[Biojava-dev] Count.java, Distribution.java and Alignment.java

[Schreiber, Mark]

> -----Original Message-----
> From: Lachlan Coin [mailto:lc1 at sanger.ac.uk] 
> Sent: Thursday, 13 February 2003 11:42 p.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] Count.java, Distribution.java and 
> Alignment.java
> 
> 
> I just had a few comments about these interfaces, which would 
> make them easier/more efficient for me to use.
> 
> It would be great if both these interfaces enforced a 
> nonZeroSymbols() method which returned the set of symbols 
> have a non-zero count / probability respectively.  
> Particularly if you are working with sparse counts over high 
> dimensional cross-product alphabets, it seems pretty 
> inefficient to iterate through all the members of a 
> cross-product alphabet when only a  small fraction of these 
> have counts.  This also relates to storage - it would be good 
> to have a DistributionFactory that could create sparse distributions.
> 

My vote would be to add two static nonZeroSymbols methods to
DistributionTools (one over Distributions the other over counts). This
avoids breaking the API but makes the functionality available.

> Also, this is more minor, but Count uses doubles rather than 
> integers, which is certainly more flexible, but would seem to 
> take more memory.  Is this flexibility needed - isn't 
> Distribution supposed to be for this?
> 

I use the double for resovling the counts of ambiguity symbols (which
Count formally doesn't count). Eg, if I am doing a count over DNA and I
see an n I add 0.25 to each symbol.

> 
> Finally, in Alignment.java, there are two methods, which use 
> inconsitent container classes for the labels of the alignment.
> 
> java.util.List getLabels()
> 
> Alignment subAlignment(java.util.Set labels, Location loc)
> 
> so that to get a subAlignment over all labels, you have to 
> convert a List to a Set.
> 

I think they should both be Sets.

> 
> Thanks,
> 
> Lachlan
> 
> -------------------------------------------------------------
> Lachlan Coin
> Wellcome Trust Sanger Institute		Magdalene College
> Cambridge  CB10 1SA			Cambridge CB30AG
> Ph: +44 1223 494 820
> Fax: +44 1223 494 919
> ------------------------------------------------------------
> 
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