Directory src/dr/app/beagle/evomodel/branchratemodel/

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rambaut 2010-06-03 01:12 Rev.: 3219

Deleting redundant dr.app.beagle.evomodel.branchratemodel.MarkovJumpsBranchRateModel.

0 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/branchratemodel: MarkovJumpsBranchRateModel.java (del)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

2 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/branchratemodel: MarkovJumpsBranchRateModel.java (new)

rambaut 2010-05-28 03:44 Rev.: 3193

Started to implement a branch rate model that takes a realization of a discrete location provided by a MarkovJumpsTreeLikelihood and produces a continuous diffusion rate based on the proportion of time spent in each location and a vector of relative rates and indicators. Builds but not finished implementing.

90 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/branchratemodel: MarkovJumpsBranchRateModel.java (+90)