Closed nathandunn closed 8 years ago
Create fold method:
Rightedge - left edge .. Projection .. Note (json)
Project feature:
Fmin fmax .. Projection .. Note (json)
Multiple projections e.g. Reverse complement .. Store a list of projections to apply
Display .. Sketch note
Projection notation should be (red is flipped, blue is not or vice versa):
With Genes:
A Gene crossing scaffold:
Note: 1-base vs interbase: http://transvar.org/6111/interbase.pdf
We are using 1-base (same as GFF3), though internally, I think that JBrowse is using interbase (bed files, etc.).
will try adding an extra track for the display . . should be REST based initially
so there are a few different approaches that we've looked at. Our biggest hinderances are: 1) we don't want to rewrite JBrowse and 2) we need appropriate visualizations 3) we don't have an appropriate model store / alternate view for our data.
I'm curious why . . . instead of modifying store functions, if we used REST directly, but this is sort of what we were already doing with the server-side mangling.
To create the REST-side alternate "view" track, I think we could just display a "feature" labelled "Projection Legend (785-913)". This will allow counting. You could even count by 10's or something, internally, displaying as exons, etc. From here you could
closing in favor of #895
TODO:
trackData.json
-> projectTrackData has a bad offset)Use-cases
Datastructure: Putative datastructure used for display. Note that the "folding" is different as it indicates the areas we are hiding (and need to indicate). Features indicate the areas that we are showing. In the sequenceList we need to be able to the region. The "features" portion is for decoration as is the "folding" region.