Class: Bioroebe::Gene

Inherits:
Sequence show all
Defined in:
lib/bioroebe/gene/gene.rb

Overview

Bioroebe::Gene

Constant Summary

Constants inherited from Sequence

Sequence::REMOVE_INVALID_CHARACTERS, Sequence::SHALL_WE_UPCASE

Instance Method Summary collapse

Methods inherited from Sequence

[], #automatic_support_for_nucleotides, #description?, #index, #infer_type, #is_DNA?, #is_RNA?, #is_a_protein?, #is_a_protein_now, #map, #n_uracil?, #randomize, #remove_invalid_entries_from_the_dna_sequence, #remove_invalid_entries_from_the_dna_sequence!, #return_string_nucleotides_or_aminoacids, #sanitize_dataset, #sanitize_rna, #save_sequence_to_this_file, sequence_from_file, #set_description, #set_dna, #set_protein, #set_rna, #set_save_file, #set_sequence, #set_type, #shall_we_upcase?, #size?, #to_genbank, #to_regexp, #type?

Methods inherited from RawSequence

#+, #<<, #[]=, #calculate_levensthein_distance, #chars?, #complement, #composition?, #count, #delete, #delete!, #downcase, #each_char, #empty?, #find_substring_indices, #first_position=, #freeze, #gsub, #gsub!, #include?, #insert_at_this_position, #prepend, #remove_n_characters_from_the_left_side, #reverse, #reverse!, #reverse_complement, #scan, #set_raw_sequence, #shuffle, #size?, #split, #start_with?, #strip, #subseq, #to_s, #to_str, #tr!, #upcase!

Constructor Details

#initialize(sequence_to_use = '', optional_use_this_name = nil) ⇒ Gene

#

initialize

#


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# File 'lib/bioroebe/gene/gene.rb', line 25

def initialize(
    sequence_to_use        = '',
    optional_use_this_name = nil
  )
  reset
  super(sequence_to_use)
  if optional_use_this_name
    set_name(optional_use_this_name)
  end
end

Instance Method Details

#name? ⇒ Boolean

#

name?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gene/gene.rb', line 56

def name?
  @hash.fetch :name
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gene/gene.rb', line 39

def reset
  # ======================================================================= #
  # === @hash
  # ======================================================================= #
  @hash = {}
end

#set_name(i) ⇒ Object

#

set_name

#


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# File 'lib/bioroebe/gene/gene.rb', line 49

def set_name(i)
  @hash[:name] = i
end