Module: Bio::Alignment::HashExtension

Bio::Alignment::HashExtension is a set of useful methods for multiple sequence alignment. It is designed to be extended to hash objects or included in your own classes which inherit Hash. (It can also be included in Hash, though not recommended.)

It possesses all methods defined in EnumerableExtension. For usage of methods, please refer to EnumerableExtension.

Because SequenceHash#alignment_collect is redefined, some methods’ return value‘s class are changed to SequenceHash instead of SequenceArray.

Because the order of the objects in a hash is inconstant, some methods strictly affected with the order of objects might not work correctly, e.g. EnumerableExtension#convert_match and convert_unmatch.

Methods

alignment_collect alignment_concat each_seq number_of_sequences sequence_names

Public Instance methods

alignment_collect() {|str| ...}

Iterates over each sequence and each results running block are collected and returns a new alignment as a Bio::Alignment::SequenceHash object.

Note that it would be redefined if you want to change return value‘s class.

[Source]

# File lib/bio/alignment.rb, line 1390
      def alignment_collect
        a = SequenceHash.new
        a.set_all_property(get_all_property)
        each_pair do |key, str|
          a.store(key, yield(str))
        end
        a
      end

alignment_concat(align)

Concatenates the given alignment. If align is a Hash (or SequenceHash), sequences of same keys are concatenated. Otherwise, align must have each_seq or each method and works same as EnumerableExtension#alignment_concat.

Returns self.

Note that it is a destructive method.

[Source]

# File lib/bio/alignment.rb, line 1410
      def alignment_concat(align)
        flag = nil
        begin
          align.each_pair do |key, seq|
            flag = true
            if origseq = self[key]
              origseq.concat(seq)
            end
          end
          return self
        rescue NoMethodError, ArgumentError =>evar
          raise evar if flag
        end
        a = values
        i = 0
        begin
          align.each_seq do |seq|
            flag = true
            a[i].concat(seq) if a[i] and seq
            i += 1
          end
          return self
        rescue NoMethodError, ArgumentError => evar
          raise evar if flag
        end
        align.each do |seq|
          a[i].concat(seq) if a[i] and seq
          i += 1
        end
        self
      end

each_seq( {|seq| ...}

Iterates over each sequences. Yields a sequence.

It works the same as Hash#each_value.

[Source]

# File lib/bio/alignment.rb, line 1378
      def each_seq #:yields: seq
        #each_value(&block)
        each_key { |k| yield self[k] }
      end

number_of_sequences()

Returns number of sequences in this alignment.

[Source]

# File lib/bio/alignment.rb, line 1443
      def number_of_sequences
        self.size
      end

sequence_names()

Returns an array of sequence names. The order of the names must be the same as the order of each_seq.

[Source]

# File lib/bio/alignment.rb, line 1450
      def sequence_names
        self.keys
      end

Methods

Included Modules

Public Instance methods