Class: TopPred::Index

Inherits:
Hash show all
Includes:
TransmemIndex
Defined in:
lib/transmembrane/toppred.rb

Instance Method Summary collapse

Constructor Details

#initialize(file, kind = :default) ⇒ Index

Returns a new instance of Index.



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# File 'lib/transmembrane/toppred.rb', line 31

def initialize(file, kind=:default)
  case kind
  when :default
    TopPred.default_index(file, self)
  else
    abort "can't do #{kind}"
  end
end

Instance Method Details

#reference_to_key(reference) ⇒ Object

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



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# File 'lib/transmembrane/toppred.rb', line 12

def reference_to_key(reference)
  if reference
    ri = reference.index(' ')
    frst =
      if ri 
        reference[0...reference.index(' ')]
      else 
        reference
      end
    if frst
      frst.gsub(/[^0-9a-zA-Z]/,'_')
    else
      nil
    end
  else
    nil
  end
end