On Tue, May 26, 2009 at 08:07:50AM -0700, Alexander Alekseyenko wrote: -> Here's what has been bothering me for a long time. I have touched on -> this previously in different contexts, but I thought I'd share in a -> dedicated thread. I think that NLMSA class starts to become too bulky. -> The main reason I see for this is that in effect it performs several -> separate functions for completely different modes of usage.
[ ... ] Alex, I generally agree. See: http://groups.google.com/group/pygr-dev/browse_thread/thread/d4d02149022e5a6/5f6ff9b7b327f31d?lnk=gst&q=titus+build+cnestedlist#5f6ff9b7b327f31d search for "Right now, this gives a confusing", which is the part of my e-mail where I complain about BuildMSASlice vs NLMSASlice. -> 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. I like the idea of separating build from query. 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 -~----------~----~----~----~------~----~------~--~---
