BEAUTi: Crash when trying to generate an XML file with the covarion.

BEAUTi crashes when trying to generate an XML file with the covarion. The 
attached patch should fix this. 

Problems encountered include: 
 - BEAST expects the covarion to have the parameters bcov.alpha, bcov.frequencies and bcov.hfrequencies. BEAUTi tried to generate "frequencies", 
"hfrequencies", "alpha"
- BEAUTi would still add a parameter and an operator on "frequencies" - which 
hadn't been defined. I've caught this in addFrequencyParams and 
addFrequencyOps respectively. This may not be the most elegant way to do this 
however.

NOTE: there is still one issue that this patch does NOT address, and the 
resulting XML DOES NOT WORK. The Two state covarion model expects the 
datatype of the alignment to be twoStateCovarion not binary (e.g.   <alignment 
id="alignment" dataType="twoStateCovarion">
not     <alignment id="alignment" dataType="binary">)

If the datatype is binary, then BEAST will crash raising a 
java.lang.ArrayIndexOutOfBoundsException. I'm not sure what's the best way to 
fix this - 
should the alignment in the XML have the attr "twoStateCovarion", or should the 
BEAST catch this exception, or does the datatype have to change to 
be analysed under a different model (the latter seems a bit odd to me?).

Original issue reported on code.google.com by dev@simon.net.nz on 28 Nov 2009 at 11:00

Attachments:

beauti-covarion.diff

dbabox / beast-mcmc

BEAUTi: Crash when trying to generate an XML file with the covarion. #258