region.rb in scaffolder-0.4.0

- old
+ new
@@ -1,138 +1,276 @@
-Scaffolder::Region = Struct.new(:entry_type,:sequence)
+require 'scaffolder'
+
+class Scaffolder::Region
+  include Scaffolder::Errors
+
+  class << self
+    include Scaffolder::Errors
+
+    # @return [Scaffolder::Region] Returns subclassed instances of
+    #   Scaffolder::Region by name
+    def [](type)
+      self.const_get(type.capitalize)
+    end
+
+    # Links the specification of values in the scaffold file to the assignment
+    # of instance variables.
+    #
+    # @param [Symbol] Define attributes for this type of scaffold
+    #   region. Attributes are read from the scaffold file and stored as
+    #   instance variables.
+    # @param [Hash] options Attribute options.
+    # @option options [Object,Proc] Default Specify a default value for this
+    #   attribute if a value is not defined in the scaffold file.
+    # @example Simple specification
+    #   class MyRegion < Scaffolder::Region
+    #     attribute :value # "value" usable as a keyword in the scaffold file
+    #   end
+    # @example Specification with a default value
+    #   attribute :value, :default => 1
+    # @example Specification with where proc is evaluated for the default
+    #   attribute :value, :default => lamdba{ Time.now.to_s }
+    # @example Specification with proc where the region instance is avaiable
+    #   attribute :value, :default => lamdba{|s| s.other_variable + 1 }
+    def attribute(name,options = {})
+      define_method(name) do |*arg|
+        var = "@#{name}"
+        default = options[:default]
+        unless arg.first # Is an argument is passed to the method?
+          value = instance_variable_get(var)
+          return value if value
+          return default.respond_to?(:call) ? default.call(self) : default
+        end
+        instance_variable_set(var,arg.first)
+      end
+    end
+
+    # Parse each key-value pair in the scaffold hash calling the corresponding
+    # attribute method for the key and passing the value as an argument.
+    #
+    # @param [Hash] region_data Key-Value pairs of the data required to define
+    #   this scaffolder region.
+    # @return [Scaffolder::Region] Returns an region object where the
+    #   instance variables have been assigned according to the region data
+    #   hash.
+    # @raise [UnknownAttributeError] If a keyword in the scaffold file does not
+    #   have a corresponding attribute in the class.
+    # @see Scaffolder::Region.attribute
+    def generate(region_data)
+      region = self.new
+      region_data.each_pair do |attribute,value|
+        begin
+          region.send(attribute.to_sym,value)
+        rescue NoMethodError => e
+          raise UnknownAttributeError.new(e)
+        end
+      end
+      region
+    end
+
+  end
+
+  # The raw sequence for this region.
+  #
+  # @param [String]
+  # @return [String]
+  attribute :raw_sequence
+
+  # Trim the start of sequence to this position. Default is 1.
+  #
+  # @param [Interger]
+  # @return [Interger]
+  attribute :start, :default => 1
+
+  # Trim the end of sequence to this position. Default is the sequence length..
+  #
+  # @param [Interger]
+  # @return [Interger]
+  attribute :stop, :default => lambda{|s| s.sequence_hook.length}
+
+
+  # Should the sequence be reverse complemented. Reverse complementation is
+  # performed after the start and end of the sequence has been trimmed.
+  #
+  # @param [Boolean]
+  # @return [Boolean]
+  attribute :reverse
+
+  # Override this to manipulate the sequence before it's subsequenced, reverse
+  # complemented etc. by Scaffolder::Region#sequence.
+  #
+  # @return [String] The value of the raw_sequence attribute
+  # @see Scaffolder::Region#sequence
+  def sequence_hook
+    raw_sequence
+  end
+
+  # The name of the class. Useful for selecting specific region types.
+  #
+  # @return [Symbol]
+  def entry_type
+    self.class.name.split('::').last.downcase.to_sym
+  end
+
+  # Returns the value of the Scaffolder::Region#raw_sequence after
+  # subsequencing and reverse complementation (if specified in the
+  # scaffold file).
+  #
+  # @return [String] Sequence after all modifications
+  # @raise [CoordinateError] if the start position is less than 1.
+  # @raise [CoordinateError] if the stop position is greater than the sequence
+  #   length.
+  # @raise [CoordinateError] if the start position is greater than the stop
+  #   position.
+  def sequence
+    seq = sequence_hook
+
+    raise CoordinateError.new if start < 1
+    raise CoordinateError.new if stop  > seq.length
+    raise CoordinateError.new if start > stop
+
+    seq = seq[(start-1)..(stop-1)]
+    seq = Bio::Sequence::NA.new(seq).reverse_complement if reverse
+    seq.to_s.upcase
+  end
+
+  require 'scaffolder/region/unresolved'
+  require 'scaffolder/region/insert'
+  require 'scaffolder/region/sequence'
+end