[Biojava-dev] AbstractULAlignment

[Schreiber, Mark]

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?

- 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
> 
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