Class: Bioroebe::ShowThisDNASequence
Overview
Bioroebe::ShowThisDNASequence
Constant Summary
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- DEFAULT_STRING =
'GATCGC'
CommandlineApplication::OLD_VERBOSE_VALUE
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
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-
.[](i) ⇒ Object
# === ShowThisDNASequence[] ========================================================================= #.
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(i = DEFAULT_STRING, run_already = true) ⇒ ShowThisDNASequence
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 34
def initialize(
i = DEFAULT_STRING,
run_already = true
)
reset
set_input(i)
run if run_already
end
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Class Method Details
.[](i) ⇒ Object
#
ShowThisDNASequence[]
#
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 140
def self.[](i)
new(i)
end
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Instance Method Details
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 78
def input?
@input
end
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#leading_three_prime ⇒ Object
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 109
def leading_three_prime
"3' "
end
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#report ⇒ Object
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 123
def report
e if @use_two_newlines_when_displaying_the_result
show_the_input_sequence
show_the_complementary_sequence
e if @use_two_newlines_when_displaying_the_result
end
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#reset ⇒ Object
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 46
def reset
super()
@padding = ' '.dup
@use_two_newlines_when_displaying_the_result = true
end
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#run ⇒ Object
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 133
def run
report
end
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 66
def set_input(i = DEFAULT_STRING)
if i.is_a? Array
i = i.join.strip
end
i = i.dup if i
i = DEFAULT_STRING if i.nil?
@input = i
end
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#show_the_complementary_sequence ⇒ Object
#
show_the_complementary_sequence
#
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 96
def show_the_complementary_sequence
erev @padding+
leading_three_prime+
colourize_this_nucleotide_sequence(
return_the_complementary_nucleotide_sequence_to(@input)
)+
rev+
trailing_five_prime
end
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 85
def show_the_input_sequence
erev @padding+
leading_five_prime+
colourize_this_nucleotide_sequence(@input)+
rev+
trailing_three_prime
end
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#trailing_five_prime ⇒ Object
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# File 'lib/bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb', line 116
def trailing_five_prime
" 5'"
end
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