Class: Bioroebe::Taxonomy::Node

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/taxonomy/node.rb

Overview

Bioroebe::Taxonomy::Node

Constant Summary

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

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(optional_read_in_from_this_file = nil) ⇒ Node

#

initialize

#


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# File 'lib/bioroebe/taxonomy/node.rb', line 37

def initialize(
    optional_read_in_from_this_file = nil
  )
  reset
  if optional_read_in_from_this_file
    @data = nodes?(optional_read_in_from_this_file)
  end
end

Instance Attribute Details

#comments ⇒ Object

Returns the value of attribute comments.



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# File 'lib/bioroebe/taxonomy/node.rb', line 32

def comments
  @comments
end

#division_id ⇒ Object

Returns the value of attribute division_id.



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# File 'lib/bioroebe/taxonomy/node.rb', line 24

def division_id
  @division_id
end

#embl_code ⇒ Object

Returns the value of attribute embl_code.



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# File 'lib/bioroebe/taxonomy/node.rb', line 23

def embl_code
  @embl_code
end

#genbank_hidden_flag ⇒ Object

Returns the value of attribute genbank_hidden_flag.



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# File 'lib/bioroebe/taxonomy/node.rb', line 30

def genbank_hidden_flag
  @genbank_hidden_flag
end

#genetic_code_id ⇒ Object

Returns the value of attribute genetic_code_id.



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# File 'lib/bioroebe/taxonomy/node.rb', line 26

def genetic_code_id
  @genetic_code_id
end

#hidden_subtree_root_flag ⇒ Object

Returns the value of attribute hidden_subtree_root_flag.



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# File 'lib/bioroebe/taxonomy/node.rb', line 31

def hidden_subtree_root_flag
  @hidden_subtree_root_flag
end

#inherited_div_flag ⇒ Object

Returns the value of attribute inherited_div_flag.



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# File 'lib/bioroebe/taxonomy/node.rb', line 25

def inherited_div_flag
  @inherited_div_flag
end

#inherited_gc_flag ⇒ Object

Returns the value of attribute inherited_gc_flag.



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# File 'lib/bioroebe/taxonomy/node.rb', line 27

def inherited_gc_flag
  @inherited_gc_flag
end

#inherited_mgc_flag ⇒ Object

Returns the value of attribute inherited_mgc_flag.



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# File 'lib/bioroebe/taxonomy/node.rb', line 29

def inherited_mgc_flag
  @inherited_mgc_flag
end

#mitochondrial_genetic_code_id ⇒ Object

Returns the value of attribute mitochondrial_genetic_code_id.



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# File 'lib/bioroebe/taxonomy/node.rb', line 28

def mitochondrial_genetic_code_id
  @mitochondrial_genetic_code_id
end

#parent_taxid ⇒ Object

Returns the value of attribute parent_taxid.



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# File 'lib/bioroebe/taxonomy/node.rb', line 21

def parent_taxid
  @parent_taxid
end

#rank ⇒ Object

Returns the value of attribute rank.



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# File 'lib/bioroebe/taxonomy/node.rb', line 22

def rank
  @rank
end

#taxid ⇒ Object

#

13 entries. Will include taxid, parent_taxid, rank and so forth.

#


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# File 'lib/bioroebe/taxonomy/node.rb', line 20

def taxid
  @taxid
end

Class Method Details

.parse(i) ⇒ Object

#

Node.parse()

Parse an input string which should be a Node. This method will setup the corresponding fields.

#


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# File 'lib/bioroebe/taxonomy/node.rb', line 59

def self.parse(i)
  _ = split(i.chomp)
  node = Node.new
  node.taxid                         = _[0]
  node.parent_taxid                  = _[1]
  node.rank                          = _[2]
  node.embl_code                     = _[3]
  node.division_id                   = _[4]
  node.inherited_div_flag            = _[5]
  node.genetic_code_id               = _[6]
  node.inherited_gc_flag             = _[7]
  node.mitochondrial_genetic_code_id = _[8]
  node.inherited_mgc_flag            = _[9]
  node.genbank_hidden_flag           = _[10]
  node.hidden_subtree_root_flag      = _[11]
  node.comments = sanitize_content(_[12])
  return node
end

Instance Method Details

#parent? ⇒ Boolean

#

parent?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/taxonomy/node.rb', line 81

def parent? # Give back our parent.
  parent_taxid
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/taxonomy/node.rb', line 49

def reset
  super()
end