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|
#
# bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange
#
# Copyright:: Copyright (C) 2011
# Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
module Bio
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
class RestrictionEnzyme
# a class to store sorted numerics.
#
# Bio::RestrictionEnzyme internal use only.
# Please do not create the instance outside Bio::RestrictionEnzyme.
class SortedNumArray
# 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
@hash = {}
#clear_cache
end
# initialize copy
def initialize_copy(other)
super(other)
@hash = @hash.dup
end
# sets internal hash object
def internal_data_hash=(h)
#clear_cache
@hash = h
self
end
protected :internal_data_hash=
# gets internal hash object
def internal_data_hash
@hash
end
protected :internal_data_hash
#---
## clear the internal cache
#def clear_cache
# @sorted_keys = nil
#end
#protected :clear_cache
#+++
# sorted keys
def sorted_keys
#@sorted_keys ||= @hash.keys.sort
#@sorted_keys
@hash.keys.sort
end
private :sorted_keys
# adds a new element
def push_element(n)
#return if @hash.has_key?(n) #already existed; do nothing
@hash.store(n, true)
#if @sorted_keys then
# if thelast = @sorted_keys[-1] and n > thelast then
# @sorted_keys.push n
# else
# clear_cache
# end
#end
nil
end
private :push_element
# adds a new element in the beginning of the array
def unshift_element(n)
#return if @hash.has_key?(n) #already existed; do nothing
@hash.store(n, true)
#if @sorted_keys then
# if thefirst = @sorted_keys[0] and n < thefirst then
# @sorted_keys.unshift n
# else
# clear_cache
# end
#end
nil
end
private :unshift_element
# Same usage as Array#[]
def [](*arg)
#$stderr.puts "SortedNumArray#[]"
sorted_keys[*arg]
end
# Not implemented
def []=(*arg)
raise NotImplementedError, 'SortedNumArray#[]= is not implemented.'
end
# Same usage as Array#each
def each(&block)
sorted_keys.each(&block)
end
# Same usage as Array#reverse_each
def reverse_each(&block)
sorted_keys.reverse_each(&block)
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
new_hash = @hash.merge(other.internal_data_hash)
result = self.class.new
result.internal_data_hash = new_hash
result
end
# Same usage as Array#==
def ==(other)
if r = super(other) then
r
elsif other.is_a?(self.class) then
other.internal_data_hash == @hash
else
false
end
end
# Same usage as Array#concat
def concat(ary)
ary.each { |elem| push_element(elem) }
self
end
# Same usage as Array#push
def push(*args)
args.each do |elem|
push_element(elem)
end
self
end
# Same usage as Array#unshift
def unshift(*arg)
arg.reverse_each do |elem|
unshift_element(elem)
end
self
end
# Same usage as Array#<<
def <<(elem)
push_element(elem)
self
end
# Same usage as Array#include?
def include?(elem)
@hash.has_key?(elem)
end
# Same usage as Array#first
def first
sorted_keys.first
end
# Same usage as Array#last
def last
sorted_keys.last
end
# Same usage as Array#size
def size
@hash.size
end
alias length size
# Same usage as Array#delete
def delete(elem)
#clear_cache
@hash.delete(elem) ? elem : nil
end
# Does nothing
def sort!(&block)
# does nothing
self
end
# Does nothing
def uniq!
# does nothing
self
end
# Converts to an array
def to_a
#sorted_keys.dup
sorted_keys
end
end #class SortedNumArray
end #class RestrictionEnzyme
end #module Bio
|
