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.
Public Instance Methods
Source
# File lib/bio/alignment.rb 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
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 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
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 1378 def each_seq #:yields: seq 1379 #each_value(&block) 1380 each_key { |k| yield self[k] } 1381 end
Iterates over each sequences. Yields a sequence.
It works the same as Hash#each_value.
Source
# File lib/bio/alignment.rb 1443 def number_of_sequences 1444 self.size 1445 end
Returns number of sequences in this alignment.
Source
# File lib/bio/alignment.rb 1450 def sequence_names 1451 self.keys 1452 end
Returns an array of sequence names. The order of the names must be the same as the order of each_seq.