On Jul 16, 2009, at 9:50 PM, C. Titus Brown wrote:
> -> > -> 2. handling of self-alignment in pairwise mode. We proposed > -> > changing > -> > -> pairwise mode to report self-alignments, rendering obsolete > the > -> > -> current annoying warning message. > > Am I correct that this boils down to setting bidirectionalRule=None in > the NLMSA constructor? No. We just need to add a conditional that retains self-alignments under our desired condition, in the NLMSASlice.__init__(). I'll have to look at the code to see exactly where. I think it'll be easier for me to just make the change and push it to the simpleframe branch for your approval... Should the condition be pairwiseMode == true or bidirectional == false? It's been a while since we discussed this. Blast alignments set both of these conditions. My original logic: in true MSA mode (pairwiseMode false and bidirectional true), the self-alignment is ALWAYS present (just due to the nature of the data-structure), so reporting it would be useless and misleading. That is not the case for blast alignments. I'll go back to our discussion and figure this out. Then we can get rid of the annoying warning messages about self- alignments in the blast methods. -- 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 -~----------~----~----~----~------~----~------~--~---
