-
dong.w.xie
2010-08-31 15:29
#109
Rev.: 3476
-
45 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+15 -4),
TreeModelGenerator.java (+23 -23)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+7 -27)
-
beth.shapiro
2010-08-31 10:48
#108
Rev.: 3475
-
1 lines of code changed in 1 file:
-
rambaut
2010-08-31 10:42
#107
Rev.: 3474
-
8 lines of code changed in 2 files:
-
src/dr/evoxml:
AttributePatternsParser.java (new)
-
mandevsgill
2010-08-31 08:06
#106
Rev.: 3473
-
1 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (+1 -1),
GMRFSkyrideLikelihood.java (-1)
-
dong.w.xie
2010-08-30 11:04
#105
Rev.: 3472
-
154 lines of code changed in 8 files:
-
release/Windows:
BEAST_launch4j.xml (+1 -1),
BEAUTi_launch4j.xml (new),
LogAnalyser_launch4j.xml (+1 -1),
LogCombiner_launch4j.xml (+1 -1),
TreeAnnotator_launch4j.xml (+1 -1)
-
release/common:
README.txt (+39 -17),
VERSION HISTORY.txt (+110 -16)
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
-
rambaut
2010-08-29 12:06
#104
Rev.: 3471
-
60 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+60 -41)
-
rambaut
2010-08-29 09:17
#103
Rev.: 3470
-
2 lines of code changed in 1 file:
-
src/dr/inference/model:
CompoundLikelihood.java (+2)
-
rambaut
2010-08-29 04:29
#102
Rev.: 3469
-
2 lines of code changed in 1 file:
-
examples/release/Benchmarks:
benchmark1.xml (+2 -2)
-
rambaut
2010-08-29 01:47
#101
Rev.: 3468
-
11535 lines of code changed in 6 files:
-
examples/release:
benchmark.xml (del),
benchmark2.xml (del),
new_benchmark.xml (del)
-
examples/release/Benchmarks:
benchmark1.xml (+10296),
benchmark2.xml (+877),
old_benchmark.xml (new 362)
-
dong.w.xie
2010-08-27 16:15
#100
Rev.: 3467
-
0 lines of code changed in 2 files:
-
examples/unrelease:
Msat (del),
Phylogeography (del)
-
dong.w.xie
2010-08-27 16:07
#99
Rev.: 3466
-
0 lines of code changed in 1 file:
-
src/dr/app/beast:
development_parsers.properties (-1)
-
dong.w.xie
2010-08-27 16:03
#98
Rev.: 3465
-
5966 lines of code changed in 51 files:
-
examples/incorrect:
logisticDoubling+uncorrelatedLn.xml (new 347),
testCTMCMap.xml (new 312),
testCompleteHistorySimulator.xml (new 200),
testConjugateTraitLikelihood.xml (+124),
testDiscreteMapDiffusion.xml (new 112),
testIntegratedTraitLikelihood.xml (new 115),
testLewisMk.xml (new 31),
testLinearRegression.xml (new 126),
testMLCalculator.xml (new 6),
testMSSD.xml (new 203),
testMultivariateComparativeMethod.xml (new 310),
testNewLikelihood.xml (new 477),
testOTFPCLikelihood.xml (new 477),
testRobustCounting.xml (new 452),
testTransmission.xml (new 742)
-
examples/release:
testAlignmentStatistics.xml (new 23),
testAutocorrelatedRelaxedClock.xml (new 460),
testMarkovJumps.xml (new 150),
testMissingIntegratedTraitLikelihood.xml (new 115),
testPopTreeModel.xml (new 39),
testRestrictedAncestralReconstruction.xml (new 255),
testSimplePathSampling.xml (new 251),
testTreePathSampling.xml (+262),
testUniformizedMarkovJumps.xml (new 152),
testYuleOneSite.xml (new 225)
-
examples/release/starBEAST:
gopher_mapping.txt (del)
-
examples/unrelease:
testAlignmentStatistics.xml (del),
testAutocorrelatedRelaxedClock.xml (del),
testBinaryDollo.xml (del),
testCTMCMap.xml (del),
testCompleteHistorySimulator.xml (del),
testConjugateTraitLikelihood.xml (del),
