstring

Constant Summary collapse

STRING1 =
#

STRING1

#
'AAAAGATAAACAAAAGGGG'
STRING2 =
#

STRING2

#
'ATATCCTAAACAAAAGGGG'

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(string1 = nil, string2 = nil, run_already = true) ⇒ FindLongestSubstring

#

initialize

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 37

def initialize(
    string1     = nil,
    string2     = nil,
    run_already = true
  )
  super()
  reset
  set_string1(string1)
  set_string2(string2)
  run if run_already
end

Instance Method Details

#record(i = @_, start_position = nil) ⇒ Object

#

record

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 103

def record(
    i              = @_,
    start_position = nil
  )
  if i.size > @longest_substring.size
    @longest_substring = i
    @start_position = (start_position-1) if start_position
  end
end

#report_longest_substring ⇒ Object Also known as: report

#

report_longest_substring

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 127

def report_longest_substring
  e "The longest substring is: #{sfancy(@longest_substring)}"
  if @start_position
    e "It starts after position: #{sfancy(@start_position)}"
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 52

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @start_position
  # ======================================================================= #
  @start_position = nil
  # ======================================================================= #
  # === @longest_substring
  # ======================================================================= #
  @longest_substring = ''
  # ======================================================================= #
  # === @_
  # ======================================================================= #
  @_ = ''.dup # Throwaway string.
end

#result? ⇒ Boolean Also known as: result

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 96

def result? # query method.
  @longest_substring
end

#run ⇒ Object

#

run (run tag)

#


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

def run
  startup_message
  @string1.chars.each_with_index {|entry, index|
    if entry == @string2[index]
      @_ << entry
      record(@_, index)
    else
      @_ = ''.dup
    end
  }
  report_longest_substring
end

#set_string1(i = :default) ⇒ Object

#

set_string1

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 72

def set_string1(i = :default)
  i = i.first if i.is_a? Array
  case i
  when nil, :default
    i = STRING1
  end
  @string1 = i
end

#set_string2(i = :default) ⇒ Object

#

set_string2

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 84

def set_string2(i = :default)
  i = i.first if i.is_a? Array
  case i
  when nil, :default
    i = STRING2
  end 
  @string2 = i
end

#startup_message ⇒ Object

#

startup_message

#


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# File 'lib/bioroebe/string_matching/find_longest_substring.rb', line 116

def startup_message
  opnn
  e
  e 'We will try to find the longest common substring between'
  e "  string1 `#{sfancy(@string1)}` and "
  e "  string2 `#{sfancy(@string2)}` now."
end