Class: Bioroebe::SimpleStringComparer

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

Overview

Bioroebe::SimpleStringComparer

Constant Summary collapse

STRING1 =
#

STRING1

#
'gelfand'
STRING2 =
#

STRING2

#
'gandalf'
VERTICAL_BAR =
#

VERTICAL_BAR

#
'|'
DEFAULT_MATCH_TOKEN =
#

DEFAULT_MATCH_TOKEN

This token is used to indicate a matching position. By default it will be the '|' character.

#
VERTICAL_BAR

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, #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(i = nil, run_already = true, &block) ⇒ SimpleStringComparer

#

initialize

#

60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 60

def initialize(
    i           = nil,
    run_already = true,
    &block
  )
  reset
  case i
  when nil # Pass through in this case.
  when :dont_run_yet
    i = nil
    run_already = false
  else
    guess_from_this_input(i)
  end
  # ======================================================================= #
  # === Handle blocks given to this method
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :disable_colours
      disable_colours
    # ===================================================================== #
    # === :use_vertical_bar
    # ===================================================================== #
    when :use_vertical_bar
      set_match_token :vertical_bar
    end
  end
  run if run_already
end

Instance Method Details

#consider_notifying_the_user_if_the_sequences_are_not_equal_in_lengthObject

#

consider_notifying_the_user_if_the_sequences_are_not_equal_in_length

#

269
270
271
272
273
274
275
276
277
278
279
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 269

def consider_notifying_the_user_if_the_sequences_are_not_equal_in_length
  if @string1.size == @string2.size
    # In this case, all is fine.
  else
    # else notify the user
    e
    e '(Note that the two sequences are not equal in length. This class'
    e 'will only try to align from the starting position of both'
    e 'sequences as-is.)'
  end
end

#do_compareObject Also known as: compare

#

do_compare

#

237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 237

def do_compare
  e rev # A newline for easier reading.
  chars1 = string1?.chars
  array1 = chars1.each_slice(80).to_a.map {|entry|
    entry.join
  }
  chars2 = string2?.chars
  array2 = chars2.each_slice(80).to_a.map {|entry|
    entry.join
  }
  # ======================================================================= #
  # Combine the two Arrays in order to find the "third" array.
  # ======================================================================= #
  array3 = chars1.zip(chars2).map {|entry|
    match_or_no_match_for(entry[0], entry[1])
  }.each_slice(80).to_a.map {|entry|
    entry.join
  }.map {|line|
    line.gsub(/\|/, seagreen(match_token?)+rev) # Colourize the match-token in the colour seagreen.
  }
  0.upto(array1.size-1) {|index|
    e array1[index]
    e array3[index] # Middle position.
    e array2[index]
  }
  consider_notifying_the_user_if_the_sequences_are_not_equal_in_length
  e
end

#guess_from_this_input(i) ⇒ Object

#

guess_from_this_input

#

117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 117

def guess_from_this_input(i)
  # ======================================================================= #
  # === Handle the case when the user did input two Arrays
  # ======================================================================= #
  i.flatten! if i.is_a? Array
  if i.is_a? Array and i.empty?
    # ===================================================================== #
    # If our Array is empty, assign a default here.
    # ===================================================================== #
    splitted = [STRING1, STRING2]
  else
    splitted = i
  end
  splitted = splitted.split(N) unless splitted.is_a? Array
  splitted.map!(&:strip) # Get rid of trailing and leading newspaces.
  if splitted.is_a? Array
    if splitted.size == 1
      if splitted.first.include? '|'
        splitted = splitted.first.split('|')
      end
    end
  end
  set_string_one(splitted.first)
  set_string_last(splitted.last)
end

#match_or_no_match_for(char1, char2) ⇒ Object

#

match_or_no_match_for

#

199
200
201
202
203
204
205
206
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 199

def match_or_no_match_for(char1, char2)
  if char1 == char2
    @n_matches += 1
    return_match_token
  else
    return_non_match_token
  end
end

#match_token?Boolean

#

match_token?

#

Returns:

  • (Boolean)

230
231
232
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 230

def match_token?
  @match_token
end

#n_matches?Boolean

#

n_matches?

#

Returns:

  • (Boolean)

192
193
194
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 192

def n_matches?
  @n_matches
end

#resetObject

#

reset (reset tag)

Set default values for the two Strings.

#

97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 97

def reset
  super()
  # ======================================================================= #
  # Set up default strings first.
  # ======================================================================= #
  set_string1 STRING1
  set_string2 STRING2
  # ======================================================================= #
  # === @n_matches
  #
  # This counter will keep track how many matches we found.
  # ======================================================================= #
  @n_matches = 0
  set_match_token
  @non_match_token = '.' # This is the token that will be displayed for non-matches.
end

#return_match_tokenObject

#

return_match_token

#

185
186
187
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 185

def return_match_token
  @match_token
end

#return_non_match_tokenObject

#

return_non_match_token

#

177
178
179
180
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 177

def return_non_match_token
  return swarn(@non_match_token)+rev if use_colours? # Colourize this in red if we use colours.
  @non_match_token # Else just return it.
end

#runObject

#

run (run tag)

#

284
285
286
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 284

def run
  do_compare
end

#set_match_token(i = DEFAULT_MATCH_TOKEN) ⇒ Object Also known as: set_main_alignment_token_to

#

set_match_token

You can define another match token here. The default is '+', another popular variant would be '|'.

#

214
215
216
217
218
219
220
221
222
223
224
225
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 214

def set_match_token(
    i = DEFAULT_MATCH_TOKEN
  )
  case i
  # ======================================================================= #
  # === :vertical_bar
  # ======================================================================= #
  when :vertical_bar
    i = VERTICAL_BAR
  end
  @match_token = i
end

#set_string1(i) ⇒ Object Also known as: string1=, set_string_one

#

set_string1

#

146
147
148
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 146

def set_string1(i)
  @string1 = i
end

#set_string2(i) ⇒ Object Also known as: string2=, set_string_two, set_string_last

#

set_string2

#

154
155
156
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 154

def set_string2(i)
  @string2 = i
end

#string1?Boolean Also known as: input?

#

string1?

#

Returns:

  • (Boolean)

163
164
165
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 163

def string1?
  @string1
end

#string2?Boolean Also known as: string2

#

string2

#

Returns:

  • (Boolean)

170
171
172
# File 'lib/bioroebe/string_matching/simple_string_comparer.rb', line 170

def string2?
  @string2
end