O(N) Garbage collection?

[dsimcha]

On 2/19/2011 12:50 PM, Ulrik Mikaelsson wrote:
> Just a thought; I guess the references to the non-GC-scanned strings
> are held in GC-scanned memory, right? Are the number of such
> references also increased linearly?

Well, first of all, the benchmark I posted seems to indicate otherwise. 
  Second of all, I was running this program before on yeast DNA and it 
was ridiculously fast.  Then I tried to do the same thing on human DNA 
and it became slow as molasses.  Roughly speaking, w/o getting into the 
biology much, I've got one string for each gene.  Yeast have about 1/3 
as many genes as humans, but the genes are on average about 100 times 
smaller.  Therefore, the difference should be at most a small constant 
factor and in actuality it's a huge constant factor.

Note:  I know I could make the program in question a lot more space 
efficient, and that's what I ended up doing.  It works now.  It's just 
that it was originally written for yeast, where space efficiency is 
obviously not a concern, and I would have liked to just try a one-off 
calculation on the human genome without having to rewrite portions of it.