Binomial likelihood now takes non-fixed counts.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5243 ca793f91-a31e-0410-b540-2769d408b6a1
renamed integratedMixtureModel to MixtureModelLikelihood. Preserved an alias parser <integratedMixtureModel> per Marc's request. Updated the class, such that the mixtures are always normalized internally when likelihood is calculated.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5244 ca793f91-a31e-0410-b540-2769d408b6a1
resolving Issue 630.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5245 ca793f91-a31e-0410-b540-2769d408b6a1
Implemented user-specified starting transmission trees

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5246 ca793f91-a31e-0410-b540-2769d408b6a1
adding multiple trees

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5247 ca793f91-a31e-0410-b540-2769d408b6a1
set tree for partition using hash map

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5248 ca793f91-a31e-0410-b540-2769d408b6a1
Now repeatedly tries to find a starting transmission tree with nonzero likelihood rather than giving up after one try

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5249 ca793f91-a31e-0410-b540-2769d408b6a1
starting to work on XML generator

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5250 ca793f91-a31e-0410-b540-2769d408b6a1
Cleaned up the format of the complete history logging. Now has {SITE,{TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5251 ca793f91-a31e-0410-b540-2769d408b6a1
Cleaned up the format of the complete history logging. Now has {{SITE,TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5252 ca793f91-a31e-0410-b540-2769d408b6a1
Various improvements and bugfixes to starting transmission trees

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5253 ca793f91-a31e-0410-b540-2769d408b6a1
Inserting the old ASTL back in to the deep inheritance chain of OTL. MJTL next.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5254 ca793f91-a31e-0410-b540-2769d408b6a1
Inserting the old MJTL back in to the deep inheritance chain of OTL. For testing purposes only. If it has a line through it - it is going to go at some point.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5255 ca793f91-a31e-0410-b540-2769d408b6a1
Forgot to change the parser name.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5256 ca793f91-a31e-0410-b540-2769d408b6a1
Old TL/ASTL/MJTL in parser list.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5257 ca793f91-a31e-0410-b540-2769d408b6a1
Fix for complete history logging; this may break code elsewhere

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5258 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed (hopefully) an issue that was causing systematic under-estimation of incubation periods

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5259 ca793f91-a31e-0410-b540-2769d408b6a1
Incomplete implementation of multi-state stochastic Dollo under BEAGLE.  Needs considerably more work.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5260 ca793f91-a31e-0410-b540-2769d408b6a1
Composition parameters; should really be a Statistic with signaling ability

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5261 ca793f91-a31e-0410-b540-2769d408b6a1
More tip date shenaningans. Also added method to dump the current transmission tree to a file.

git-svn-id: http://beast-mcmc.googlecode.com/svn/trunk@5262 ca793f91-a31e-0410-b540-2769d408b6a1