Class: Bioroebe::Ruler
Overview
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, #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
#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_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(for_this_sequence = ARGV, group_together_n_nucleotides = 72, run_already = true) ⇒ Ruler
#
initialize
The second argument determines which grouping is to be applied, that is, how many nucleotides are shown per line.
#
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# File 'lib/bioroebe/misc/ruler.rb', line 42
def initialize(
for_this_sequence = ARGV,
group_together_n_nucleotides = 72,
run_already = true
)
reset
set_use_this_sequence(
for_this_sequence
)
set_group_together_n_nucleotides(
group_together_n_nucleotides
)
if block_given?
yielded = yield
if yielded.is_a? Hash
if yielded.has_key? :ruler
_ = yielded.delete(:ruler)
case _
when :no_colours,
:without_colours
@highlight_numbers = false
end
end
else
case yielded
when :no_colours,
:without_colours
@highlight_numbers = false
end
end
end
run if run_already
end
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Instance Method Details
#main_sequence? ⇒ Boolean
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# File 'lib/bioroebe/misc/ruler.rb', line 138
def main_sequence?
@use_this_sequence
end
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#reset ⇒ Object
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# File 'lib/bioroebe/misc/ruler.rb', line 92
def reset
super()
@result = []
@group_together_n_nucleotides = 72
@highlight_numbers = true
end
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#result? ⇒ Boolean
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# File 'lib/bioroebe/misc/ruler.rb', line 145
def result?
@result
end
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#result_as_string? ⇒ Boolean
Also known as:
result_as_string
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# File 'lib/bioroebe/misc/ruler.rb', line 152
def result_as_string?
@result.join.strip
end
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#run ⇒ Object
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# File 'lib/bioroebe/misc/ruler.rb', line 159
def run
chunks = main_sequence?.to_s.split(/(.{#{@group_together_n_nucleotides}})/).reject(&:empty?)
array = chunks.each_slice(@group_together_n_nucleotides).to_a.flatten
array.each {|sequence| _ = ''.dup
sequence.chars.each_with_index {|char, index| index += 1
result = index % 10
if @highlight_numbers
case result
when 1
result = crimson(result)+rev
when 5, 0
result = royalblue(result)+rev
else
result = result.to_s
end
end
_ << result.to_s
}
@result << _
}
end
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#set_group_together_n_nucleotides(i = 72) ⇒ Object
#
set_group_together_n_nucleotides
#
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# File 'lib/bioroebe/misc/ruler.rb', line 112
def set_group_together_n_nucleotides(
i = 72
)
case i
when :default
i = 72
end
@group_together_n_nucleotides = i
end
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#set_use_this_sequence(i) ⇒ Object
#
set_use_this_sequence
#
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# File 'lib/bioroebe/misc/ruler.rb', line 128
def set_use_this_sequence(i)
if i.is_a? Array
i = i.join(' ').strip
end
@use_this_sequence = i
end
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