Class: Bioroebe::MirrorRepeat
Overview
Constant Summary
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
collapse
Instance Method Summary
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#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
#initialize(commandline_arguments = nil, run_already = true) ⇒ MirrorRepeat
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 31
def initialize(
commandline_arguments = nil,
run_already = true
)
reset
set_commandline_arguments(
commandline_arguments
)
if block_given?
yielded = yield
if yielded.is_a? Hash
if yielded.has_key? :use_separator_token
commandline_arguments? << '--use-spacer'
elsif yielded.has_key? :separator_token
commandline_arguments? << '--use-spacer'
end
if yielded.has_key? :use_colours
set_use_colours(
yielded.delete(:use_colours)
)
end
if yielded.has_key? :be_verbose
set_be_verbose(
yielded.delete(:be_verbose)
)
end
end
end
run if run_already
end
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Class Method Details
.[](i = '', &block) ⇒ Object
#
Bioroebe::MirrorRepeat[]
#
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 196
def self.[](i = '', &block)
new(i, &block)
end
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Instance Method Details
#determine_the_main_sequence ⇒ Object
#
determine_the_main_sequence
#
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 113
def determine_the_main_sequence
@sequence = return_commandline_arguments_without_hyphen.join
end
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#determine_the_result ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 127
def determine_the_result
if @sequence.nil?
e 'Please supply some proper input to this class.'
return
end
if @use_spacer
@result = "#{rev}#{@sequence}#{return_spacer}#{rev}#{@sequence.reverse}"
else
@result = @sequence + @sequence.reverse
end
end
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 142
def (
i = commandline_arguments?
)
if i.is_a? Array
i.each {|entry| (entry) }
else
case i when /^-?-?spacer$/i,
/^-?-?use(-|_)?spacer$/i,
/^-?-?with(-|_)?separator$/i
@use_spacer = true
when /^-?-?disable(-|_)?colours?$/i
disable_colours
when /^-?-?help$/i
show_help
exit
end
end
end
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#report(i = @result) ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 120
def report(i = @result)
e i if i and be_verbose?
end
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#reset ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 77
def reset
super()
@use_spacer = false
@result = nil
end
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#result? ⇒ Boolean
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 106
def result?
@result
end
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#return_spacer ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 95
def return_spacer
_ = '|'
if use_colours?
_ = ::Colours.steelblue(_)
end
_
end
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#run ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 185
def run
remove_hyphens_from_the_commandline_arguments
determine_the_main_sequence
determine_the_result
report
end
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#show_help ⇒ Object
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# File 'lib/bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb', line 175
def show_help
e 'Currently the following options are supported by this class:'
e
e ' --spacer # use a spacer to denote where the mirror repeat begins'
e
end
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