Module | Bio::Alignment::OriginalPrivate |
In: |
lib/bio/alignment.rb
|
Bio::Alignment::OriginalPrivate is a set of private methods for Bio::Alignment::OriginalAlignment.
Gets the name or the definition of the sequence from given object.
# File lib/bio/alignment.rb, line 1498 1498: def extract_key(obj) 1499: sn = nil 1500: for m in [ :definition, :entry_id ] 1501: begin 1502: sn = obj.send(m) 1503: rescue NameError, ArgumentError 1504: sn = nil 1505: end 1506: break if sn 1507: end 1508: sn 1509: end
Gets the sequence from given object.
# File lib/bio/alignment.rb, line 1478 1478: def extract_seq(obj) 1479: seq = nil 1480: if obj.is_a?(Bio::Sequence::NA) or obj.is_a?(Bio::Sequence::AA) then 1481: seq = obj 1482: else 1483: for m in [ :seq, :naseq, :aaseq ] 1484: begin 1485: seq = obj.send(m) 1486: rescue NameError, ArgumentError 1487: seq = nil 1488: end 1489: break if seq 1490: end 1491: seq = obj unless seq 1492: end 1493: seq 1494: end