[Biojava-l] Equals method in for gap symbols

[Lachlan Coin]

Hi,

I am trying to read in an alignment, and get a count of frequencies of
symbols in columns of the alignment.  My problem is that biojava seems to
not recognize two gap symbols as being equal, so each time I come across
a gap symbol my (probably naive!) implementation puts a new gap symbol in
my HashMap, rather than incrementing the overall gap symbol count.
Is it possible to set things up so that two gap symbols are equal?  I
realize that this is probably not the right thing to do for other
applications.

Thanks a lot,

Lachlan