Class: Bio::RestrictionEnzyme::DenseIntArray

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/bio/util/restriction_enzyme/dense_int_array.rb

Overview

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.

Defined Under Namespace

Classes: MutableRange

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ DenseIntArray

creates a new object



33
34
35
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 33

def initialize
  @data = []
end

Class Method Details

.[](*args) ⇒ Object

Same usage as Array.[]



24
25
26
27
28
29
30
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 24

def self.[](*args)
  a = self.new
  args.each do |elem|
    a.push elem
  end
  a
end

Instance Method Details

#+(other) ⇒ Object

Same usage as Array#+, but accepts only the same classes instance.



85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 85

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

#<<(elem) ⇒ Object

Same usage as Array#<<



136
137
138
139
140
141
142
143
144
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 136

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

#==(other) ⇒ Object

Same usage as Array#==



106
107
108
109
110
111
112
113
114
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 106

def ==(other)
  if r = super(other) then
    r
  elsif other.is_a?(self.class) then
    other.internal_data == @data
  else
    false
  end
end

#[](*arg) ⇒ Object

Same usage as Array#[]



58
59
60
61
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 58

def [](*arg)
  #$stderr.puts "SortedIntArray#[]"
  to_a[*arg]
end

#[]=(*arg) ⇒ Object

Not implemented

Raises:

  • (NotImplementedError) 


64
65
66
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 64

def []=(*arg)
  raise NotImplementedError, 'DenseIntArray#[]= is not implemented.'
end

#concat(ary) ⇒ Object

Same usage as Array#concat



117
118
119
120
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 117

def concat(ary)
  ary.each { |elem| self.<<(elem) }
  self
end

#delete(elem) ⇒ Object

Same usage as Array#delete

Raises:

  • (NotImplementedError) 


177
178
179
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 177

def delete(elem)
  raise NotImplementedError, 'DenseIntArray#delete is not implemented.'
end

#each ⇒ Object

Same usage as Array#each



69
70
71
72
73
74
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 69

def each
  @data.each do |elem|
    elem.first.upto(elem.last) { |num| yield num }
  end
  self
end

#first ⇒ Object

Same usage as Array#first



155
156
157
158
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 155

def first
  elem = @data.first
  elem ? elem.first : nil
end

#include?(elem) ⇒ Boolean

Same usage as Array#include?

Returns:

  • (Boolean) 


147
148
149
150
151
152
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 147

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

#initialize_copy(other) ⇒ Object

initialize copy



38
39
40
41
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 38

def initialize_copy(other)
  super(other)
  @data = @data.collect { |elem| elem.dup }
end

#last ⇒ Object

Same usage as Array#last



161
162
163
164
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 161

def last
  elem = @data.last
  elem ? elem.last : nil
end

#push(*args) ⇒ Object

Same usage as Array#push



123
124
125
126
127
128
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 123

def push(*args)
  args.each do |elem|
    self.<<(elem)
  end
  self
end

#reverse_each ⇒ Object

Same usage as Array#reverse_each



77
78
79
80
81
82
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 77

def reverse_each
  @data.reverse_each do |elem|
    elem.last.downto(elem.first) { |num| yield num }
  end
  self
end

#size ⇒ Object Also known as: length

Same usage as Array#size



167
168
169
170
171
172
173
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 167

def size
  sum = 0
  @data.each do |range|
    sum += (range.last - range.first + 1)
  end
  sum
end

#sort!(&block) ⇒ Object

Does nothing



182
183
184
185
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 182

def sort!(&block)
  # does nothing
  self
end

#uniq! ⇒ Object

Does nothing



188
189
190
191
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 188

def uniq!
  # does nothing
  self
end

#unshift(*arg) ⇒ Object

Same usage as Array#unshift

Raises:

  • (NotImplementedError) 


131
132
133
 
# File 'lib/bio/util/restriction_enzyme/dense_int_array.rb', line 131

def unshift(*arg)
  raise NotImplementedError, 'DenseIntArray#unshift is not implemented.'
end