August 2009 Commit Log

Number of Commits:
192
Number of Active Developers:
9
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

0 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-08-31 18:03 Rev.: 2167

Changed println statement in NormaliseMeanTreeRate

1 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-08-31 18:01 Rev.: 2166

Added NormaliseMeanTreeRate (incomplete)

302 lines of code changed in 1 file:

dong.w.xie 2009-08-31 16:57 Rev.: 2165

BEAUTi: fix the bug of no other elements in <substitutionModel> besides Substitution Model Type.

3 lines of code changed in 1 file:

rambaut 2009-08-29 01:58 Rev.: 2164

Fixed an issue with the generation of the SequenceErrorModel. Altered the screen log to only give the 'rate of evolution' under the rate column.

7 lines of code changed in 4 files:

rambaut 2009-08-29 01:43 Rev.: 2163

Changed order of the rate statistics of the BranchRatesModel in the log files

6 lines of code changed in 1 file:

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).

3 lines of code changed in 2 files:

dong.w.xie 2009-08-28 17:29 Rev.: 2161

BEAUTi: fix more bugs regarding calibration GUI event and log.

23 lines of code changed in 5 files:

dong.w.xie 2009-08-28 15:03 Rev.: 2160

update xml example of *BEAST generated by BEAUTi.

0 lines of code changed in 8 files:

dong.w.xie 2009-08-28 15:02 Rev.: 2159

BEAUTi: add some GUI event for triggering codon model.

7 lines of code changed in 1 file:

dong.w.xie 2009-08-28 14:36 Rev.: 2158

BEAUTi: fixing a bug of reseting *BEAST.

0 lines of code changed in 1 file:

dong.w.xie 2009-08-28 13:31 Rev.: 2157

BEAUTi: fix a big bug in Substitution Model panel, for linking and unlinking subst model, frequency, rate hererog, when having codon model.

137 lines of code changed in 3 files:

dong.w.xie 2009-08-28 10:40 Rev.: 2156

BEAUTi: correct some wrong validation.

18 lines of code changed in 2 files:

dong.w.xie 2009-08-28 10:11 Rev.: 2155

BEAUTi: add some GUI event, and reset panel.

31 lines of code changed in 3 files:

jheled 2009-08-28 06:12 Rev.: 2154

Fix TN93 update (issue 134)

12 lines of code changed in 1 file:

dong.w.xie 2009-08-27 17:24 Rev.: 2153

BEAUTi: bug fixing for clock setting in calibrication.

89 lines of code changed in 10 files:

jheled 2009-08-27 15:29 Rev.: 2152

Even slower at startup - have more detailed printouts

4 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-08-27 15:23 Rev.: 2151

Changed todo to TODO

1 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-08-27 15:15 Rev.: 2150

Commented out my discretizedBranchRates Beauti stuff

4 lines of code changed in 1 file:

dong.w.xie 2009-08-27 13:38 Rev.: 2149

BEAUTi: add some useful message.

63 lines of code changed in 4 files:

dong.w.xie 2009-08-27 13:37 Rev.: 2148

BEAUTi: Issue #116.
Finish BEAUTi part, but there is problem for parser.

4 lines of code changed in 3 files:

dong.w.xie 2009-08-27 10:47 Rev.: 2147

BEAUTi: more Issue 133: changing treelogger xml generating in beauti.
Need Sibon to test.

13 lines of code changed in 2 files:

dong.w.xie 2009-08-27 10:29 Rev.: 2146

BEAUTi: solve Issue 133: changing treelogger xml generating in beauti.
Need Sibon to test.

24 lines of code changed in 1 file:

rambaut 2009-08-27 00:14 Rev.: 2145

Renamed column in data to 'subst. model' to match link/unlink buttons.

5 lines of code changed in 2 files:

dong.w.xie 2009-08-26 18:13 Rev.: 2144

BEAUTi: cotinue Issue #116. But got exception regarding siteModel block in XML.

141 lines of code changed in 6 files:

dong.w.xie 2009-08-26 17:52 Rev.: 2143

BEAUTi: finish Issue #100 and Issue #124.
But it still needs improvement of initial values referring each partition.

