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rambaut 2009-08-20 07:59 Rev.: 2109

Merged in changes removing the use of STL vectors from the CPU implementation. Also removed a few try blocks round calls to functions that don't and needn't throw exceptions.

1 lines of code changed in 2 files:

• src/dr/app/misc: Coevolve.java (new)

rambaut 2009-04-08 11:19 Rev.: 1542

Forgot to check in changes to Coevolve. What is Coevolve? Looks like old crud that should be deleted.

10 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+10 -10)

jheled 2008-11-19 12:11 Rev.: 1318

Code Police

2 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+2 -1)

rambaut 2008-07-02 02:25 Rev.: 969

OK. Automatic scaling is now working. If the initial evaluation of the log likelihood returns -Inf then it turns on. It will impact performance but is better than not working at all. There are a number of improvements that could be made: one is to switch it off again once the tree is significantly improved. The other is to only rescale on certain nodes.

I tested it by comparing with the ArbitraryPrecisionLikelihoodCore (see ExperimentalTreeLikelihood) which is a form of GeneralLikelihoodCore that uses BigDecimal to a specified precision.

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

rambaut 2008-07-01 03:23 Rev.: 967

Am working on a partial likelihood scaling mechanism that will allow us to calculate likelihoods of very bad trees and very big trees. The aim is that this is dynamic and switches off if no longer needed. It is crude at the moment but compiles and runs (and shouldn't affect anything that doesn't explicitly ask for it).

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

rambaut 2008-06-21 06:01 Rev.: 963

Added the ability to force the use of a Java nucleotide core (rather than native) in order to assist debugging.

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

rambaut 2008-05-27 11:38 Rev.: 896

Added a flag to TreeLikelihood to allow missing taxa (defaults to false so that missing taxa throw an exception). If true then missing taxa are given missing data at all sites.

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

rambaut 2008-03-14 09:50 Rev.: 754

Fixes for DNA damage model

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

alexei.drummond 2006-12-05 20:49 Rev.: 103

oops, fixed inadvertent compile error due to reversing some of my changes to TreeLikelihood in my last commit

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)

rambaut 2006-12-05 10:51 Rev.: 97

I have removed the org.virion.jam package from the Trunk. This was the Java 1.4 version of JAM. The trunk now compiles against JEBL v0.3 which includes JAM and is based on Java 1.5. The jebl-0.3.jar can now be found in the lib/ folder.

1 lines of code changed in 1 file:

• src/dr/app/misc: Coevolve.java (+1 -1)