Re: [Gmod-ajax] lazy feature loading and long features

[Mitch S. <mit...@be...>]

On 11/20/2009 03:48 AM, Martin A. Hansen wrote:
> I was reading about lazy loading: 
> http://biowiki.org/view/JBrowse/LazyFeatureLoading
>
> How to handle long features that would result in uneven large chunks 
> and possible overloading?
>
>    1. One could disallow long features.
>    2. or break them into smaller features with a hidden "link" between
>       them?
>
>

If there's a large real feature, the generated fake features can be 
within it.  For example, suppose you have the following four real features:

A: [10, 100)
B: [20, 30)
C: [40, 50)
D: [50, 60)

And suppose you want to split this set of features into chunks that each 
contain two features.  JBrowse will generate two fake features:

F1: [10, 101)
F2: [40,61)

And the NCList tree will look something like:

F1: (A B *F2)
F2: (C D)

Where *F2 is a URL pointing to the F2 chunk.

I hope that makes sense, maybe I'll add another diagram to that wiki 
page to try and make it clearer.

The one failure case that I know about (with the current code) is when 
there are lots of features with the exact same boundaries.  I think that 
could be addressed by making the NCList.pm code aware of the fake 
features (currently, NCList.pm doesn't know anything about the fake 
features; those are all created and handled by the code that calls 
NCList.pm).

Mitch