Module Bio::Alignment::HashExtension
In: lib/bio/alignment.rb

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

Included Modules

EnumerableExtension

Public Instance methods

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
1390:       def alignment_collect
1391:         a = SequenceHash.new
1392:         a.set_all_property(get_all_property)
1393:         each_pair do |key, str|
1394:           a.store(key, yield(str))
1395:         end
1396:         a
1397:       end

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
1410:       def alignment_concat(align)
1411:         flag = nil
1412:         begin
1413:           align.each_pair do |key, seq|
1414:             flag = true
1415:             if origseq = self[key]
1416:               origseq.concat(seq)
1417:             end
1418:           end
1419:           return self
1420:         rescue NoMethodError, ArgumentError =>evar
1421:           raise evar if flag
1422:         end
1423:         a = values
1424:         i = 0
1425:         begin
1426:           align.each_seq do |seq|
1427:             flag = true
1428:             a[i].concat(seq) if a[i] and seq
1429:             i += 1
1430:           end
1431:           return self
1432:         rescue NoMethodError, ArgumentError => evar
1433:           raise evar if flag
1434:         end
1435:         align.each do |seq|
1436:           a[i].concat(seq) if a[i] and seq
1437:           i += 1
1438:         end
1439:         self
1440:       end

Iterates over each sequences. Yields a sequence.

It works the same as Hash#each_value.

[Source]

      # File lib/bio/alignment.rb, line 1378
1378:       def each_seq #:yields: seq
1379:         #each_value(&block)
1380:         each_key { |k| yield self[k] }
1381:       end

Returns number of sequences in this alignment.

[Source]

      # File lib/bio/alignment.rb, line 1443
1443:       def number_of_sequences
1444:         self.size
1445:       end

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
1450:       def sequence_names
1451:         self.keys
1452:       end

[Validate]