testDiscreteMapDiffusion.xml (del),
testIntegratedTraitLikelihood.xml (del),
testLewisMk.xml (del),
testLinearRegression.xml (del),
testMLCalculator.xml (del),
testMSSD.xml (del),
testMarkovJumps.xml (del),
testMissingIntegratedTraitLikelihood.xml (del),
testMultivariateComparativeMethod.xml (del),
testNewLikelihood.xml (del),
testOTFPCLikelihood.xml (del),
testPopTreeModel.xml (del),
testRestrictedAncestralReconstruction.xml (del),
testRobustCounting.xml (del),
testSimplePathSampling.xml (del),
testTransmission.xml (del),
testTreePathSampling.xml (del),
testUniformizedMarkovJumps.xml (del),
testYuleOneSite.xml (del)
-
dong.w.xie
2010-08-27 15:49
#97
Rev.: 3464
-
9 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
RandomLocalClockModel.java (+8 -3)
-
src/dr/evomodel/tree:
TreeModel.java (+1 -1)
-
dong.w.xie
2010-08-27 13:28
#96
Rev.: 3463
-
3370 lines of code changed in 56 files:
-
examples/incorrect:
Mdor phygeo ages1.xml (new 1475),
demoCodonHistorySimulator.xml (new 88),
testCovarionHKY.xml (new 339),
testGeneralSubstitutionModel.xml (new 183),
testIA.xml (new 120),
testPathSampling.xml (new),
testRandomLocalClock.xml (new)
-
examples/release:
arg-ecoli.xml (new),
benchmark2.xml (new),
testBSP.xml (del),
testCovarionHKY.xml (del),
testGeneralSubstitutionModel.xml (del),
testIA.xml (del),
testLocalClock.xml (del),
testPathSampling.xml (del),
testRandomLocalClock.xml (del),
testStrictClock.xml (del),
testUncorrelatedRelaxedClock.xml (del)
-
examples/release/clockModels:
testLocalClock.xml (new 413),
testStrictClock.xml (new 334),
testUncorrelatedRelaxedClock.xml (new 418)
-
examples/unrelease:
Mdor phygeo ages1.xml (del),
arg-ecoli.xml (del),
arg-lepto.xml (del),
arg-rokas.xml (del),
benchmark.xml (del),
benchmark2.xml (del),
demoCodonHistorySimulator.xml (del),
new_benchmark.xml (del),
testAncestralReconstruction.xml (del),
testAscertainment.xml (del),
testBSP.xml (del),
testCodonLikelihood.xml (del),
testComparativeMethod.xml (del),
testCovarionHKY.xml (del),
testGeneralSubstitutionModel.xml (del),
testIA.xml (del),
testIBDweights.xml (del),
testLikelihood.xml (del),
testLocalClock.xml (del),
testLognormalPrior.xml (del),
testMC3.xml (del),
testMCMC.xml (del),
testML.xml (del),
testMVOU.xml (del),
testMixedModel.xml (del),
testMultiThreading.xml (del),
testNormalModelGibbs.xml (del),
testPMD.xml (del),
testPathSampling.xml (del),
testPosteriorIBD.xml (del),
testRandomLocalClock.xml (del),
testSequenceSimulator.xml (del),
testStrictClock.xml (del),
testTransmissionStatistic.xml (del),
testUncorrelatedRelaxedClock.xml (del)
-
dong.w.xie
2010-08-27 11:20
#95
Rev.: 3462
-
0 lines of code changed in 2 files:
-
examples/release:
treeOpsTest (new)
-
examples/unrelease:
calibrations (del)
-
dong.w.xie
2010-08-27 11:12
#94
-
422 lines of code changed in 6 files:
-
examples/incorrect/treePriors:
testBirthDeath.xml (new 221),
testBirthDeathPrior.xml (new 201)
-
examples/release:
Virus Practical (del)
-
examples/release/treePriors:
testGMRFCoalescent.xml (new),
testYuleCase3.xml (new)
-
examples/unrelease:
treePriors (del)
-
dong.w.xie
2010-08-26 16:40
#93
-
3 lines of code changed in 2 files:
-
build.xml (+3 -3)
-
examples/unrelease:
Data (del)
-
dong.w.xie
