[Biojava-l] adding toSequenceIterator method for Alignment

[Matthew Pocock]

Cool. Looks good. Commit away. Could you add some javadocs (class & 
constructor)?

Matthew

Singh, Nimesh wrote:
>      I've created a class called AlignmentSequenceIterator that I intend to put in the org.biojava.bio.seq package.  It will do the real work.  I've also added
>         public SequenceIterator sequenceIterator() {
>             return new AlignmentSequenceIterator(this);
>         }
> to each alignment class.  It should work fine in every alignment, because AlignmentSequenceIterator uses the getLabels and symbolListForLabel methods from the Alignment interface.  
>  
>      If this is fine, then I'll upload everything later today.  If you have any suggestions for changes, then let me know.
>  
> Nimesh
>  
>  
> Here is the cod for AlignmentSequenceIterator:
>  
> public class AlignmentSequenceIterator implements SequenceIterator {
>     private Alignment align;
>     private Iterator labels;
>     private SequenceFactory sf;
>     public AlignmentSequenceIterator(Alignment align) {
>         this.align = align;
>         labels = align.getLabels().iterator();
>         sf = new SimpleSequenceFactory();
>     }
>     public boolean hasNext() {
>         return labels.hasNext();
>     }
>     public Sequence nextSequence() throws NoSuchElementException, BioException {
>         if (!hasNext()) {
>             throw new NoSuchElementException("No more sequences in the alignment.");
>         }
>         else {
>             try {
>                 Object label = labels.next();
>                 SymbolList symList = align.symbolListForLabel(label);
>                 Sequence seq = sf.createSequence(symList, label.toString(), label.toString(), null);
>                 return seq;
>             } catch (Exception e) {
>          throw new BioException(e, "Could not read sequence");
>      }
>         }
>     }
> }
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