Class: Bioroebe::ScanForRepeat
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::ScanForRepeat
- Defined in:
- lib/bioroebe/patterns/scan_for_repeat.rb
Overview
Bioroebe::ScanForRepeat
Constant Summary
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Class Method Summary collapse
-
.[](i = '') ⇒ Object
# === Bioroebe::ScanForRepeat[] ========================================================================= #.
Instance Method Summary collapse
-
#determine_the_main_sequence ⇒ Object
# === determine_the_main_sequence ========================================================================= #.
-
#do_scan_for_the_main_pattern_in_use ⇒ Object
# === do_scan_for_the_main_pattern_in_use ========================================================================= #.
-
#initialize(commandline_arguments = nil, run_already = true) ⇒ ScanForRepeat
constructor
# === initialize ========================================================================= #.
-
#n_repeats? ⇒ Boolean
(also: #n_patterns?)
# === @n_repeats ========================================================================= #.
-
#report ⇒ Object
# === report (report tag) ========================================================================= #.
-
#reset ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#run ⇒ Object
# === run (run tag) ========================================================================= #.
-
#set_scan_for_this_repeat(i = 'TAAG') ⇒ Object
(also: #set_use_this_pattern)
# === set_scan_for_this_repeat ========================================================================= #.
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(commandline_arguments = nil, run_already = true) ⇒ ScanForRepeat
#
initialize
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 25 def initialize( commandline_arguments = nil, run_already = true ) reset set_commandline_arguments( commandline_arguments ) # ======================================================================= # # === Handle blocks given next # ======================================================================= # if block_given? yielded = yield if yielded.is_a? Hash # =================================================================== # # === :pattern # =================================================================== # if yielded.has_key? :pattern set_use_this_pattern(yielded[:pattern]) end # =================================================================== # # === :verbose # =================================================================== # if yielded.has_key? :verbose set_be_verbose(:be_quiet) end end end run if run_already end |
Class Method Details
.[](i = '') ⇒ Object
#
Bioroebe::ScanForRepeat[]
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 127 def self.[](i = '') new(i) end |
Instance Method Details
#determine_the_main_sequence ⇒ Object
#
determine_the_main_sequence
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 90 def determine_the_main_sequence @main_sequence = first? end |
#do_scan_for_the_main_pattern_in_use ⇒ Object
#
do_scan_for_the_main_pattern_in_use
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 97 def do_scan_for_the_main_pattern_in_use @n_repeats = @main_sequence.scan(/#{@scan_for_this_repeat}/).size report if be_verbose? end |
#n_repeats? ⇒ Boolean Also known as: n_patterns?
#
@n_repeats
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 105 def n_repeats? @n_repeats end |
#report ⇒ Object
#
report (report tag)
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 112 def report e @n_repeats end |
#reset ⇒ Object
#
reset (reset tag)
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 59 def reset super() infer_the_namespace # ======================================================================= # # === @n_repeats # ======================================================================= # @n_repeats = 0 # ======================================================================= # # === @scan_for_this_repeat # # Try to find the following repeat. # # We may also need to allow for syntax such as '(TAAG)n' as valid # input. # ======================================================================= # set_scan_for_this_repeat end |
#run ⇒ Object
#
run (run tag)
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 119 def run determine_the_main_sequence do_scan_for_the_main_pattern_in_use end |
#set_scan_for_this_repeat(i = 'TAAG') ⇒ Object Also known as: set_use_this_pattern
#
set_scan_for_this_repeat
#
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# File 'lib/bioroebe/patterns/scan_for_repeat.rb', line 80 def set_scan_for_this_repeat(i = 'TAAG') i = i.dup i.chop! if i.end_with? 'n' i.delete!('()') if i.include?('(') @scan_for_this_repeat = i end |