4 lines of code changed in 1 file:

alexei.drummond 2009-08-26 17:11 Rev.: 2142

estimating initial root height from node calibrations

17 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-08-26 17:07 Rev.: 2141

Extra parameter option for TreeLogger: normaliseMeanRateTo. More on this later

40 lines of code changed in 2 files:

alexei.drummond 2009-08-26 16:56 Rev.: 2140

estimating initial root height from node calibrations

708 lines of code changed in 5 files:

dong.w.xie 2009-08-26 12:56 Rev.: 2139

BEAUTi: cotinue Issue #100 and Issue #124.
TODO for Alexei.

10 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-08-25 17:06 Rev.: 2138

Tracer tweaks

368 lines of code changed in 1 file:

dong.w.xie 2009-08-25 16:32 Rev.: 2137

BEAUTi: cotinue Issue #100 and Issue #124.
1) add some events in GUI to fire Tip Calibration and Node Calibration;
2) tidy up 5 FixRateType;
3) TODO: the calculation of ini rate and root height for Node Calibration.

119 lines of code changed in 9 files:

dong.w.xie 2009-08-25 14:29 Rev.: 2136

BEAUTi: cotinue Issue #100 and Issue #124.
1) implement isTipCalibration() by whether maximumTipHeight > 0;
2) if isTipCalibration(), then Tip Dates check box is checked;
3) if any calibration, then fix mean check box in clock panel is disabled.

9 lines of code changed in 4 files:

dong.w.xie 2009-08-25 13:51 Rev.: 2135

BEAUTi: cotinue Issue #100 and Issue #124.
Fix the bug of Op: there is alway upDown(rate, allInternalNodeHeight), but if FIX_MEAN (delta), then no rate in up part of updown OP.

44 lines of code changed in 2 files:

dong.w.xie 2009-08-25 13:12 Rev.: 2134

BEAUTi: cotinue Issue #100 and Issue #124. implement getMeanDistance in each PartitionData and getAveWeightedMeanDistance(List partitionData) in BeautiOptions.

53 lines of code changed in 4 files:

dong.w.xie 2009-08-25 11:24 Rev.: 2133

BEAUTi: solve #Issue 118: Beauti defaults - clock.rate in starbeast, which is changed to GAMMA, where shape = 0.1, scale = 10*x, offset = 0, init = x, and where x
is the fixed rate value.

51 lines of code changed in 6 files:

dong.w.xie 2009-08-25 10:57 Rev.: 2132

BEAUTi engineering work: big refactorying of *BEAST, and create STARBEASToptions.

233 lines of code changed in 14 files:

dong.w.xie 2009-08-25 10:25 Rev.: 2131

BEAUTi engineering work: add new abstract class for Partition????.

54 lines of code changed in 16 files:

rambaut 2009-08-24 18:50 Rev.: 2130

Fixed an issue with what LogCombiner did with attributes at the root of the tree (it was putting them after a ':' but with no branch length). Added an option to TimeSlicer to write frequencies of discrete traits.

420 lines of code changed in 2 files:

dong.w.xie 2009-08-24 18:25 Rev.: 2129

BEAUTi:
1) cotinue Issue #100;
2) start Issue #124.

294 lines of code changed in 16 files:

dong.w.xie 2009-08-24 10:57 Rev.: 2128

BEAUTi: add abstract method selectParameters and selectOperators in ModelOptions.

53 lines of code changed in 4 files:

dong.w.xie 2009-08-21 17:14 Rev.: 2127

BEAUTi: make initRootHeight and inti rate value to fit with multi-partition structure.
Not completed.

355 lines of code changed in 10 files:

dong.w.xie 2009-08-21 14:29 Rev.: 2126

BEAUTi: improve error message of guess trait.

4 lines of code changed in 1 file:

dong.w.xie 2009-08-21 11:52 Rev.: 2125

fix build of r2124.

105 lines of code changed in 1 file:

dong.w.xie 2009-08-21 11:50 Rev.: 2124

Fix the problem of BEAST using BEAUTi code, finding from r2123.

413 lines of code changed in 16 files:

dong.w.xie 2009-08-21 11:01 Rev.: 2123

BEAUTi big refactory: move all enum into dr.app.beauti.enumTypes to spearate logic from GUI.
Note: some BEAST classes are using BEAUTi enum.

779 lines of code changed in 72 files:

dong.w.xie 2009-08-21 10:13 Rev.: 2122

BEAUTi: solve Issue #114: Beauti Priors panel, rootHeight is disabled for starbeast.

