[Bioperl-l] Exonerate vulgar lines; SearchIO model

[Ewan Birney]

I have added vulgar line parsing to the exonerate output. I made
a simpler model than the cigar line parsing of having just the M
state durations as being HSPs.

(this will get checked into the main trunk)


This brings up an issue - should HSPs in the SearchIO objects
be ungapped or gapped? It looks as if gapped cases are allowed
- is this the case? Should we flag ungapped vs gapped (or is
this done already somehow?)


I am starting to grok more why this event passing system is useful
(abstracts out parsing from object creation, more graceful about
partial information etc) but it does seem... quite alot of 
scaffolding...


I guess we should make SeqIO work like this at some point, but
that's definitely not in my critical path at the moment.