# taxa issue - AA frequencies matrix incorrectly initialised

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SitewiseSpecificLikelihoodSupportAaml.parseAamlOutput() can fail when the 
float[][] freqMat dimensions initialised, and those parsed from paml's 
aaml.out, do not match. 

As a result an java.lang.ArrayIndexOutOfBoundsException can be thrown 
(SitewiseSpecificLikelihoodSupportAaml:603), or else the matrix will have 
spurious. 

This will almost always occur when either:

a) One or more RAxML trees haven't run, and the # trees in the matrix is 
actually smaller than expected
b) The # sequences present in the AlignedSequenceRepresentation are < the #taxa 
in the taxa list because of missing data, again the matrix will be smaller than 
expected.
c) The # sequences present in the AlignedSequenceRepresentation are > the #taxa 
in the taxa list because the taxa list was misspecified. In this case an 
exception will be thrown, and the SSLS initialisation (and serialisation of 
results) will fail. 

(a) and (b) are not priorities but should be fixed ASAP as this behaviour is 
not safe. 
(c) has been fixed partially (r193) in that an Exception is thrown if the taxon 
list can't be read.

Original issue reported on code.google.com by joeparke...@gmail.com on 1 Aug 2013 at 12:53