[Biojava-l] Counting Gaps

[Schreiber, Mark]

Hi -

This is reminiciscent of something I was trying to do with
DistributionTools. You can't store a frequency of the Gap symbol in a
Distribution even though a gap symbol is a perfectly valid addition to
most alphabets.

Is there a way of counting gaps in a distribution? Sometimes its really
useful to know that

A = 0.2
C = 0.3
G = 0.2
T = 0.2
- = 0.1

 - Mark

> -----Original Message-----
> From: Lachlan Coin [mailto:lc1 at sanger.ac.uk] 
> Sent: Friday, 7 February 2003 3:11 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Equals method in for gap symbols
> 
> 
> 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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> 
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