tests for dpp cluster configuration likelihood, fixed a small bug

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6484 ca793f91-a31e-0410-b540-2769d408b6a1
Committed various older changes

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6485 ca793f91-a31e-0410-b540-2769d408b6a1
Implemented getInverseIntensity

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6486 ca793f91-a31e-0410-b540-2769d408b6a1
Various cosmetic changes (comments etc)

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6487 ca793f91-a31e-0410-b540-2769d408b6a1
Now works from the command line

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6488 ca793f91-a31e-0410-b540-2769d408b6a1
Fix to issue 681 as suggested by Graham853 in comments; MCMCMC is now more verbose if DEBUG=true

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6489 ca793f91-a31e-0410-b540-2769d408b6a1
Moved stable CTC parsers to release version

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6490 ca793f91-a31e-0410-b540-2769d408b6a1
Moving code around a bit.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6491 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed some issues generating XML with multiple trees and joint discrete traits. Resolves Issue 743

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6492 ca793f91-a31e-0410-b540-2769d408b6a1
Local Clocks started

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6493 ca793f91-a31e-0410-b540-2769d408b6a1
Reverting

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6494 ca793f91-a31e-0410-b540-2769d408b6a1
The default is now to try to use the BEAGLE library (and SSE extensions). Turn this off with -beagle_off option (and -beagle_sse_off).

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6495 ca793f91-a31e-0410-b540-2769d408b6a1
Tweaks to JAM for OS X integration.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6496 ca793f91-a31e-0410-b540-2769d408b6a1
Prettyficating the options dialog

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@6497 ca793f91-a31e-0410-b540-2769d408b6a1