Class: Bioroebe::ElectronMicroscopy::ParseCoordinates

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/electron_microscopy/parse_coordinates.rb

Overview

Bioroebe::ElectronMicroscopy::ParseCoordinates

Constant Summary collapse

DEFAULT_FILE =
#

DEFAULT_FILE

#
'test_coordinates.pos'
DEFAULT_RUN_MODE =
#

DEFAULT_RUN_MODE

#
true

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 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(i = nil, run_already = DEFAULT_RUN_MODE) ⇒ ParseCoordinates

#

initialize

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 37

def initialize(
    i           = nil,
    run_already = DEFAULT_RUN_MODE
  )
  reset
  set_file(i)
  case run_already
  when :be_quiet
    be_silent
    run_already = DEFAULT_RUN_MODE
  end
  run if run_already
end

Instance Method Details

#clear_coordinates ⇒ Object

#

clear_coordinates

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 71

def clear_coordinates
  @array_coordinates = []
end

#coordinates? ⇒ Boolean

#

coordinates?

Return the coordinates.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 172

def coordinates?
  @array_coordinates
end

#dataset? ⇒ Boolean Also known as: dataset

#

dataset?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 78

def dataset?
  @dataset
end

#determine_coordinates ⇒ Object

#

determine_coordinates

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 156

def determine_coordinates
  clear_coordinates
  @dataset.each {|line|
    next unless line.include? '   '
    coordinates = parse_x_y_coordinate(line)
    @array_coordinates << coordinates
  } if @dataset
  # @array_coordinates.sort!
  # For some reason, sorting this dataset is not working for xmipp.
end

#file? ⇒ Boolean

#

file?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 126

def file?
  @file
end

#grab_dataset(use_this_file = file? ) ⇒ Object

#

grab_dataset

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 113

def grab_dataset(
    use_this_file = file?
  )
  if File.exist? use_this_file
    @dataset = File.readlines(use_this_file).map(&:strip)
  else
    no_file_exists_at(use_this_file)
  end
end

#no_file?(i = file? ) ⇒ Boolean

#

no_file?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 133

def no_file?(
    i = file?
  )
  !File.exist?(i)
end

#parse_x_y_coordinate(line) ⇒ Object

#

parse_x_y_coordinate

This method will parse x/y coordinates.

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 102

def parse_x_y_coordinate(line)
  line = line.split('  ').map(&:strip)
  line.reject!(&:empty?)
  x = line[0]
  y = line[1]
  return [x,y]
end

#report_stats ⇒ Object

#

report_stats

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 142

def report_stats
  _ = file?
  if no_file?
    opnerev 'No statistics can be reported because there is'
    opnerev 'no file at `'+sfile(_)+'`.'
  else
    opnerev "We have #{sfancy(@array_coordinates.size.to_s)} "\
            "#{rev}coordinates in #{sfile(_)}#{rev}."
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 54

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @dataset
  # ======================================================================= #
  @dataset = nil
  # ======================================================================= #
  # === :be_verbose
  # ======================================================================= #
  set_be_verbose
  clear_coordinates
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 179

def run
  grab_dataset
  determine_coordinates
  report_stats # Show some information about our dataset in question.
end

#set_file(i = DEFAULT_FILE) ⇒ Object

#

set_file

#


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# File 'lib/bioroebe/electron_microscopy/parse_coordinates.rb', line 85

def set_file(
    i = DEFAULT_FILE
  )
  i = i.first if i.is_a? Array
  i = DEFAULT_FILE if i.nil?
  i = i.to_s.dup
  if be_verbose?
    opne "#{rev}Next assigning to the file #{sfile(i)}#{rev}."
  end
  @file = i
end