lib/bio/appl/clustalw/report.rb in bio-1.4.0 vs lib/bio/appl/clustalw/report.rb in bio-1.4.1

@@ -1,9 +1,11 @@
 #
 # = bio/appl/clustalw/report.rb - CLUSTAL W format data (*.aln) class
 #
 # Copyright:: Copyright (C) 2003 GOTO Naohisa <[e-mail]>
+#             Copyright (C) 2010 Pjotr Prins <[e-mail]> 
+#
 # License::   The Ruby License
 #
 #  $Id: report.rb,v 1.13 2007/07/18 08:47:39 ngoto Exp $
 #
 # Bio::ClustalW::Report is a CLUSTAL W report (*.aln file) parser.
@@ -68,9 +70,25 @@
       # Shows first line of the result data, for example,
       # 'CLUSTAL W (1.82) multiple sequence alignment'.
       # Returns a string.
       def header
         @header or (do_parse or @header)
+      end
+
+      # Returns the Bio::Sequence in the matrix at row 'row' as
+      # Bio::Sequence object. When _row_ is out of range a nil is returned.
+      # ---
+      # *Arguments*:
+      # * (required) _row_: Integer
+      # *Returns*:: Bio::Sequence
+      def get_sequence(row)
+        a = alignment
+        return nil if row < 0 or row >= a.keys.size
+        id  = a.keys[row]
+        seq = a.to_hash[id]
+        s = Bio::Sequence.new(seq.seq)
+        s.definition = id
+        s
       end
 
       # Shows "match line" of CLUSTAL's alignment result, for example,
       # ':* :* .*   *       .*::*.   ** :* . *    .        '.
       # Returns a string.