Class: Bioroebe::Digestion
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::Digestion
- Defined in:
- lib/bioroebe/cleave_and_digest/digestion.rb
Overview
Bioroebe::Digestion
Direct Known Subclasses
Constant Summary
Constants inherited from CommandlineApplication
CommandlineApplication::OLD_VERBOSE_VALUE
Constants included from ColoursForBase
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited from Base
Instance Method Summary collapse
-
#consider_reading_from_a_file_if_given_as_input_argument_to_this_class ⇒ Object
# === consider_reading_from_a_file_if_given_as_input_argument_to_this_class.
-
#mediumturquoise_1_to_10 ⇒ Object
# === mediumturquoise_1_to_10 ========================================================================= #.
-
#reset ⇒ Object
# === reset ========================================================================= #.
-
#return_1_to_10 ⇒ Object
# === return_1_to_10 ========================================================================= #.
-
#sequence? ⇒ Boolean
# === sequence? ========================================================================= #.
-
#set_first(i) ⇒ Object
# === set_first ========================================================================= #.
-
#show_the_weight_of_these_aminoacids? ⇒ Boolean
# === show_the_weight_of_these_aminoacids? ========================================================================= #.
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?, #initialize, #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
This class inherits a constructor from Bioroebe::Base
Instance Method Details
#consider_reading_from_a_file_if_given_as_input_argument_to_this_class ⇒ Object
#
consider_reading_from_a_file_if_given_as_input_argument_to_this_class
This method allows us to use a fasta file (.fa or .fasta as extension) for input.
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 76 def consider_reading_from_a_file_if_given_as_input_argument_to_this_class if first? and File.file?(first?) _ = ParseFasta.new(first?) { :be_quiet } set_first(_.content?) end end |
#mediumturquoise_1_to_10 ⇒ Object
#
mediumturquoise_1_to_10
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 52 def mediumturquoise_1_to_10 mediumturquoise(return_1_to_10) end |
#reset ⇒ Object
#
reset
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 26 def reset super() reset_the_internal_hash # Always allow for @internal_hash to exist here. # ======================================================================= # # === :show_the_weight_of_these_aminoacids # ======================================================================= # @internal_hash[:show_the_weight_of_these_aminoacids] = true end |
#return_1_to_10 ⇒ Object
#
return_1_to_10
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 59 def return_1_to_10 '1234567890' end |
#sequence? ⇒ Boolean
#
sequence?
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 66 def sequence? first? end |
#set_first(i) ⇒ Object
#
set_first
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 45 def set_first(i) @commandline_arguments[0] = i end |
#show_the_weight_of_these_aminoacids? ⇒ Boolean
#
show_the_weight_of_these_aminoacids?
#
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# File 'lib/bioroebe/cleave_and_digest/digestion.rb', line 38 def show_the_weight_of_these_aminoacids? @internal_hash[:show_the_weight_of_these_aminoacids] end |