Hi, your first solution (new constructor: new GappedSymbolList(origSyms, mergeOriginalGaps) sounds good to me These new constructors for GappedSymbolList and GappedSequence would be very helpful.
Thanks in advance. David ----- Original Message ----- From: "Matthew Pocock" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: <[EMAIL PROTECTED]>; <[EMAIL PROTECTED]> 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 > > [EMAIL PROTECTED] 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 > > > > > > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
