Class: Bioroebe::AminoacidsMassTable

Inherits:
Base
  • Object
show all
Defined in:
lib/bioroebe/aminoacids/aminoacids_mass_table.rb

Overview

Bioroebe::AminoacidsMassTable

Constant Summary collapse

PADDING_TO_USE =
#

PADDING_TO_USE

#
'  '

Constants inherited from Base

Base::NAMESPACE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

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 BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

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 included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize ⇒ AminoacidsMassTable

#

initialize

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 25

def initialize
  reset
  Bioroebe::AminoacidsMassTable.show
end

Class Method Details

.e(i = '') ⇒ Object

#

AminoacidsMassTable.e

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 47

def self.e(i = '')
  puts i
end

.erev(i) ⇒ Object

#

AminoacidsMassTable.erev

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 40

def self.erev(i)
  ::Bioroebe.erev(i)
end

.report_which_file_is_used ⇒ Object

#

AminoacidsMassTable.report_which_file_is_used

The purpose of this method is to simply report which file we use to read in the mass table.

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 101

def self.report_which_file_is_used
  erev 'We will read from the file `'+
        Colours.sfile(FILE_AMINO_ACIDS_MASS_TABLE)+
        Colours.rev+'`.'
end

.show(optional_padding = PADDING_TO_USE) ⇒ Object

#

Bioroebe::AminoacidsMassTable.show

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 54

def self.show(
    optional_padding = PADDING_TO_USE
  )
  sum = 0
  erev 'Aminoacids Mass Table - Molecular Weight of '\
       'Amino Acids:'; e # Need a newline here.
  AMINO_ACIDS_MASS_TABLE.each {|key, value|
    long_amino_acid = AMINO_ACIDS[key].select {|inner_key, _|
      inner_key.size == 3
    }.values.first
    left = optional_padding+
           key.to_s+
           ' ('+long_amino_acid+')'+': '
    sum += value # Add to the sum.
    # ===================================================================== #
    # Next pad the value.
    # ===================================================================== #
    value = value.to_s.rjust(10)
    value = '%.3f' % value
    value = value.rjust(10)
    left = left.ljust(23)
    # ===================================================================== #
    # The variable left may look like this:
    #   "  T (threonine): "
    # ===================================================================== #
    if left.include? '('
      splitted = left.split('(')
      splitted[0] = ::Bioroebe.springgreen(splitted[0])+::Bioroebe.rev
      left = splitted.join('(')
    end
    erev left+
         Colours.sfancy(value)
  }
  e
  erev 'Average weight of an amino acid: '+
    Colours.simp(
      (sum.to_f / AMINO_ACIDS_MASS_TABLE.keys.size).round(2).to_s
    )
  e # Trailing newline.
end

Instance Method Details

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/aminoacids/aminoacids_mass_table.rb', line 33

def reset
  super()
end