[Biojava-l] removeGap problem with SimpleGappedSequence

david de beule daviddebeule at pandora.be
Thu Feb 12 15:03:26 EST 2004


your first solution (new constructor: new GappedSymbolList(origSyms,
sounds good to me
These new constructors for GappedSymbolList and GappedSequence would be very

Thanks in advance.

----- Original Message -----
From: "Matthew Pocock" <matthew_pocock at yahoo.co.uk>
To: <mark.schreiber at group.novartis.com>
Cc: <daviddebeule at pandora.be>; <biojava-l at biojava.org>
Sent: Thursday, February 12, 2004 12:02 PM
Subject: Re: [Biojava-l] removeGap problem with SimpleGappedSequence

> Hi,
> Seems like we have a bit of an 'expected behavior' and 'implemented
> behavior' gap. If we decide to modify the GappedSymbolList constructor
> to find all gaps in the original sequence, I think we should add it as
> an option:
>   new GappedSymbolList(origSyms, mergeOriginalGaps)
> and make the current constructor equivalent to this(syms, false).
> Finding all these gaps, making an ungapped underlying symbol list, and
> building the gap insertion data structures is a potentialy expensive
> operation (imagine gapping a genome! you would pull the whole thing into
> memory and do a linear scan), so we should be careful not to force it
> upon the world.
> This would also change the contract of getSourceSymbolList() and also
> what happens if that source is modified, wether changes to it are tracked.
> This could be worked around by implementing an "UnGappedView" class that
> does the oposite mapping of GappedSymbolList - removes all gaps in the
> source - then we could gap this putting them all back, making it
> editable. I don't wan't to be the one to write it though - writing
> GappedSymbolList made my brain hurt.
> Matthew
> mark.schreiber at group.novartis.com wrote:
> >Sounds like a pretty sensible suggestion. Can anyone think of why this
> >might not be a 'good idea'?
> >
> >If not, i'll add it to the list of things to fix :)
> >
> >- Mark
> >
> >

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