-> > Here's how this could work. The -> > construction of the alignment can be handled via a separate hierarchy -> > -> > NLMSABuilderBase: base class for construction methods -> > NLMSABuilderMAF: construction from MAF files -> > NLMSABuilderBlast: construction from Blast output -> > NLMSABuilderManual: interactive construction -> > NLMSABuilderYourFavouriteMSAFormat: ... -> > -> > These classes would all have a build() method, which would yield an -> > NLMSA object that is ready for querying. This top-level NLMSA object -> > is very similar in function to the SeqPath concept, in that it -> > provides a reference for all sub-alignments. The sub-alignments in -> > turn could also be queried in a very similar fashion to the top-level -> > NLMSA. -> -> It sounds like you are saying that we would subclass NLMSA to add new -> constructor methods, rather than adding them all directly to the -> original NLMSA class definition. I have been wondering about that -> myself. I don't remember whether / how Pyrex supports this kind of -> subclassing pattern. You can of course always subclass a Pyrex -> extension class *in Python*, but that just drops you back into the -> world of lousy performance. I don't know whether one Pyrex module can -> subclass a Pyrex extension class defined in another Pyrex module. We -> need to find out about this, as we need a way for users to be able to -> extend classes like NLMSA with their own high-performance methods, -> taking advantage of high-speed access to the NLMSA C methods.
Quick comment -- how about using just a regular module-level function, instead of a class method, for creating NLMSAs with specialized data formats? cheers, --titus -- C. Titus Brown, c...@msu.edu --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
