Class: Bio::BioAlignment::Sequence

Inherits:
Object
  • Object
show all
Includes:
State, Enumerable
Defined in:
lib/bio-alignment/sequence.rb

Overview

A Sequence is a simple and efficient container for String sequences. To add state to elements unpack it into an Elements object with to_elements.

Instance Attribute Summary collapse

Attributes included from State

#state

Instance Method Summary collapse

Constructor Details

#initialize(id, seq) ⇒ Sequence

Returns a new instance of Sequence.



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# File 'lib/bio-alignment/sequence.rb', line 12

def initialize id, seq
  @id = id
  @id.freeze
  @seq = seq
end

Instance Attribute Details

#id ⇒ Object (readonly)

Returns the value of attribute id.



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# File 'lib/bio-alignment/sequence.rb', line 11

def id
  @id
end

#seq ⇒ Object (readonly)

Returns the value of attribute seq.



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# File 'lib/bio-alignment/sequence.rb', line 11

def seq
  @seq
end

Instance Method Details

#<<(element) ⇒ Object 



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# File 'lib/bio-alignment/sequence.rb', line 40

def << element
  @seq += element.to_s
end

#[](index) ⇒ Object 



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# File 'lib/bio-alignment/sequence.rb', line 18

def [] index
  @seq[index]
end

#clone ⇒ Object 



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# File 'lib/bio-alignment/sequence.rb', line 48

def clone
  Sequence.new(@id,@seq.clone)
end

#each ⇒ Object

Return each element in the Sequence as an Element opbject, so it can be queried for gap? and undefined?



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# File 'lib/bio-alignment/sequence.rb', line 32

def each
  @seq.each_char { | c | yield Element.new(c) }
end

#empty_copy ⇒ Object 



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# File 'lib/bio-alignment/sequence.rb', line 44

def empty_copy
  Sequence.new(@id,"")
end

#length ⇒ Object

def []= index, value — we should not implement this for reasons of purity

@seq[index] = value

end



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# File 'lib/bio-alignment/sequence.rb', line 26

def length
  @seq.length
end

#to_elements ⇒ Object

Return Sequence (string) as an Elements object



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# File 'lib/bio-alignment/sequence.rb', line 53

def to_elements
  Elements.new(@id,@seq)
end

#to_s ⇒ Object 



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# File 'lib/bio-alignment/sequence.rb', line 36

def to_s
  @seq.to_s
end