[Biojava-dev] AbstractULAlignment

[Schreiber, Mark]

Hi -

It turns out that the AbstractULAlignment would require a bit of a
re-engineer to cope with non-contigous locations as arguments to the
subAlignment() method. As a work around I have added a warning to that
method that users of non-contiguous locations may prefer an alternative
strategy. I have also added a subAlignment() method that takes two ints
instead of a Location which provides a possible alternative.

Finally I have made the constructor of the inner SubULAlignment
protected as construction should really be limited to the subAlignment
method.

If any of this doesn't work let me know.

- Mark


> -----Original Message-----
> From: Lachlan Coin [mailto:lc1 at sanger.ac.uk] 
> Sent: Wednesday, 12 March 2003 10:18 p.m.
> To: Schreiber, Mark
> Cc: biojava-dev at biojava.org
> Subject: RE: [Biojava-dev] AbstractULAlignment
> 
> 
> 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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