Class: Bioroebe::AdvancedDotplot

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/dotplots/advanced_dotplot.rb

Overview

Bioroebe::AdvancedDotplot

Constant Summary collapse

DEFAULT_VALUE_FOR_A_MATCH =
#

DEFAULT_VALUE_FOR_A_MATCH

This is the default value to use for a dotplot. We could also use a ‘*’ token of course.

#
'*'
MATCH =

2

DEFAULT_VALUE_FOR_A_MATCH
NON_MATCH =
#

NON_MATCH

#
0
USE_COLOURS_IN_THIS_CLASS =
#

USE_COLOURS_IN_THIS_CLASS

Whether to have this class handle colours on the commandline or not.

#
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

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(string1 = ARGV[0], string2 = nil, run_already = true) ⇒ AdvancedDotplot

#

initialize

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 51

def initialize(
    string1     = ARGV[0],
    string2     = nil,
    run_already = true
  )
  reset
  # ======================================================================= #
  # If the first argument is an Array, and if it has at the least two
  # elements, then we need to assign the last element to string2.
  # ======================================================================= #
  if string1.is_a?(Array) and (string1.size > 1) and string2.nil?
    string2 = string1.pop
  end
  set_string1(string1)
  set_string2(string2)
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :use_asterisk
    # ===================================================================== #
    when :use_asterisk
      set_match_token('*')
    end
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::AdvancedDotplot.[]

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 201

def self.[](i = ARGV)
  new(i)
end

Instance Method Details

#explain_to_the_user_what_the_asterisk_mean ⇒ Object

#

explain_to_the_user_what_the_asterisk_mean

We have to explain to the user what the meaning of this is.

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 164

def explain_to_the_user_what_the_asterisk_mean
  e
  erev "Note that the #{@match}#{rev} denotes a dot (== match) here."
  e
end

#match? ⇒ Boolean Also known as: match

#

match?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 148

def match?
  @match
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 82

def reset
  super()
  set_match # Use the default in this case.
  # ======================================================================= #
  # === @non_match
  # ======================================================================= #
  @non_match = NON_MATCH
  if USE_COLOURS_IN_THIS_CLASS
    @non_match = lightgreen(@non_match)
  end
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 173

def run
  e
  e rev+top_row
  left_side = string1?
  left_side.each_with_index {|token, index|
    # ===================================================================== #
    # Also show that token
    # ===================================================================== #
    print rev, token, ' '
    # ===================================================================== #
    # Inner loop
    # ===================================================================== #
    string2.each_with_index {|inner_token, inner_index|
      if inner_token == token
        print @match
      else
        print @non_match
      end
      print ' '
    }
    e
  }
  explain_to_the_user_what_the_asterisk_mean
end

#set_match(i = MATCH) ⇒ Object Also known as: set_match_token

#

set_match

This method will determine which character is to be used when a match was found. Typically this is the ‘*’ character, but the constant defined on top of this .rb file can be changed to use another character.

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 102

def set_match(i = MATCH)
  @match = i
  if USE_COLOURS_IN_THIS_CLASS # And use colours.
    @match = orange(@match)
  end
end

#set_string1(i) ⇒ Object

#

set_string1

string1 is on the left side of the 2d diagramm.

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 114

def set_string1(i)
  i = i.join  if i.is_a? Array
  i = i.chars if i.is_a? String
  @string1 = i
end

#set_string2(i) ⇒ Object

#

set_string2

string2 is on the top side of the 2d diagramm.

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 125

def set_string2(i)
  i = i.join  if i.is_a? Array
  i = i.chars if i.is_a? String
  @string2 = i
end

#string1? ⇒ Boolean Also known as: string1

#

string1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 141

def string1?
  @string1
end

#string2? ⇒ Boolean Also known as: string2

#

string2?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 134

def string2?
  @string2
end

#top_row ⇒ Object

#

top_row

#


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# File 'lib/bioroebe/dotplots/advanced_dotplot.rb', line 155

def top_row
  "  #{string2.join(' ')}"
end