Re: [Gmod-ajax] rendered larger chromsome

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

I wrote:
> One of the things I like about the feature density plot is that it's 
> obvious that there's nothing to click on.

As an experiment I implemented this:
http://genome.biowiki.org/gbrowse/dmel51/prototype_gbrowse.html

On the conference call yesterday Lincoln said that there was some 
feature density functionality already in GBrowse, and I see some code 
for it in Bio::DB::GFF but AFAICS it's not implemented for 
Bio::DB::SeqFeature, so I did my own version.  The stuff in Bio::DB::GFF 
is per-datasource (there's some SQL to count the number of features in 
each histogram bin) and that's more efficient than retrieving all the 
features and sorting them into bins, but since we have to get all of the 
features anyway a generic implementation doesn't cost us much.  Point 
being, I don't think I'm duplicating effort by doing things this way.

Also (at Lincoln's suggestion) I made it so it doesn't generate imagemap 
regions for 1-pixel wide features.  I'm a little concerned that this 
might be confusing, since you can mouseover some features but not 
others, but then again I don't think it's too likely that people will 
try to mouseover 1-pixel targets but will probably try to zoom in some 
more before trying it.  I'd be interested to hear opinions on this--try 
looking at the exon track at 500kbp.  I should try to measure how much 
this saves on HTML size.

Unfortunately, the scale is currently getting rendered off-tile, and I 
think the only way to change this is to add some padding on the side, 
which will throw off a lot of other position calculations (on both the 
client and server side).  The Right Thing to do in this case is have 
special client-side support for always showing the scale at the edge of 
the view, so trying to add padding is not only problematic but it 
doesn't really solve the problem either.  Point being, when judging the 
usefulness of the feature density histogram, imagine that there's a 
scale on the side.

Mitch