2010-08-26 16:31
#92
-
0 lines of code changed in 164 files:
-
examples/Data:
Dengue4.env.aminoacid.nex (del),
Dengue4.env.nex (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del)
-
release/common/examples:
Darwins-finches.nex (del),
Dengue4.env.nex (del),
Gopher Data (del),
Mdor phygeo ages1.xml (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del),
arg-ecoli.xml (del),
arg-lepto.xml (del),
arg-rokas.xml (del),
benchmark.xml (del),
new_benchmark.xml (del),
testAncestralReconstruction.xml (del),
testAscertainment.xml (del),
testAutocorrelatedRelaxedClock.xml (del),
testBSP.xml (del),
testBinaryDollo.xml (del),
testCTMCMap.xml (del),
testCodonLikelihood.xml (del),
testComparativeMethod.xml (del),
testCovarionHKY.xml (del),
testDiscreteMapDiffusion.xml (del),
testGeneralSubstitutionModel.xml (del),
testIA.xml (del),
testIBDweights.xml (del),
testLikelihood.xml (del),
testLinearRegression.xml (del),
testLocalClock.xml (del),
testLognormalPrior.xml (del),
testMC3.xml (del),
testMCMC.xml (del),
testML.xml (del),
testMLCalculator.xml (del),
testMSSD.xml (del),
testMVOU.xml (del),
testMixedModel.xml (del),
testMultiThreading.xml (del),
testMultivariateComparativeMethod.xml (del),
testNewLikelihood.xml (del),
testNormalModelGibbs.xml (del),
testOTFPCLikelihood.xml (del),
testPMD.xml (del),
testPathSampling.xml (del),
testPosteriorIBD.xml (del),
testRandomLocalClock.xml (del),
testRelaxedClock.xml (del),
testSequenceSimulator.xml (del),
testStrictClock.xml (del),
testTransmission.xml (del),
testTransmissionStatistic.xml (del),
testUncorrelatedRelaxedClock.xml (del)
-
release/common/examples/Data:
Darwins-finches.nex (del),
Dengue4.env.nex (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del),
primates.nex (del)
-
release/common/examples/Data/Gopher Data:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del),
gopher_mapping.txt (del)
-
release/common/examples/Phylogeography:
H5N1_HA_discrete.xml (del)
-
release/common/examples/Virus Practical/FPV:
FPV.nex (del),
FPV.xml (del),
FPV1.xml (del)
-
release/common/examples/Virus Practical/Flu:
Flu.nex (del),
Flu.xml (del)
-
release/common/examples/Virus Practical/RSVA:
RSVA.nex (del),
RSVA.xml (del),
RSVA1.xml (del)
-
release/common/examples/beauti1.5:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del),
Darwins-finches.nex (del)
-
release/common/examples/beauti1.5/Gopher Data:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del)
-
release/common/examples/beauti1.5/Virus Practical/FPV:
FPV.nex (del),
FPV.xml (del),
FPV1.xml (del)
-
release/common/examples/beauti1.5/Virus Practical/Flu:
Flu.nex (del),
Flu.xml (del)
-
release/common/examples/beauti1.5/Virus Practical/RSVA:
RSVA.nex (del),
RSVA.xml (del),
RSVA1.xml (del)
-
release/common/examples/beauti1.5/starBEAST:
g10.xml (del),
g11.xml (del),
x10.xml (del),
x11.xml (del)
-
release/common/examples/beauti1.5/treePrior+clockModel:
x1.xml (del),
x2.xml (del),
x3.xml (del),
x4.xml (del),
x5.xml (del),
x6.xml (del),
x7.xml (del),
x8.xml (del),
x9.xml (del)
-
release/common/examples/calibrations:
constrainedTaxaTest1.xml (del),
constrainedTaxaTest2.xml (del),
constrainedTaxaTest3.xml (del),
constrainedTaxaTest4.xml (del),
constrainedTaxaTest5.xml (del),
constrainedTaxaTest6.xml (del),
