Class: Bioroebe::FindLongestSubstringViaLCSalgorithm
Overview
Bioroebe::FindLongestSubstring
Constant Summary
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Instance Method Summary
collapse
#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
#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
#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
#internal_hash?, #reset_the_internal_hash
#infer_the_namespace, #namespace?
Constructor Details
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 31
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
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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 127
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
opnerev 'The gem '+sfancy('diff-lcs')+rev+' is not installed. '\
'Please install it if you'
opnerev 'wish to make use of this gem here.'
end
end
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#diff_lcs_is_available? ⇒ Boolean
#
diff_lcs_is_available?
#
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 115
def diff_lcs_is_available?
unless Object.const_defined? :Diff
begin
require 'diff-lcs'
rescue LoadError; end
end
Object.const_defined? :Diff
end
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#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 149
def do_show_the_two_sequences
erev 'Sequence 1: '+sfancy(seq1?)
erev 'Sequence 2: '+sfancy(seq2?)
end
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#reset ⇒ Object
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 51
def reset
super()
infer_the_namespace
@string1 = nil
@string2 = nil
@also_show_the_two_sequences = false end
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#run ⇒ Object
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 157
def run
determine_whether_diff_lcs_is_available
end
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#set_string1(i) ⇒ Object
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 71
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
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#set_string2(i) ⇒ Object
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 92
def set_string2(i)
@string2 = i
end
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#string1? ⇒ Boolean
Also known as:
seq1, seq1?
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 99
def string1?
@string1
end
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#string2? ⇒ Boolean
Also known as:
seq2, seq2?
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# File 'lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb', line 107
def string2?
@string2
end
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