5 lines of code changed in 1 file:

alexander.alekseyenko 2009-08-21 09:56 Rev.: 2121

making stochastic Dollo compliant with the new DataType stuff...

7 lines of code changed in 1 file:

rambaut 2009-08-20 21:06 Rev.: 2120

Just added a comment explaning the lower bound on the gamma shape parameter.

6 lines of code changed in 1 file:

dong.w.xie 2009-08-20 17:32 Rev.: 2119

BEAUTi engineering work: delete initGlobalParaAndOp from BeautiOptions.

14 lines of code changed in 3 files:

dong.w.xie 2009-08-20 17:22 Rev.: 2118

BEAUTi engineering work: rename TreePriorType.

148 lines of code changed in 15 files:

dong.w.xie 2009-08-20 17:06 Rev.: 2117

BEAUTi engineering work: create BeautiTemplate to reduce the lines of BeautiOptions.

599 lines of code changed in 5 files:

dong.w.xie 2009-08-20 16:30 Rev.: 2116

BEAUTi engineering work: create SubstitutionModelOptions to contain deltaMus.

143 lines of code changed in 4 files:

dong.w.xie 2009-08-20 16:16 Rev.: 2115

BEAUTi: complete r2114.

17 lines of code changed in 1 file:

dong.w.xie 2009-08-20 16:04 Rev.: 2114

BEAUTi: fix a PartitionTreePriorPanel bug.

5 lines of code changed in 1 file:

dong.w.xie 2009-08-20 15:57 Rev.: 2113

BEAUTi: dsicard shareSameTreePrior boolean variable in BeautiOptions, and replaced by isShareSameTreePrior().

18 lines of code changed in 7 files:

dong.w.xie 2009-08-20 15:13 Rev.: 2112

BEAUTi: solve Issue #125:
1) discard activedSameTreePrior and use treePrior in each PartitionTreeModel;
2) implement resetPanel() to make sure to reset BEAUTi when no data;
3) when linking or unlinking, each new partition is created, insteady of copying;
4) refactory code, and further tidying up is expected.

270 lines of code changed in 13 files:

msuchard 2009-08-20 12:42 Rev.: 2111

Hard lower bound on shape parameter of GammaSite*Model

2 lines of code changed in 2 files:

rambaut 2009-08-20 08:02 Rev.: 2110

New benchmark XML

371 lines of code changed in 1 file:

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.

6 lines of code changed in 6 files:

msuchard 2009-08-20 06:17 Rev.: 2108

My apologies for forgetting this file!

7 lines of code changed in 1 file:

msuchard 2009-08-20 06:14 Rev.: 2107

Can not force rescaling in TreeLikelihood; useful for speed comparisons and planning optimal rescaling schemes.

13 lines of code changed in 1 file:

msuchard 2009-08-20 04:44 Rev.: 2106

Can now specify scaling scheme at tree construction and in XML (none, alwaysRescale, dynamicRescaling)

53 lines of code changed in 5 files:

msuchard 2009-08-19 16:56 Rev.: 2105

No scaling, full rescaling and dynamic rescaling appear to work in BeagleTreeLikelihood

15 lines of code changed in 1 file:

dong.w.xie 2009-08-19 14:50 Rev.: 2104

BEAUTi: Issue #100, assign correct intial value of rate, and fix bug of rate not changing according user's input.

72 lines of code changed in 5 files:

msuchard 2009-08-19 06:31 Rev.: 2103

Typos

2 lines of code changed in 2 files:

msuchard 2009-08-19 06:28 Rev.: 2102

More connectedness checks in BSSSVS substitution models

57 lines of code changed in 3 files:

msuchard 2009-08-18 21:30 Rev.: 2101

Standardizing likelihood checks in BSSVS across BEAGLE and BEAST

19 lines of code changed in 3 files:

Sibon.Li@gmail.com 2009-08-18 17:57 Rev.: 2100

Fixed NormalDistributionTest

1 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-08-18 17:53 Rev.: 2099

Lognormal now uses the cdf calculation as used in R. Renamed the method to cdf()

5 lines of code changed in 4 files:

dong.w.xie 2009-08-18 16:36 Rev.: 2098

BEAUTi: continue Issue #100:
1) if FIX_MEAN_RATE, then do delta exchange for all clock rates, which has to be multi-clock rates situation;
2) if ESTIMATE, then has scale op for each non-fixed rate except fixed rate, updown op for each non-fixed rate and tree, updownAll op for all non-fixed rates and all trees;
3) need TODO prior parameters calculations in selectParameters and selectOperators;

52 lines of code changed in 7 files:

dong.w.xie 2009-08-18 14:08 Rev.: 2097

BEAUTi: refactory for Issue #114: Beauti Priors panel for starbeast.

