Directory src/dr/evomodel/beagle/treelikelihood/

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rambaut 2009-08-04 03:47 Rev.: 2009

Moving BEAGLE/BEAST out of the main package into dr.app. This will allow us to deploy the jar file separately from BEAST.

0 lines of code changed in 2 files:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (del), BeagleTreeLikelihood.java (del)

rambaut 2009-08-03 05:05 Rev.: 1997

The helper class for handling store/restore now works with BEAGLE.

51 lines of code changed in 2 files:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (new)

rambaut 2009-08-02 23:13 Rev.: 1996

Implemented a helper class to handle the buffer indexing.

94 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+94 -81)

rambaut 2009-08-02 21:57 Rev.: 1995

Updated BeagleTreeLikelihood to use the new scaling API including store/restore. As this is not yet implemented in BEAGLE, this is untested.

87 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+87 -44)

rambaut 2009-08-01 01:52 Rev.: 1971

More BEAST/BEAGLE fixes

2 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+2 -2)

rambaut 2009-07-31 22:40 Rev.: 1970

Added more detail to the comments in 'beagle.h' about what is expected in the arrays passed to setPartials, setTipStates and setMatrix.

9 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+9 -1)

rambaut 2009-07-31 12:11 Rev.: 1963

Java implementation (GeneralBeagleImpl) now works for categories. Native BEAGLE returns NaN.

0 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (-13)

rambaut 2009-07-31 11:58 Rev.: 1962

BEAST/Beagle now samples a simple (single category) model returning exactly the same sequence as normal BEAST. Multiple categories still returning NaN.

28 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+28 -25)

rambaut 2009-07-31 10:29 Rev.: 1961

BeagleTreeLikelihood now works with testLikelihood.xml except when multiple categories are used. Work continues...

32 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+32 -29)

msuchard 2009-07-31 09:59 Rev.: 1960

Started rescaling mechanism; should not interfere with Andrew's work

26 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+26 -7)

rambaut 2009-07-31 07:56 Rev.: 1958

beagle library update to fix build failure

1 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+1 -1)

rambaut 2009-07-31 07:14 Rev.: 1956

The JNIWrapper now seems to work - the 'TinyTest' in BeagleFactory now reports:

BEAGLE library loaded
BEAGLE bootstrap: CPU - Success
logL = -1574.6362268149937 (PAUP logL = -1574.63623)

50 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+50 -48)

rambaut 2009-07-30 00:55 Rev.: 1947

Updates to BEAST/BEAGLE. Not working yet.

12 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+12 -23)

alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

3 lines of code changed in 2 files:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (+3 -2)

rambaut 2009-06-03 09:08 Rev.: 1759

Made some changes to the BEAGLE/BEAST interface to reflect the new BEAGLE API.

109 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+109 -50)

rambaut 2009-05-31 07:32 Rev.: 1756

Updated tinyTest

2 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+2 -2)

rambaut 2009-05-31 04:48 Rev.: 1755

Removed setStateFrequencies as calculateLogLikelihood gets passed these.

3 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+3)

msuchard 2009-04-20 06:05 Rev.: 1605

Refactored LikelihoodColumn as protected class in AbstractModelLikelihood (thanks, Joseph ... this was a good idea); removed subclassing of getLogColumns in several AMLs to see if this break things. I do not suspect that it will and we can/should now remove subclassing getLogColumns and redefinition of LikelihoodColumn in most AMLs, saving hundreds of lines of code .. or shotting myself in the foot :-)

0 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (-23)

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

2 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (+2 -3)

rambaut 2009-04-08 04:20 Rev.: 1538

Added a demo Beagle core that uses the dependencies of node operations to add additional parallelization. Probably not worth doing in Java but maybe worth porting to CUDA.

46 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+46 -48)

msuchard 2009-03-28 09:18 Rev.: 1520

BeagleTreeLikelihood and the BEAGLE library now support the dynamic partials rescaling that we have come to know and love.

2 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+2 -2)

msuchard 2009-03-25 07:34 Rev.: 1515

Changed BEAGLE tree parser so user can specify a precision preference instead of requirement. Removed some redundant code (static names)

7 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+7 -5)

rambaut 2009-03-24 05:11 Rev.: 1510

Import optimization

8 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+8 -12)

rambaut 2009-03-21 23:08 Rev.: 1506

Improved interface of calculateTransitionProbabilityMatrices to allow multiple branches to be updated. Eliminated use of getCriticalPrimativeArray over calls to BEAGLE. Elimated mallocs within JNIWrapper calls. However, the native CPU version seems not to work yet (zero likelihood).

1 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+1 -3)

rambaut 2009-03-20 05:08 Rev.: 1504

Towards a working beagle library

6 lines of code changed in 2 files:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (+3 -2), BeagleTreeLikelihood.java (+3 -5)

rambaut 2009-03-19 05:23 Rev.: 1502

Towards a working beagle library

22 lines of code changed in 1 file:

• src/dr/evomodel/beagle/treelikelihood: BeagleTreeLikelihood.java (+22 -20)

rambaut 2009-03-19 02:15 Rev.: 1501

I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.

812 lines of code changed in 2 files:

• src/dr/evomodel/beagle/treelikelihood: AbstractTreeLikelihood.java (+292), BeagleTreeLikelihood.java (+520)