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rambaut 2012-03-03 23:50 Rev.: 4759

Removing 'blue.jar' from lib folder. Need to work out other solution - either it is part of BEAST or it isn't.

0 lines of code changed in 1 file:

• lib: blue.jar (del)

sibon.li 2012-03-03 21:38 Rev.: 4758

Commented out all of my last commit until issues resolved

0 lines of code changed in 2 files:

• lib: blue-beast.jar (del), blue.jar (new)

sibon.li 2012-03-03 18:14 Rev.: 4756

Added blue-beast.jar and modified build xmls

0 lines of code changed in 1 file:

• lib: blue-beast.jar (new)

fbielejec 2012-02-02 03:26 Rev.: 4625

reverting

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• lib: beagle.jar (changed)

fbielejec 2012-02-01 20:40 Rev.: 4620

recompiled beagle.jar

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• lib: beagle.jar (changed)

fbielejec 2012-01-18 09:20 Rev.: 4588

recompiled beagle.jar

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• lib: beagle.jar (changed)

rambaut 2011-07-27 23:43 Rev.: 4123

Removed commons-maths-2.0.jar from lib folder

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• lib: commons-math-2.0.jar (del)

rambaut 2011-07-24 06:30 Rev.: 4117

Switched GammaDistributionModel to use Common Math version to see if that has better numerical stability. Also updated commons-math to the latest version.

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• lib: commons-math-2.2.jar (new)

msuchard 2010-09-11 00:27 Rev.: 3525

Changing default BEAST behavior to throw exception if BEAGLE not found, instead of trying to run the Java BEAGLE implementation that is incomplete and crashes anyway.

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• lib: beagle.jar (changed)

rambaut 2010-09-09 23:33 Rev.: 3515

A few more bits of clean up.

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• lib: jam.jar (changed)

msuchard 2010-08-22 08:39 Rev.: 3423

In the middle of trying to get BEAGLE's dynamic scaling to work in BEAST

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2010-06-05 02:18 Rev.: 3224

Fixed TreeTrait to deal with a null trait value array (for example from the root of a tree).

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• lib: beagle.jar (changed)

rambaut 2010-03-02 01:23 Rev.: 2998

Updated beagle.jar

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2010-02-10 03:57 Rev.: 2906

Resolved an arbitrary contraction of a constant name.

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• lib: beagle.jar (changed)

rambaut 2010-01-22 04:53 Rev.: 2828

Updates to Java BEAGLE. BEAST now compiles and runs but make not be correct yet when using BEAGLE.

0 lines of code changed in 3 files:

• lib: beagle.jar (changed), jebl.jar (new)

rambaut 2009-12-12 01:47 Rev.: 2691

Minor correction of intercapitalization.

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• lib: jam.jar (changed)

rambaut 2009-12-02 00:07 Rev.: 2642

Trying to get JVM 1.5 linking compatibility

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• lib: figtreepanel.jar (changed)

rambaut 2009-12-01 10:37 Rev.: 2639

Recompilation of beagle.jar to try and fix a JVM mismatch

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-11-26 04:04 Rev.: 2612

Another little tree processing main.

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-11-13 01:32 Rev.: 2534

New library to add to the project. Only required for dr.app.phylogeography.* so either exclude this from your build or add kmlframework_20090320.jar to your libraries.

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• lib: org.boehn.kmlframework_20090320.jar (new)

rambaut 2009-10-28 01:38 Rev.: 2479

Updated the Mac/Linux build scripts: the command line shell scripts now provide linking for BEAGLE if required. Added spaces _back_ into Mac and Windows application/package names. There was no need to remove them and users expect spaces in the names of applications. Issue 220: http://code.google.com/p/beast-mcmc/issues/detail?id=220 still needs to be dealt with but the solution is _NOT_ just to remove spaces - see the issue for details.

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-10-24 00:49 Rev.: 2452

Updated the JEBL jar file and BeastDialog to use longs for the RNG seed text box.

0 lines of code changed in 1 file:

• lib: jebl.jar (changed)

msuchard 2009-10-23 11:29 Rev.: 2450

Implemented getTransitionMatrix in BEAGLE for use with microsat models and ancestral state reconstruction. Reconstruction no longer crashes; still need to confirm results

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-10-16 08:13 Rev.: 2420

figtreepanel.jar in 1.5 byte code.

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• lib: figtreepanel.jar (changed)

rambaut 2009-10-15 09:53 Rev.: 2410

Updated figtreepanel

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• lib: figtreepanel.jar (changed)

rambaut 2009-10-15 09:06 Rev.: 2406

Updated figtreepanel

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• lib: figtreepanel.jar (changed)

jheled 2009-10-15 09:04

version 2.0

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• lib: commons-math-1.2.jar (del), commons-math-2.0.jar (new)

msuchard 2009-09-24 12:55 Rev.: 2283

Trying another build

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• lib: beagle.jar (changed)

msuchard 2009-09-24 11:52 Rev.: 2280

Preparing BEAST for complex computation in BEAGLE ... ready for fast microsat models?

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• lib: beagle.jar (changed)

msuchard 2009-09-11 09:16 Rev.: 2235

BeagleTreeLikelihood now takes advantage of BEAGLE's resource flexibility

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

msuchard 2009-09-11 06:47 Rev.: 2234

Switched default BEAGLE CPU version from hybrid to pure C
; appears to offer performance gains

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-08-31 20:37 Rev.: 2168

'beagle.jar' should now be targetted at a 1.5 JVM as required to link with BEAST

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• lib: beagle.jar (changed)

rambaut 2009-08-29 01:26 Rev.: 2162

Removed some extraneous columns that were being written to the screen log (with very large numbers of decimal places).

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• lib: beagle.jar (changed)

rambaut 2009-08-15 12:16 Rev.: 2075

Updated 'beagle.jar'.

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• lib: beagle.jar (changed)

rambaut 2009-08-14 12:09 Rev.: 2071

Some experiments on CPU efficiency. NNLCBeagleImpl.java is a Java BeagleImpl which calls the NativeNucleotideLikelihoodCore (BEAST's old JNI library) directly for the 3 main calls (calculateStatesStates, calculateStatesPartials, calculatePartialsPartials). This JNI implementation is considerably faster than BEAGLE CPU.

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• lib: beagle.jar (changed)

rambaut 2009-08-10 20:40 Rev.: 2051

Forgot to update the beagle.jar library (again).

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

rambaut 2009-08-06 23:45 Rev.: 2039

BeagleTreeLikelihood now prints info about the BEAGLE resource it is running on.

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• lib: beagle.jar (changed)

msuchard 2009-08-06 08:28 Rev.: 2030

Changed beagle.jar

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• lib: beagle.jar (changed)

rambaut 2009-08-05 03:26 Rev.: 2019

Forgot to update beagle.jar causing a broken build.

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

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.

0 lines of code changed in 1 file:

• lib: beagle.jar (changed)

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