127 lines of code changed in 10 files:

dong.w.xie 2009-08-18 12:11 Rev.: 2096

BEAUTi: solve Issue #120: Beauti silliness - warn about not saving when nothing was done.

1 lines of code changed in 1 file:

dong.w.xie 2009-08-18 12:04 Rev.: 2095

BEAUTi: Issue #100, fix a bug of upDownAllRates.

2 lines of code changed in 1 file:

dong.w.xie 2009-08-18 11:57 Rev.: 2094

BEAUTi:
1) solve Issue #115: when FixMean && isEstimatedRate() = false, write nothing on up part of upDownOp;
2) solve Issue #119;
3) continue #100: add weights for detal exchange operator of Clock Relative Rates.

47 lines of code changed in 5 files:

jheled 2009-08-18 11:18 Rev.: 2093

Offer stem as default file name

3 lines of code changed in 1 file:

msuchard 2009-08-18 06:52 Rev.: 2092

Connectedness checks in BSSSVS substitution models

164 lines of code changed in 4 files:

dong.w.xie 2009-08-17 17:33 Rev.: 2091

BEAUTi: Issue #100, continue delta exchange on allClockRates, TODO: the weight length.

174 lines of code changed in 6 files:

msuchard 2009-08-17 17:12 Rev.: 2090

Tweak to BeagleTreeLikelihood

26 lines of code changed in 2 files:

jheled 2009-08-17 16:57 Rev.: 2089

MIndless cleanup

8 lines of code changed in 3 files:

jheled 2009-08-17 16:56 Rev.: 2088

Give more info upon error

2 lines of code changed in 1 file:

dong.w.xie 2009-08-17 16:27 Rev.: 2087

BEAUTi: fix the bug of r2086.

1 lines of code changed in 1 file:

dong.w.xie 2009-08-17 13:07 Rev.: 2086

BEAUTi: add upDownAllRatesHeights operator and available only for *BEAST and EBSP.

28 lines of code changed in 5 files:

dong.w.xie 2009-08-17 12:55 Rev.: 2085

BEAUTi: binary model.

3 lines of code changed in 1 file:

dong.w.xie 2009-08-17 12:06 Rev.: 2084

BEAUTi: Issue #100, complete allClockRate delta operator and its generator.
Need test.

50 lines of code changed in 3 files:

msuchard 2009-08-17 09:02 Rev.: 2083

Resolving incompatibility issues between BSSVS models and dynamic rescaling in BEAGLE; I recommend setting alwaysRescale="true" in BeagleTreeLikelihoods that use BSSVS

38 lines of code changed in 4 files:

msuchard 2009-08-16 15:16 Rev.: 2082

Overloaded several standard BEAST XML labels, so BEAGLE does not mask standard classes completely. A better solution is to have BeastParser do this automatically when it replaces parsers.

24 lines of code changed in 4 files:

msuchard 2009-08-16 14:35 Rev.: 2081

Just place holders for ancestral reconstruction on a BEAGLE tree. Unfortunately, API currently does support not getting transition probability matrices, so this is not currently possible. I also introduced a bug into BeagleTreeLikelihood such that alwaysRescale must remain true or likelihoods get messed up. Must fix this.

376 lines of code changed in 4 files:

msuchard 2009-08-16 11:56 Rev.: 2080

Implemented BSSVS reversible model in BEAGLE. I see ~7-fold speed-up for a 40-state phylogeography problem on my midrange iMac-GT120.

