Module: Bio::Protparam::Remote

Defined in:
lib/bio/util/protparam.rb

Constant Summary collapse

PROTPARAM_URL = 
'http://web.expasy.org/cgi-bin/protparam/protparam'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#result ⇒ Object

Returns the value of attribute result.



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# File 'lib/bio/util/protparam.rb', line 376

def result
  @result
end

Class Method Details

.cast_method(type) ⇒ Object 



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# File 'lib/bio/util/protparam.rb', line 378

def self.cast_method(type)
  case type.to_s
  when "Fixnum"
    ".to_i"
  when "Float"
    ".to_f"
  when "String"
    ""
  else
    ""
  end
end

.extract_options(*args) ⇒ Object 



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# File 'lib/bio/util/protparam.rb', line 391

def self.extract_options(*args)
  # label, class, regex
  # label, class, regex, lambda
  # label, lambda
  label, type, regex, block = [nil, nil, nil, nil]
  if args.size > 2
    label = args.shift
    type  = args.shift
    if args.size > 1
      regex, block = args
    elsif args.size > 0
      regex, block = if args.first.kind_of?(Regexp)
                       [args.first, nil]
                     elsif args.first.respond_to?(:call)
                       [nil, args.first]
                     end
    end
  end
  [label, type, regex, block]
end

.rule(*args) ⇒ Object 



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# File 'lib/bio/util/protparam.rb', line 412

def self.rule(*args)
  (label, type, regex, block) = extract_options(*args)
  if regex && block
    self.class_eval <<-METHOD
    METHOD
  elsif regex && !block
    self.class_eval <<-METHOD
        def #{label}
          response = self.request
          matched  = %r/#{regex}/.match(response)
          if matched.size > 1
            matched[1]#{cast_method(type)}
          else
            nil
          end
        end
            METHOD
  elsif !regex && block
    wrapped_block = Proc.new {|*method_args|
      response = self.request
      method_args.unshift response
      block.call(method_args)
    }
    self.send(:define_method, label, &wrapped_block)
  else
    raise ArgumentError,
      "Invalid arguments.rule(:label, :type, :regex) or rule(:label, :type, :lambda)"
  end
end

Instance Method Details

#fallback! ⇒ Object 



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# File 'lib/bio/util/protparam.rb', line 500

def fallback!
  self.class.class_eval do
    include Local
  end
end

#request ⇒ Object 



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# File 'lib/bio/util/protparam.rb', line 492

def request
  @result ||= begin
                res = Net::HTTP.post_form(URI(PROTPARAM_URL),
                                          {'sequence' => @seq.to_s})
                res.body
              end
end

#stable? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/util/protparam.rb', line 488

def stable?
  (stablity == 'stable')
end