constrainedTaxaTest7.xml (del),
constrainedTaxaTest8.xml (del),
constrainedTaxaTest9.xml (del)
-
release/common/examples/starBEAST:
YuleMultiLoci.xml (del),
YuleSingleLocus.xml (del),
birthDeathMultiLoci.xml (del),
brithDeathSingleLocus.xml (del),
g10.xml (del),
g11.xml (del),
gopher_mapping.txt (del),
x10.xml (del),
x11.xml (del)
-
release/common/examples/treePrior+clockModel:
BayesianSkyline+unccorelatedExp.xml (del),
GMRFBayesianSkyride+strict .xml (del),
Yule+unccorelatedExp.xml (del),
birthDeath+unccorelatedLn.xml (del),
constant+uncorrelatedExp.xml (del),
expansionDoubling+strict.xml.xml (del),
exponentialDoubling+strict.xml (del),
extendedBayesianSkyline+uncorrelatedLn.xml (del),
logisticDoubling+uncorrelatedLn.xml (del),
x1.xml (del),
x2.xml (del),
x3.xml (del),
x4.xml (del),
x5.xml (del),
x6.xml (del),
x7.xml (del),
x8.xml (del),
x9.xml (del)
-
release/common/examples/treePriors:
testBSP.xml (del),
testBirthDeath.xml (del),
testBirthDeathAsYule.xml (del),
testBirthDeathPrior.xml (del),
testCataclysmCoalescent.xml (del),
testCoalescent.xml (del),
testGMRFCoalescent.xml (del),
testLinearBSP.xml (del),
testPiecewiseExponential.xml (del),
testYule.xml (del),
testYuleModel.xml (del),
testYuleModel_10taxa.xml (del),
testYulePrior.xml (del)
-
dong.w.xie
2010-08-26 16:18
#91
-
0 lines of code changed in 11 files:
-
release/common/examples/Data/Gopher Data:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del)
-
release/common/examples/starBEAST:
YuleMultiLoci.xml (del),
YuleSingleLocus.xml (del),
birthDeathMultiLoci.xml (del),
brithDeathSingleLocus.xml (del)
-
dong.w.xie
2010-08-26 16:11
#90
-
17429 lines of code changed in 220 files:
-
examples:
Mdor phygeo ages1.xml (del),
Msat (del),
arg-ecoli.xml (del),
arg-lepto.xml (del),
arg-rokas.xml (del),
benchmark.xml (del),
benchmark2.xml (del),
demoCodonHistorySimulator.xml (del),
new_benchmark.xml (del),
testAlignmentStatistics.xml (del),
testAncestralReconstruction.xml (del),
testAscertainment.xml (del),
testAutocorrelatedRelaxedClock.xml (del),
testBSP.xml (del),
testBinaryDollo.xml (del),
testCTMCMap.xml (del),
testCodonLikelihood.xml (del),
testComparativeMethod.xml (del),
testCompleteHistorySimulator.xml (del),
testConjugateTraitLikelihood.xml (del),
testCovarionHKY.xml (del),
testDiscreteMapDiffusion.xml (del),
testGeneralSubstitutionModel.xml (del),
testIA.xml (del),
testIBDweights.xml (del),
testIntegratedTraitLikelihood.xml (del),
testLewisMk.xml (del),
testLikelihood.xml (del),
testLinearRegression.xml (del),
testLocalClock.xml (del),
testLognormalPrior.xml (del),
testMC3.xml (del),
testMCMC.xml (del),
testML.xml (del),
testMLCalculator.xml (del),
testMSSD.xml (del),
testMVOU.xml (del),
testMarkovJumps.xml (del),
testMissingIntegratedTraitLikelihood.xml (del),
testMixedModel.xml (del),
testMultiThreading.xml (del),
testMultivariateComparativeMethod.xml (del),
testNewLikelihood.xml (del),
testNormalModelGibbs.xml (del),
testOTFPCLikelihood.xml (del),
testPMD.xml (del),
testPathSampling.xml (del),
testPopTreeModel.xml (del),
testPosteriorIBD.xml (del),
testRandomLocalClock.xml (del),
testRestrictedAncestralReconstruction.xml (del),
testRobustCounting.xml (del),
testSequenceSimulator.xml (del),