153 lines of code changed in 3 files:

msuchard 2009-08-16 10:50 Rev.: 2079

Added a wrapper around a DistributionLikelihood such that its likelihood is only recomputed after a handleVariableChangedEvent; this results in substantial speed-up for models with priors on parameter with high dimension (such as 100s or 1000s)

128 lines of code changed in 4 files:

msuchard 2009-08-16 05:53 Rev.: 2078

Fixed BeagleTreeLikelihood store/restore of scalingBufferIndices and the use of rate parameter in beagle.GammaSiteRateModel

22 lines of code changed in 2 files:

msuchard 2009-08-16 05:03 Rev.: 2077

Added option to always rescale in BeagleTreeLikelihood for debugging purposes.

11 lines of code changed in 1 file:

msuchard 2009-08-15 13:46 Rev.: 2076

BEAGLE GammaSiteModel now accepts a mutationRate for compatibility with some BEAST XML.

10 lines of code changed in 3 files:

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

Updated 'beagle.jar'.

0 lines of code changed in 1 file:

rambaut 2009-08-15 12:15 Rev.: 2074

Some extra JNI functions for a BEAST/BEAGLE performance testing platform.

1 lines of code changed in 1 file:

msuchard 2009-08-15 11:07 Rev.: 2073

Implemented a BEAGLEize GeneralSubstitutionModel and parser

110 lines of code changed in 3 files:

dong.w.xie 2009-08-14 17:55 Rev.: 2072

BEAUTi: Issue #100,
1) complete GUI, and a further improvement will be continued;
2) need to add allClockRate delta operator, and implement it in BeastGenerator.

391 lines of code changed in 12 files:

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.

0 lines of code changed in 1 file:

dong.w.xie 2009-08-13 14:03 Rev.: 2070

Correct Linux/Unix release bin path.

5 lines of code changed in 1 file:

dong.w.xie 2009-08-13 13:27 Rev.: 2069

BEAUTi: add updown operator for all rates using EBSP.

15 lines of code changed in 2 files:

rambaut 2009-08-13 12:40 Rev.: 2068

Some performance improvements for Java implementations of BEAGLE (as it that matters). Is pretty much identical speed as BEAST's Java implementations.

299 lines of code changed in 2 files:

dong.w.xie 2009-08-13 12:20 Rev.: 2067

1) Improve Windows release and add Linux/Unix release;
2) Add extra_lib in the release folder.

84 lines of code changed in 7 files:

msuchard 2009-08-13 10:17 Rev.: 2066

Additional debug info for BeagleTreeLikelihood

37 lines of code changed in 2 files:

rambaut 2009-08-13 09:45 Rev.: 2065

Cleaned up DiscretizedBranchRates to minimize unnecessary firing of events.

14 lines of code changed in 2 files:

msuchard 2009-08-13 09:31 Rev.: 2064

Per r1837, Marc Suchard has tested this and found that DiscretizedBranchRates generates recalculations of the entire tree when only a partial update is necessary. Andrew fixed it with a single line code change. Truly impressive.

1 lines of code changed in 1 file:

rambaut 2009-08-13 02:28 Rev.: 2063

Added ability of TreeLikelihood and BeagleTreeLikelihood to count the total number of node evaluations. This is hidden by a static constant COUNT_TOTAL_OPERATIONS=false when not required. benchmark.xml now reports this number at the end.

29 lines of code changed in 5 files:

rambaut 2009-08-12 23:45 Rev.: 2062

Added a 'show' button to show the alignments. Will also add a panel to the frame that gives information (such as number of patterns etc).

58 lines of code changed in 1 file:

rambaut 2009-08-12 22:41 Rev.: 2061

Added some existing code for displaying alignments.

1175 lines of code changed in 19 files:

dong.w.xie 2009-08-12 17:20 Rev.: 2060

Double.MAX_EXPONENT is Java 1.6 feature

1 lines of code changed in 1 file:

dong.w.xie 2009-08-12 16:57 Rev.: 2059

Continue Issue #98, need to develop some mouse events late.

81 lines of code changed in 4 files:

Sibon.Li@gmail.com 2009-08-12 14:42 Rev.: 2058

Code tidying

6 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-08-12 14:39 Rev.: 2057

Updated Inverse Gaussian distribution with a much more flexible, accurate and faster algorithm for the quantile function. Improved its unit test.

262 lines of code changed in 2 files:

dong.w.xie 2009-08-12 12:55 Rev.: 2056

Continue Issue #98, but JScrollPanel does not work with Dialog.

