[Biojava-dev] AbstractULAlignment

[Lachlan Coin]

On Wed, 12 Mar 2003, Schreiber, Mark wrote:

> Hi -
>
> I guess the thing to do would be to test for contiguousness (if that's a
> word) and use the Locations block iterator to retreive each subalignment
> and then concatenate them before returning them.
>
> The Location getMin() and getMax() methods should be documented to
> indicate that it is very wise to test for a contiguous location before
> relying on them to give a sensible result. I'll do that now. Do you want
> me to change the AbstractULAlignment so that it internally copes with
> this problem?



Yes, thanks a lot for that - I'm not overly familiar with the
AbstractULAlignment code myself.

Cheers,

Lachlan




>
> - Mark
>
>
> > -----Original Message-----
> > From: Lachlan Coin [mailto:lc1 at sanger.ac.uk]
> > Sent: Wednesday, 12 March 2003 3:38 a.m.
> > To: biojava-dev at biojava.org
> > Subject: [Biojava-dev] AbstractULAlignment
> >
> >
> > Hi,
> >
> > I have been using AbstractULAlignment, and I have noticed that  the
> > subAlignment() method does not deal with non-contiguous
> > Location objects
> > properly:  it takes the getMin() and getMax() from location
> > and returns a contiguous sub-alignment with this minimum and maximum.
> >
> > I guess we should document this in the api, and throw and
> > error for non-contiguous locations in the method, at least at
> > a short-term fix, before fixing the method.  Am I missing
> > something? Does anyone have code which fixes this problem?
> >
> > Thanks,
> >
> > Lachlan
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org
> > http://biojava.org/mailman/listinfo/biojava-dev
> >
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Lachlan Coin
Wellcome Trust Sanger Institute		Magdalene College
Cambridge  CB10 1SA			Cambridge CB30AG
Ph: +44 1223 494 820
Fax: +44 1223 494 919
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