testSimplePathSampling.xml (del),
testStrictClock.xml (del),
testTransmission.xml (del),
testTransmissionStatistic.xml (del),
testTreePathSampling.xml (del),
testUncorrelatedRelaxedClock.xml (del),
testUniformizedMarkovJumps.xml (del),
testYuleOneSite.xml (del)
-
examples/Data:
Dengue4.env.aminoacid.nex (del),
Dengue4.env.nex (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del)
-
examples/Phylogeography:
H5N1_HA_discrete.xml (del),
H5N1_HA_discrete_traits.xml (del)
-
examples/Phylogeography/continuous:
RacRABV_LogNRRW.xml (del),
RacRABV_cauchyRRW.xml (del),
RacRABV_gammaRRW.xml (del),
RacRABV_homogeneous.xml (del)
-
examples/calibrations:
constrainedTaxaTest1.xml (del),
constrainedTaxaTest2.xml (del),
constrainedTaxaTest3.xml (del),
constrainedTaxaTest4.xml (del),
constrainedTaxaTest5.xml (del),
constrainedTaxaTest6.xml (del),
constrainedTaxaTest7.xml (del),
constrainedTaxaTest8.xml (del),
constrainedTaxaTest9.xml (del)
-
examples/treeOpsTest:
treeUniformTest1.xml (del),
treeUniformTest2.xml (del),
treeUniformTest3.xml (del)
-
examples/treePriors:
testBSP.xml (del),
testBirthDeath.xml (del),
testBirthDeathAsYule.xml (del),
testBirthDeathPrior.xml (del),
testCataclysmCoalescent.xml (del),
testCoalescent.xml (del),
testGMRFCoalescent.xml (del),
testLinearBSP.xml (del),
testPiecewiseExponential.xml (del),
testYule.xml (del),
testYuleCase3.xml (del),
testYuleModel.xml (del),
testYuleModel_10taxa.xml (del),
testYulePrior.xml (del)
-
examples/unrelease:
Data (new),
Mdor phygeo ages1.xml (new 1475),
Msat (new),
Phylogeography (new),
arg-ecoli.xml (new),
arg-lepto.xml (new),
arg-rokas.xml (new),
benchmark.xml (new),
benchmark2.xml (new),
calibrations (new),
demoCodonHistorySimulator.xml (new 88),
new_benchmark.xml (new 371),
testAlignmentStatistics.xml (new 23),
testAncestralReconstruction.xml (new 245),
testAscertainment.xml (new 174),
testAutocorrelatedRelaxedClock.xml (new 460),
testBSP.xml (new 324),
testBinaryDollo.xml (new 148),
testCTMCMap.xml (new 312),
testCodonLikelihood.xml (new 1183),
testComparativeMethod.xml (new 292),
testCompleteHistorySimulator.xml (new 200),
testConjugateTraitLikelihood.xml (new 124),
testCovarionHKY.xml (new 339),
testDiscreteMapDiffusion.xml (new 112),
testGeneralSubstitutionModel.xml (new 183),
testIA.xml (new 120),
testIBDweights.xml (new 166),
testIntegratedTraitLikelihood.xml (new 115),
testLewisMk.xml (new 31),
testLikelihood.xml (new 727),
testLinearRegression.xml (new 126),
testLocalClock.xml (new 413),
testLognormalPrior.xml (new 62),
testMC3.xml (new 300),
testMCMC.xml (new 175),
testML.xml (new 165),
testMLCalculator.xml (new 6),
testMSSD.xml (new 203),
testMVOU.xml (new 302),
testMarkovJumps.xml (new 150),
testMissingIntegratedTraitLikelihood.xml (new 115),
testMixedModel.xml (new 148),
testMultiThreading.xml (new 423),
testMultivariateComparativeMethod.xml (new 310),
testNewLikelihood.xml (new 477),
testNormalModelGibbs.xml (new 109),
testOTFPCLikelihood.xml (new 477),
testPMD.xml (new 1550),
testPathSampling.xml (new 236),
testPopTreeModel.xml (new 39),
testPosteriorIBD.xml (new 194),
testRandomLocalClock.xml (new 321),
testRestrictedAncestralReconstruction.xml (new 255),
testRobustCounting.xml (new 452),
testSequenceSimulator.xml (new 143),