97 lines of code changed in 2 files:

msuchard 2009-08-12 08:34 Rev.: 2055

Tweaks to BeagleTreeLikelihood

7 lines of code changed in 1 file:

dong.w.xie 2009-08-11 16:21 Rev.: 2054

The draft of Issue #98: View Alignment Given A Partition Data.

141 lines of code changed in 2 files:

dong.w.xie 2009-08-11 11:17 Rev.: 2053

Add OSType in dr.app.util to detect OS, and replace all old isMacOS into new one.

128 lines of code changed in 12 files:

dong.w.xie 2009-08-11 10:16 Rev.: 2052

Remove Launch4j from the releases folder in the repository, to make it work, either install Launch4j under {BEAST workspace}/${release}, or install it in the default directoy and change the location of launch4j.dir.

2 lines of code changed in 32 files:

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

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

0 lines of code changed in 1 file:

rambaut 2009-08-10 20:37 Rev.: 2050

Added the ability to BeagleTreeLikelihood to pick up a System Property ("beagle_resource_order") which is a list of resource numbers (as reported by beagle.BeagleInfo.main()) to apply each BeagleTreeLikelihood in the order they are created.

42 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-08-10 18:03 Rev.: 2049

Added an alternative calculate of Normal distribution cdf. Method is faster and more accurate on tails. Also included unit test for NormalDistribution

352 lines of code changed in 2 files:

dong.w.xie 2009-08-10 17:08 Rev.: 2048

BEAUTi: Resolved issue #103: add addTxt check box in MCMC panel.

21 lines of code changed in 1 file:

dong.w.xie 2009-08-10 16:49 Rev.: 2047

BEAUTi: Resolved issue #99: spearate models panel into Site Models and Clock Models two panels.

1267 lines of code changed in 11 files:

dong.w.xie 2009-08-10 12:57 Rev.: 2046

BEAUTi: fix a critical bug in prefix, which make incoreect XML when only unlink Clock model or Tree Model.

2 lines of code changed in 2 files:

dong.w.xie 2009-08-10 11:56 Rev.: 2045

Complete ANT windows release.

1731 lines of code changed in 50 files:

rambaut 2009-08-07 20:50 Rev.: 2044

Added icons, remove old build files

0 lines of code changed in 13 files:

philippe.lemey@gmail.com 2009-08-07 17:55 Rev.: 2043

Tracer tweaks

231 lines of code changed in 1 file:

dong.w.xie 2009-08-07 16:38 Rev.: 2042

rename example/beauti1.6 into 1.5

0 lines of code changed in 27 files:

dong.w.xie 2009-08-07 16:35 Rev.: 2041

Ant build to make Windows release using Launch4j. (need to add TreeAnnotator and LogCombiner)

86 lines of code changed in 2 files:

dong.w.xie 2009-08-07 15:45 Rev.: 2040

BeastMain: replace thread.stop() with thread = null.

2 lines of code changed in 1 file:

rambaut 2009-08-06 23:44

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

9 lines of code changed in 2 files:

dong.w.xie 2009-08-06 16:57 Rev.: 2037

BEAUTi enhancement: add scroll panel in BeautiFrame to deal with low resolution screen.

6 lines of code changed in 1 file:

msuchard 2009-08-06 14:23 Rev.: 2036

BEAGLE also returns -Infinity for poorly scaled likelihoods. Sorry for the one-line change commit.

1 lines of code changed in 1 file:

dong.w.xie 2009-08-06 14:12 Rev.: 2035

BEAUTi: fix a critical bug of <patterns> when having multi data parition.

16 lines of code changed in 1 file:

jheled 2009-08-06 14:08 Rev.: 2034

comment unused code

2 lines of code changed in 1 file:

msuchard 2009-08-06 13:17 Rev.: 2033

BeagleTreeLikelihood is apparently working again for dynamic rescaling

46 lines of code changed in 1 file:

dong.w.xie 2009-08-06 12:24 Rev.: 2032

tidy up

8 lines of code changed in 2 files:

rambaut 2009-08-06 12:08 Rev.: 2031

Implemented the return of InstanceDetails. Also fixed up the main() in BeagleFactory to print resource details.

