[DAS2] feature group assembly; proposals for simplification

[Andrew Dalke]

On Sep 16, 2006, at 1:08 AM, Lincoln Stein wrote:
> Hi Andrew,
>
>  Grouping them into a <FEATURE_GROUP> set is almost equivalent to the 
> "end of
>  feature set" marker in GFF3, which is why I favor that solution. If 
> we do this, should we adopt the same convention for the GET requests 
> as well? If so, should we get rid of bidirection references?

(I did notice that the GFF3 data sets I found, like wormbase, don't have
the "end of feature set" marker.  My GFF3 parser has about 10x memory 
overhead
so parsing a 80MB input file thrashed my 1GB laptop.  Adding a single
marker in the middle, by hand, made it much happier.)

If we have a <FEATURE_GROUP> such that features in that group are all
connected to other and only to each other, then I have no problem 
getting
rid of the child link.  It adds no benefits in that case but does cause
the verification overhead of checking that both directions are correct.

					Andrew
					dalke at dalkescientific.com