[Biojava-l] Equals method in for gap symbols

Matthew Pocock matthew_pocock at yahoo.co.uk
Thu Feb 6 15:07:44 EST 2003

Hi Lachlan,

This smells like a bug. Gaps should be unique. Could you mail me an 
example program and data-file?


Lachlan Coin wrote:
> 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
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