Class: Bioroebe::BiolangParser

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/parsers/biolang_parser.rb

Overview

Bioroebe::BiolangParser

Constant Summary collapse

BIOLANG_DIR = 
'/tmp/robert'
BIO_LANG =
#

BIO_LANG

#
"#{BIOLANG_DIR}bio_lang.md"
IMMUNO_LANG =
#

IMMUNO_LANG

#
"#{BIOLANG_DIR}immuno_lang.md"
VIR_LANG =
#

VIR_LANG

#
BIOLANG_DIR+'vir_lang'

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Bioroebe::Base::NAMESPACE

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, #opne, #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, #set_be_verbose, #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 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_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?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #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

Constructor Details

#initialize(file_location = BIO_LANG, run_already = true) ⇒ BiolangParser

#

initialize

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 51

def initialize(
    file_location = BIO_LANG,
    run_already   = true
  )
  set_file_location(
    file_location
  )
  reset
  run if run_already
end

Instance Method Details

#location? ⇒ Boolean

#

location?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 92

def location?
  @file_location
end

#read_file_content ⇒ Object

#

read_file_content

Read into array.

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 80

def read_file_content
  _ = location?
  if File.exist? _
    @array_file_content = File.readlines(_)
  else
    opnn; no_file_exists_at(_)
  end
end

#report_available_entries ⇒ Object

#

report_available_entries

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 106

def report_available_entries
  e 'These entries are available:'
  e
  @array_main_entries.each_with_index { |entry, index|
    erev '  '+sfancy((index+1).to_s.rjust(3))+
         rev+' -'+entry.to_s
  }
  e
end

#report_main_file ⇒ Object

#

report_main_file

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 135

def report_main_file
  erev 'The input-file can be found at:'
  e
  e "  #{sfile(@file_location)}"
  e
end

#reset ⇒ Object

#

reset

Reset out variables.

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 67

def reset
  super()
  # ======================================================================= #
  # === @array_file_content
  # ======================================================================= #
  @array_file_content = []
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 145

def run
  read_file_content
  scan_for_available_main_entries
  report_available_entries
end

#scan_for_available_main_entries ⇒ Object

#

scan_for_available_main_entries

Will fetch all main entries out of the file. “main entries” are those that start at left entry

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 122

def scan_for_available_main_entries
  @array_main_entries = []
  @array_file_content.each { |line|
    next if line.empty? or
            line.start_with? ' '
            line.start_with? '#'
    @array_main_entries << line.gsub(/#.+/,'').strip if line =~ /^(.+)$/
  }
end

#set_file_location(i) ⇒ Object

#

set_file_location

#

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# File 'lib/bioroebe/parsers/biolang_parser.rb', line 99

def set_file_location(i)
  @file_location = i # set @file_location ivar.
end