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