1 lines of code changed in 1 file:

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

Changed beagle.jar

0 lines of code changed in 1 file:

jheled 2009-08-06 08:22 Rev.: 2029

intellij auto

22 lines of code changed in 10 files:

jheled 2009-08-06 08:22 Rev.: 2028

Allow init in constant population

12 lines of code changed in 1 file:

jheled 2009-08-06 08:21 Rev.: 2027

remove unused

1 lines of code changed in 1 file:

msuchard 2009-08-06 03:05 Rev.: 2026

No-rescaling computation works again on CPU and GPU

8 lines of code changed in 1 file:

rambaut 2009-08-06 01:56

Fixed store/restore.

5 lines of code changed in 2 files:

dong.w.xie 2009-08-05 14:03 Rev.: 2023

BEAUTi: rename Model panel into Subst & Clock Models.

1 lines of code changed in 1 file:

alexei.drummond 2009-08-05 13:05 Rev.: 2022

Fixes Constant-Exponential reconstruction in Tracer which was out of sync with current BEAST parameterization.

39 lines of code changed in 2 files:

dong.w.xie 2009-08-05 11:50 Rev.: 2021

Resolved issue #109: BEAUti: Generating XML - no file overwriting warning?

23 lines of code changed in 1 file:

msuchard 2009-08-05 08:29 Rev.: 2020

Changed logic in BeagleTreeLikelihood to either recompute or reuse (not both) scaleFactors when necessary.

16 lines of code changed in 1 file:

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:

rambaut 2009-08-05 02:51 Rev.: 2018

BEAST/BEAGLE now working with updated API (both Java impl and CPU).

53 lines of code changed in 1 file:

dong.w.xie 2009-08-04 15:23 Rev.: 2017

Correct spelling.

2 lines of code changed in 1 file:

rambaut 2009-08-04 12:39 Rev.: 2014

A few final tweaks: added a few names to the credits. Fixed issue 107 (credits appearing twice) and 101 (fixed rate box small on Mac).

23 lines of code changed in 6 files:

dong.w.xie 2009-08-04 11:23 Rev.: 2013

add tree annotator in build

53 lines of code changed in 1 file:

rambaut 2009-08-04 10:59 Rev.: 2012

Resolved issue #108: Setting the filter to the save dialog box every time generate button was called caused the file format to be added multiple times. Have add the filter once, when the dialog is created.

9 lines of code changed in 1 file:

dong.w.xie 2009-08-04 10:16 Rev.: 2011

More new BEAUTi example XML for single locus.

0 lines of code changed in 9 files:

rambaut 2009-08-04 04:03 Rev.: 2010

The build script now creates a beast-beagle.jar that contains the beagle specific stuff. This is only loaded if the -beagle flag is given and then requires the beast-beagle.jar to be on the class path. We now have our first plugin! This means we can distribute a beast-beagle.jar at a later date and it will work with the current BEAST. This is not quite perfect yet as the parser list has to be packaged in the beast.jar so we can't have arbitrary plugins. We need a way of searching jar files for parser lists. We can then have a /plugins folder into which we could drop jar files.

13 lines of code changed in 1 file:

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.

4757 lines of code changed in 68 files:

rambaut 2009-08-04 03:37 Rev.: 2008

Small fix so that only the CompoundLikelihood called 'likelihood' uses the System property to get the number of threads.

2 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-08-04 01:08 Rev.: 2007

Tracer tweaks

0 lines of code changed in 1 file:

rambaut 2009-08-04 00:16 Rev.: 2006

Fixed issue 105: http://code.google.com/p/beast-mcmc/issues/detail?id=105
and addressed 106 (made the dialog box say it is a 'Warning') rather than an error.

21 lines of code changed in 3 files:

rambaut 2009-08-03 22:37 Rev.: 2005

Fixed issue 104: http://code.google.com/p/beast-mcmc/issues/detail?id=104

1 lines of code changed in 1 file:

rambaut 2009-08-03 21:24 Rev.: 2004

Added a command-line option to enable multithreading in BEAST. The option is '-threads n', where n is the number of threads. This option actually sets a System Property called 'thread_count' (so this can also be set using -Dthread_count=n on the JVM). The thread_count property is picked up by CompoundLikelihood and overrides its XML attribute ('threads="n"') to create a thread pool in which to distribute partitions. If the alignment is not partitioned then no multithreading will be done.

22 lines of code changed in 2 files:

dong.w.xie 2009-08-03 16:59 Rev.: 2003

v1.5 starts from r2001.

