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
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