On Aug 5, 2009, at 9:55 AM, C. Titus Brown wrote:
> It's not a Pyrex problem, at least not by my understanding of how > garbage collection works in Python. There are two general areas we could look in. The first is NLMSA and other classes in cnestedlist. My point was that for all those extension classes, Pyrex takes care of releasing references to any Python objects. Pyrex does not even permit you to write a __del__() method for a Pyrex extension class. So if the reference problem turns out to be in this area, it's a Pyrex problem by definition. The other area we can look at is seqdb: SequenceDB, PrefixUnionDict and relations. I don't think SequenceDB is the likely explanation. The fact that you don't provide the NLMSA a seqDict, and thus force it to build a seqDict for you as you add sequences to the alignment, might be relevant. That makes the NLMSA set seqDict = SeqPrefixUnionDict(addAll=True), which then has to keep track of all the sequences you add to the alignment. Might be worth a look. > > -> I'll try to enumerate the various places a reference to the > sequence > -> object might be held, in another email. I'll send that to you soon. -- Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
