VPR needs to recurse into the hierarchy to link interactions

[cjmyers]

I ran into an issue with the “data2” approach in regards to CDs with hierarchy. Consider the following example:

CD pro

CD rbs

CD cds

CD gene
Comp rbs
Comp cds

CD TU
Comp pro
Comp gene

CD protein

MD production
Comp cds_prod
Comp protein_prod
Interaction production
Participation cds
Participation protein

If we apply, VPR, we get:

MD top
FuncComp cds_top
FuncComp protein_top
FuncComp TU
MapsTo cds to cds_top
Module production
MapsTo cds_prod to cds_top
MapsTo protein_prod to protein_top

This is wrong though because TU does not have the cds mapped up to it. Once again, we need to map things up, like so:

MD top
FuncComp cds_top
FuncComp protein_top
FuncComp gene_top
MapsTo cds to cds_top
FuncComp TU
MapsTo gene to gene_top
Module production
MapsTo cds_prod to cds_top
MapsTo protein_prod to protein_top

Its not so pretty, but I don’t see any easier way.