Class: Phobius::Index

Inherits:
Hash show all
Includes:
TransmembraneIndex
Defined in:
lib/transmembrane/phobius.rb

Overview

note: to implement some of the TransmembraneIndex features, the update_aaseq method must be called!

Instance Method Summary collapse

Methods included from TransmembraneIndex

#avg_overlap, filetype, new, #num_certain_index, #num_overlapping_chars, #num_transmem_aa

Constructor Details

#initialize(file) ⇒ Index

will update_aaseq if given a fasta_obj



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# File 'lib/transmembrane/phobius.rb', line 18

def initialize(file)
  Phobius.default_index(file, self)
end

Instance Method Details

#reference_to_key(reference) ⇒ Object

we need to match whatever function phobius uses to generate identifiers if we want derivative processes to be fast and accurate



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# File 'lib/transmembrane/phobius.rb', line 24

def reference_to_key(reference)
  if reference
    if reference.size > 0
      index = reference.index(' ')
      string = 
        if index
          reference[0...index]
        else
          reference
        end
      string.gsub('"','')
    else
      ''
    end
  else
    nil
  end
end