class Bio::RestrictionEnzyme::DenseIntArray

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
27 def self.[](*args)
28   a = self.new
29   args.each do |elem|
30     a.push elem
31   end
32   a
33 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
36 def initialize
37   @data = []
38 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
 88 def +(other)
 89   unless other.is_a?(self.class) then
 90     raise TypeError, 'unsupported data type'
 91   end
 92   tmpdata = @data + other.internal_data
 93   tmpdata.sort! { |a,b| a.first <=> b.first }
 94   result = self.class.new
 95   return result if tmpdata.empty?
 96   newdata = result.internal_data
 97   newdata.push tmpdata[0].dup
 98   (1...(tmpdata.size)).each do |i|
 99     if (x = newdata[-1].last) >= tmpdata[i].first then
100       newdata[-1].last = tmpdata[i].last if tmpdata[i].last > x
101     else
102       newdata.push tmpdata[i].dup
103     end
104   end
105   result
106 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
139 def <<(elem)
140   if !@data.empty? and
141       @data[-1].last + 1 == elem then
142     @data[-1].last = elem
143   else
144     @data << MutableRange.new(elem, elem)
145   end
146   self
147 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
109 def ==(other)
110   if r = super(other) then
111     r
112   elsif other.is_a?(self.class) then
113     other.internal_data == @data
114   else
115     false
116   end
117 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
61 def [](*arg)
62   #$stderr.puts "SortedIntArray#[]"
63   to_a[*arg]
64 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
67 def []=(*arg)
68   raise NotImplementedError, 'DenseIntArray#[]= is not implemented.'
69 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
120 def concat(ary)
121   ary.each { |elem| self.<<(elem) }
122   self
123 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
180 def delete(elem)
181   raise NotImplementedError, 'DenseIntArray#delete is not implemented.'
182 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
72 def each
73   @data.each do |elem|
74     elem.first.upto(elem.last) { |num| yield num }
75   end
76   self
77 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
158 def first
159   elem = @data.first
160   elem ? elem.first : nil
161 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
150 def include?(elem)
151   return false if @data.empty? or elem < self.first or self.last < elem
152   @data.any? do |range|
153     range.first <= elem && elem <= range.last
154   end
155 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
41 def initialize_copy(other)
42   super(other)
43   @data = @data.collect { |elem| elem.dup }
44 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
164 def last
165   elem = @data.last
166   elem ? elem.last : nil
167 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
126 def push(*args)
127   args.each do |elem|
128     self.<<(elem)
129   end
130   self
131 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
80 def reverse_each
81   @data.reverse_each do |elem|
82     elem.last.downto(elem.first) { |num| yield num }
83   end
84   self
85 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
170 def size
171   sum = 0
172   @data.each do |range|
173     sum += (range.last - range.first + 1)
174   end
175   sum
176 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
185 def sort!(&block)
186   # does nothing
187   self
188 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
191 def uniq!
192   # does nothing
193   self
194 end

    # File lib/bio/util/restriction_enzyme/dense_int_array.rb
134 def unshift(*arg)
135   raise NotImplementedError, 'DenseIntArray#unshift is not implemented.'
136 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
55 def internal_data
56   @data
57 end

   # File lib/bio/util/restriction_enzyme/dense_int_array.rb
47 def internal_data=(a)
48   #clear_cache
49   @data = a
50   self
51 end