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#
# bio/util/restriction_enzyme/dense_int_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange
#
# Copyright:: Copyright (C) 2011
# Naohisa Goto <ng@bioruby.org>
# Tomoaki NISHIYAMA
# License:: The Ruby License
#
module Bio
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
class RestrictionEnzyme
# a class to store integer numbers, containing many contiguous
# integral numbers.
#
# Bio::RestrictionEnzyme internal use only.
# Please do not create the instance outside Bio::RestrictionEnzyme.
class DenseIntArray
MutableRange = Struct.new(:first, :last)
include Enumerable
# Same usage as Array.[]
def self.[](*args)
a = self.new
args.each do |elem|
a.push elem
end
a
end
# creates a new object
def initialize
@data = []
end
# initialize copy
def initialize_copy(other)
super(other)
@data = @data.collect { |elem| elem.dup }
end
# sets internal data object
def internal_data=(a)
#clear_cache
@data = a
self
end
protected :internal_data=
# gets internal data object
def internal_data
@data
end
protected :internal_data
# Same usage as Array#[]
def [](*arg)
#$stderr.puts "SortedIntArray#[]"
to_a[*arg]
end
# Not implemented
def []=(*arg)
raise NotImplementedError, 'DenseIntArray#[]= is not implemented.'
end
# Same usage as Array#each
def each
@data.each do |elem|
elem.first.upto(elem.last) { |num| yield num }
end
self
end
# Same usage as Array#reverse_each
def reverse_each
@data.reverse_each do |elem|
elem.last.downto(elem.first) { |num| yield num }
end
self
end
# Same usage as Array#+, but accepts only the same classes instance.
def +(other)
unless other.is_a?(self.class) then
raise TypeError, 'unsupported data type'
end
tmpdata = @data + other.internal_data
tmpdata.sort! { |a,b| a.first <=> b.first }
result = self.class.new
return result if tmpdata.empty?
newdata = result.internal_data
newdata.push tmpdata[0].dup
(1...(tmpdata.size)).each do |i|
if (x = newdata[-1].last) >= tmpdata[i].first then
newdata[-1].last = tmpdata[i].last if tmpdata[i].last > x
else
newdata.push tmpdata[i].dup
end
end
result
end
# Same usage as Array#==
def ==(other)
if r = super(other) then
r
elsif other.is_a?(self.class) then
other.internal_data == @data
else
false
end
end
# Same usage as Array#concat
def concat(ary)
ary.each { |elem| self.<<(elem) }
self
end
# Same usage as Array#push
def push(*args)
args.each do |elem|
self.<<(elem)
end
self
end
# Same usage as Array#unshift
def unshift(*arg)
raise NotImplementedError, 'DenseIntArray#unshift is not implemented.'
end
# Same usage as Array#<<
def <<(elem)
if !@data.empty? and
@data[-1].last + 1 == elem then
@data[-1].last = elem
else
@data << MutableRange.new(elem, elem)
end
self
end
# Same usage as Array#include?
def include?(elem)
return false if @data.empty? or elem < self.first or self.last < elem
@data.any? do |range|
range.first <= elem && elem <= range.last
end
end
# Same usage as Array#first
def first
elem = @data.first
elem ? elem.first : nil
end
# Same usage as Array#last
def last
elem = @data.last
elem ? elem.last : nil
end
# Same usage as Array#size
def size
sum = 0
@data.each do |range|
sum += (range.last - range.first + 1)
end
sum
end
alias length size
# Same usage as Array#delete
def delete(elem)
raise NotImplementedError, 'DenseIntArray#delete is not implemented.'
end
# Does nothing
def sort!(&block)
# does nothing
self
end
# Does nothing
def uniq!
# does nothing
self
end
end #class DenseIntArray
end #class RestrictionEnzyme
end #module Bio
|
