[Gmod-ajax] rendered larger chromsome

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

I've put up Dmel 3R here:
http://genome.biowiki.org/gbrowse/dmel51/prototype_gbrowse.html

It rendered in less than 8 hours on one CPU, and the tiles and HTML take 
up around 13 gigabytes on disk.  Memory usage maxed out at 342 MB.  The 
3R chromosome arm is the largest Dmel one at 28 Mb, or about 20 times 
the size of chromosome 4.  So to do human we just have to scale another 
order of magnitude; it's CPU bound and we've got a fair amount of CPU to 
throw at it, but if memory usage grows linearly with the amount of 
sequence then we may start running into problems.  We could do some more 
work on rendering on demand, and that would help, but you've still got 
to have all the features in memory at the same time to do layout, so we 
may not be able to reduce max memory usage very much that way.  Maybe we 
can partition the layout job if there are empty regions of the chromosome.

One problem with the current approach is that the HTML files get quite 
large for the lower (more zoomed-out) zoom levels.  For the Genes track 
the entire_landmark HTML file is 1.6 megabytes; for CDS it's 7.7 
megabytes.  The HTML for entire_landmark for all tracks totals 24 
megabytes, which is how much you would have to download to actually view 
the entire_landmark zoom level.  Maybe we should have some kind of limit 
above which we turn off the HTML.  Also, if we had a way of lazily 
loading feature information then the HTML could be a lot smaller.

With a large number of features the browser starts to slow down; for me 
this starts to be noticeable around the 1Mbp zoom level on Windows.  On 
other platforms firefox starts to bog down at higher (less dense) zoom 
levels.  Again, if we turn off the html above some feature density 
threshold this should be less of a problem.

Mitch