1 lines of code changed in 1 file:

dong.w.xie 2009-08-03 15:35 Rev.: 2001

BEAUTi: *BEAST correct the bug, where the initial value for pop mean is the same as what used to be the value for the population size.

1873 lines of code changed in 10 files:

dong.w.xie 2009-08-03 14:45 Rev.: 2000

BEAUTi: fix the bug of getting Exception to update initial vaule for Jeffreys (1/x) prior in Prior panel.

1 lines of code changed in 1 file:

dong.w.xie 2009-08-03 11:08 Rev.: 1999

BEAUTi: change species tree prior from exponential + gamma2 into gama2 + gamma4.

28 lines of code changed in 1 file:

dong.w.xie 2009-08-03 11:06 Rev.: 1998

BEAUTi:
1) remove DisplayTree panel from Tree panel;
2) add making substTreeFileNameField disenabled when the check box is not selected, but it seems not working.

14 lines of code changed in 2 files:

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:

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:

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 2 files:

philippe.lemey@gmail.com 2009-08-02 05:13 Rev.: 1994

Tracer tweaks

4 lines of code changed in 1 file:

msuchard 2009-08-02 04:06 Rev.: 1993

Contributor list

2 lines of code changed in 1 file:

rambaut 2009-08-01 23:49 Rev.: 1992

Updated the credits for the upcoming release of BEAST. Note the list of developers in 'BeastVersion.java' is not complete. Please review and revise.

94 lines of code changed in 6 files:

akaruiws 2009-08-01 19:57 Rev.: 1991

removed enum.

1 lines of code changed in 1 file:

akaruiws 2009-08-01 19:51 Rev.: 1990

constructor fixed.

1 lines of code changed in 1 file:

akaruiws 2009-08-01 19:44 Rev.: 1989

getParserName fixed

1 lines of code changed in 1 file:

akaruiws 2009-08-01 19:35 Rev.: 1988

Implements the Asymmetric Quadratic Model for microsatellites

1 lines of code changed in 1 file:

akaruiws 2009-08-01 19:33 Rev.: 1987

Added enum MicrosatelliteModelType.

8 lines of code changed in 1 file:

akaruiws 2009-08-01 19:22 Rev.: 1986

Parser for Asymmetric Quadratic model.

0 lines of code changed in 1 file:

akaruiws 2009-08-01 19:17

JUnit test for Asymmetric quadratic model.

333 lines of code changed in 2 files:

akaruiws 2009-08-01 19:15 Rev.: 1983

Asymmetric quadratic model for microsatellites

170 lines of code changed in 1 file:

akaruiws 2009-08-01 19:13 Rev.: 1982

An abstract class for one phase microsatellite models

51 lines of code changed in 1 file:

akaruiws 2009-08-01 19:11 Rev.: 1981

An abstract class for microsatellite models

120 lines of code changed in 1 file:

akaruiws 2009-08-01 18:56 Rev.: 1980

Added a separate method which assigns the infinitesimal rates from a vector to a matrix during the setting up of the matrix.

22 lines of code changed in 1 file:

akaruiws 2009-08-01 18:27 Rev.: 1979

Add SMM distance option

3 lines of code changed in 1 file:

akaruiws 2009-08-01 18:22 Rev.: 1978

Calculates SMM distance for microsatellite alleles

35 lines of code changed in 1 file:

akaruiws 2009-08-01 18:17 Rev.: 1977

Add SMM distance option

5 lines of code changed in 1 file:

akaruiws 2009-08-01 18:16 Rev.: 1976

Parser that returns a Patterns object containing the pattern of one microsatellite locus

99 lines of code changed in 1 file:

akaruiws 2009-08-01 17:57 Rev.: 1975

Parser for microsatellite data type

51 lines of code changed in 1 file:

akaruiws 2009-08-01 17:52 Rev.: 1974

Microsatellite data type

245 lines of code changed in 1 file:

msuchard 2009-08-01 06:12 Rev.: 1973

Linked TraitLikelihood to TraitBranchRate to fix store/restore issues.

19 lines of code changed in 1 file:

rambaut 2009-08-01 04:03 Rev.: 1972

Experiments with clocks correlated with traits

97 lines of code changed in 3 files:

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

More BEAST/BEAGLE fixes

3 lines of code changed in 2 files:

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