Not finished but descent version of GPOperator

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4778 ca793f91-a31e-0410-b540-2769d408b6a1
Not finished but descent version of GPOperator - fixing imports :S

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4779 ca793f91-a31e-0410-b540-2769d408b6a1
Reverting inadvertent changes from Julia

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4780 ca793f91-a31e-0410-b540-2769d408b6a1
Reverting more silly changes

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4781 ca793f91-a31e-0410-b540-2769d408b6a1
Corrected spelling and simplified error XML reporting (commented out public ID and System ID).

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4782 ca793f91-a31e-0410-b540-2769d408b6a1
Initial, horribly slow, inefficient re-write of antigenic likelihood.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4783 ca793f91-a31e-0410-b540-2769d408b6a1
BEAST version for trunk changed to 1.8.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4784 ca793f91-a31e-0410-b540-2769d408b6a1
Added a total to the diagnostic string of compound likelihood

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4785 ca793f91-a31e-0410-b540-2769d408b6a1
Commented out a couple of debug printfs

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4786 ca793f91-a31e-0410-b540-2769d408b6a1
Finally fixed the diagnostics strings displayed after an incorrect restore so that they are genuinely before and after (as opposed to both after).

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4787 ca793f91-a31e-0410-b540-2769d408b6a1
Runtime errors galore.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4788 ca793f91-a31e-0410-b540-2769d408b6a1
Implemented TN93 under BEAGLE.


git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4789 ca793f91-a31e-0410-b540-2769d408b6a1
Added BEAGLE rescaling options to BEAST UI dialog. Added command line option to control the rescaling frequency in dynamic scaling.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4793 ca793f91-a31e-0410-b540-2769d408b6a1
Don't use a truncated distribution unless this option is selected.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4794 ca793f91-a31e-0410-b540-2769d408b6a1
TruncatedDistribution now adjusts its bounds to be inside the source distribution's (i.e., if it is an OffsetPositive). LogNormalDistribution had a lower bound of -Inf, now set to zero.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4795 ca793f91-a31e-0410-b540-2769d408b6a1
Fix to last commit.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4796 ca793f91-a31e-0410-b540-2769d408b6a1
Few more fixes to truncation of prior distributions

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4797 ca793f91-a31e-0410-b540-2769d408b6a1
Antigenic

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4801 ca793f91-a31e-0410-b540-2769d408b6a1
Merged changes from 1.7

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4802 ca793f91-a31e-0410-b540-2769d408b6a1
Implemented a "not statistics" for boolean stats (like monophylyl).  NotStatistic is now deprecated.


git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@4803 ca793f91-a31e-0410-b540-2769d408b6a1