Class: Bioroebe::Taxonomy::Chart

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

Overview

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Bioroebe::Taxonomy::Chart

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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

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(dataset = nodes?, , run_already = true) ⇒ Chart

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initialize

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

def initialize(
    dataset     = nodes?,
    run_already = true
  ) # Initialized with all nodes.
  reset
  @dataset = dataset
  run if run_already
end

Instance Attribute Details

#hash ⇒ Object

Returns the value of attribute hash.



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

def hash
  @hash
end

Instance Method Details

#[](i = ARGV) ⇒ Object Also known as: find_id

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Bioroebe::Taxonomy::Chart[]

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# File 'lib/bioroebe/taxonomy/chart.rb', line 90

def [](i = ARGV)
  i = i.to_sym unless i.is_a? Fixnum # For now these are symbols.
  return @hash[i]
end

#find_parent_of(i) ⇒ Object Also known as: find_parent

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find_parent_of

Find the parent here.

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# File 'lib/bioroebe/taxonomy/chart.rb', line 57

def find_parent_of(i)
  result = find_id(i)
  cliner {
    pp result
    pp result
    pp result
  }
  return result.parent_taxid
end

#populate_hash_from_the_dataset ⇒ Object

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populate_hash_from_the_dataset

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# File 'lib/bioroebe/taxonomy/chart.rb', line 70

def populate_hash_from_the_dataset
  @dataset.each {|entry|
    new_node = Node.parse(entry)
    id = new_node.taxid.to_sym
    @hash[id] = new_node
  }
end

#reset ⇒ Object

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reset (reset tag)

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# File 'lib/bioroebe/taxonomy/chart.rb', line 44

def reset
  super()
  # ======================================================================= #
  # === @hash
  # ======================================================================= #
  @hash = {} # Main hash to keep all of our Nodes.
end

#run ⇒ Object

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run

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

def run
  populate_hash_from_the_dataset
  remove_instance_variable :@dataset # Dont need it anymore here.
  return @hash
end