Codon alignment test

lib/bio-alignment/column.rb

@@ -22,11 +22,12 @@ def num_columns
         rows.first.length
       end
 
-      # Return an alignment which match columns
+      # Return an alignment which match columns. The originating
+      # sequences should have methods 'empty_copy' and '<<'
       def columns_where &block
         seqs = []
         rows.each do | seq | 
-          new_seq = Sequence.new(seq.id,"")
+          new_seq = seq.empty_copy
           seq.each_with_index do | e,i |
             new_seq << e if block.call(columns[i])
           end

lib/bio-alignment/sequence.rb

@@ -45,6 +45,10 @@ def to_s
       def << element
         @seq += element.to_s
       end
+
+      def empty_copy
+        Sequence.new(@id,"")
+      end
     end
   end
 end

spec/bio-alignment_spec.rb

@@ -84,10 +84,12 @@
   columns2.count { |e| e.state.deleted? }.should == 6
   aln2.columns[0].state.should == columns2[0].state
   aln2.columns[0].state.should_not == columns[0].state
-  aln3.rows.first.to_s.should == "SNSFSRPTIIFSGCSTACSGKSELVCGFRSFMLSDV"
-
+  aln2.rows.first.to_s.should == "----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV"
   # now write out the alignment with deleted columns removed
   aln3 = aln2.columns_where { |col| !col.state.deleted? }
   print aln3.to_s,"\n"
   aln3.rows.first.to_s.should == "SNSFSRPTIIFSGCSTACSGKSELVCGFRSFMLSDV"
+
+  # We are going to do the same for a codon alignment
+  test == false
 end