[Biojava-l] adding toSequenceIterator method for Alignment

[Kalle Näslund]

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
> 
>

Well, there is one big problem with this piece of code, you treat all 
objects in the alignment as being
SymbolLists only, witch in reality isnt true, as you can insert any 
object that implements the
SymbolList interface into an alignment.

For example, i am currently populating my alignment objects with custom 
Sequence objects. if i called
this code it would create new Sequence objects of the type 
SimpleSequence, and as i understand it from
a quick look at the SequenceFactory code, it wont have any of the 
annotations, features etc that the
original Sequence objects i added to the alignment had. so, instead of 
geting my custom Sequence objects
back containing feature etc, i would get nearly "empty" SimpleSequence 
objects back, witch makes it unusable.
Other problems should pop upp if you insert other objects into 
Alignments, say other alignments. and instead
of getting them back as alignments when you iterate over the SymbolLists 
in the alignemnt, you get it back
as a SimpleSequence.

But, i do agree that adding a method to the Alignment interface, that 
gives you an iterator so you can
iterate over the SymbolList's in the alignment is a good thing to add.

My suggestion would just be to have it iterate over the SymbolLists that 
are inserted into the Alignment
and avoid doing any type of alterations of the objects. That way you get 
back what you insert, and
the method will work for everyone, just not people using SimpleSequences.

regads Kalle

> 
>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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