Class: Bioroebe::PalindromeFinder

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/palindromes/palindrome_finder.rb

Constant Summary collapse

DEFAULT_SEARCH_STRING =
#

DEFAULT_SEARCH_STRING

#
'RENTNER reliefpfeiler anna ATCTA'

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(string_to_search = 'RENTNER reliefpfeiler anna ATCTA', do_display_results = false) ⇒ PalindromeFinder

#

initialize

Can also invoke it via rpalindrome. Currently we can find only palindromes which have odd numbers

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 31

def initialize(
    string_to_search   = 'RENTNER reliefpfeiler anna ATCTA',
    do_display_results = false
  )
  case do_display_results
  when :display_results
    do_display_results = true
  end
  set_string_to_search(
    string_to_search
  )
  reset
  run if do_display_results
end

Instance Method Details

#display_results ⇒ Object

#

display_results

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 179

def display_results
  e "#{rev}Looking for results in the string "\
    "`#{sfancy(@string_to_search)}#{rev}`:"
  if @array_found_palindrome.empty?
    erev 'No Palindrome was found in this string.'
  else
    @array_found_palindrome.each_with_index { |palindrome, index|
      erev 'Palindrome '+steelblue(index.to_s)
      erev "    #{palindrome.first}"
    }
  end
end

#find_complex_palindromes ⇒ Object

#

find_complex_palindromes

Please invoke this method only after find_simple_palindromes has been invoked. This is not very smart right now, but i dont wanna change it yet. :P

May be half deprecated hmmm.

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 122

def find_complex_palindromes
  @array_found_palindrome.each { |palindrome|
    palindrome_start_pos = palindrome[1]
    palindrome_content   = palindrome[0] 
    if @string_to_search[palindrome_start_pos-1,1] == @string_to_search[palindrome_start_pos+palindrome_content.size+1,1]
      e sfancy(
          @string_to_search[palindrome_start_pos - 1, 1]+
          palindrome_content+
          @string_to_search[palindrome_start_pos+palindrome_content.size+1,1]
        )
    end 
  }
end

#find_seeds ⇒ Object

#

find_seeds

This method finds every seed to a palindrome in a given string.

It will return an array with their respective positions.

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 95

def find_seeds
  index = 0
  array = []
  @string_to_search.each_char { |char|
    current_char = char
    next_char = @string_to_search[index+1, 1]
    last_char = @string_to_search[index-1, 1]
    if next_char == ' ' or last_char == ' ' or current_char == ' ' # Skip empty lines
      index += 1
      next
    else
      array << index if next_char == last_char
      index += 1
    end
  }
  return array
end

#find_simple_palindromes ⇒ Object

#

find_palindrome

What is the property of a palindrome?

anna, otto, abcba, eeegeee, RENTNER, Reliefpfeiler

Basically a property.

The “middle” part is normally static.

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 147

def find_simple_palindromes
  index = 1
  string_size = @string_to_search.size
  loop {
    if @string_to_search[index, 1] == ' '
      # safe guard to intercept (and ignore) empty positions (i.e. space char)
    elsif @string_to_search[index-1, 1] == ' ' and
          @string_to_search[index+1,1]  == ' '
      # Here too.
    else
      @last_char    = @string_to_search[index-1,1]
      @current_char = @string_to_search[index,1]
      @next_char    = @string_to_search[index+1,1]
      if @next_char == @last_char
        palindrome = @last_char+@current_char+@next_char
        pp palindrome
        # The format for @array_found_palindrome is:
        #   0 sequence
        #   1 start_position
        #   2 end_position
        @array_found_palindrome << [ palindrome, index-1 ]
      end
    end
    index += 1
    break if string_size == index
  }
  e
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 49

def reset
  super()
  # ======================================================================= #
  # === @array_found_palindrome
  #
  # This array will keep the palindromes.
  # ======================================================================= #
  @array_found_palindrome = []
  # ======================================================================= #
  # === @last_char
  # ======================================================================= #
  @last_char    = ''
  # ======================================================================= #
  # === @current_char
  # ======================================================================= #
  @current_char = ''
  # ======================================================================= #
  # === @next_char
  # ======================================================================= #
  @next_char    = ''
  # ======================================================================= #
  # === @longest_palindrome
  # ======================================================================= #
  @longest_palindrome = nil # if we did found a palindrome, this counter
                            # tells us how many chars it has.
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 195

def run
  display_results
end

#set_string_to_search(i = DEFAULT_SEARCH_STRING) ⇒ Object

#
#


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# File 'lib/bioroebe/palindromes/palindrome_finder.rb', line 79

def set_string_to_search(
    i = DEFAULT_SEARCH_STRING
  )
  i = i.first if i.is_a? Array
  i = DEFAULT_SEARCH_STRING if i.nil?
  i = DEFAULT_SEARCH_STRING if i.is_a?(Array) and i.empty?
  @string_to_search = i
end