testSimplePathSampling.xml (new 251),
testStrictClock.xml (new 334),
testTransmission.xml (new 742),
testTransmissionStatistic.xml (new 682),
testTreePathSampling.xml (new 262),
testUncorrelatedRelaxedClock.xml (new 418),
testUniformizedMarkovJumps.xml (new 152),
testYuleOneSite.xml (new 225),
treePriors (new)
-
release/common/examples:
arg-lepto.xml (del),
arg-rokas.xml (del),
benchmark.xml (del),
new_benchmark.xml (del),
testAncestralReconstruction.xml (del),
testAscertainment.xml (del),
testBSP.xml (del),
testBinaryDollo.xml (del),
testCodonLikelihood.xml (del),
testComparativeMethod.xml (del),
testCovarionHKY.xml (del),
testGeneralSubstitutionModel.xml (del),
testIA.xml (del),
testIBDweights.xml (del),
testLikelihood.xml (del),
testLocalClock.xml (del),
testLognormalPrior.xml (del),
testMC3.xml (del),
testMCMC.xml (del),
testML.xml (del),
testMVOU.xml (del),
testMixedModel.xml (del),
testMultiThreading.xml (del),
testNormalModelGibbs.xml (del),
testPMD.xml (del),
testPathSampling.xml (del),
testPosteriorIBD.xml (del),
testRandomLocalClock.xml (del),
testSequenceSimulator.xml (del),
testStrictClock.xml (del),
testTransmissionStatistic.xml (del),
testUncorrelatedRelaxedClock.xml (del)
-
release/common/examples/Data:
Darwins-finches.nex (del),
Dengue4.env.nex (del),
Primates.nex (del),
Shankarappa.Patient9.nex (del),
anolis.nex (del)
-
release/common/examples/treePrior+clockModel:
BayesianSkyline+unccorelatedExp.xml (del),
GMRFBayesianSkyride+strict .xml (del),
Yule+unccorelatedExp.xml (del),
birthDeath+unccorelatedLn.xml (del),
constant+uncorrelatedExp.xml (del),
expansionDoubling+strict.xml.xml (del),
exponentialDoubling+strict.xml (del),
extendedBayesianSkyline+uncorrelatedLn.xml (del),
logisticDoubling+uncorrelatedLn.xml (del)
-
release/common/examples/treePriors:
testBSP.xml (del),
testBirthDeathAsYule.xml (del),
testCataclysmCoalescent.xml (del),
testCoalescent.xml (del),
testLinearBSP.xml (del),
testPiecewiseExponential.xml (del),
testYule.xml (del),
testYuleModel.xml (del),
testYuleModel_10taxa.xml (del),
testYulePrior.xml (del)
-
src/dr/app/beauti/generator:
TreePriorGenerator.java (-2)
-
mandevsgill
2010-08-26 11:29
#89
Rev.: 3449
-
58 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (+47 -150),
GMRFSkyrideLikelihood.java (+5 -4)
-
src/dr/evomodel/coalescent/operators:
GMRFMultiocusSkyrideBlockUpdateOperator.java (new 6)
-
dong.w.xie
2010-08-26 10:49
#88
Rev.: 3448
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+2 -2)
-
rambaut
2010-08-25 23:32
#87
Rev.: 3447
-
116 lines of code changed in 2 files:
-
examples:
benchmark2.xml (new 3)
-
src/dr/inference/model:
CompoundLikelihood.java (+113 -13)
-
jheled
2010-08-25 21:58
#86
Rev.: 3446
-
11 lines of code changed in 1 file:
-
src/dr/app/tracer/application:
TracerFrame.java (+11 -3)
-
rambaut
2010-08-25 19:06
#85
Rev.: 3445
-
14 lines of code changed in 2 files:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+4 -4)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+10 -11)
-
dong.w.xie
2010-08-25 18:04
#84
Rev.: 3444
-
44 lines of code changed in 1 file:
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+44 -51)
-
msuchard
2010-08-25 12:15
#83
Rev.: 3443
-
19 lines of code changed in 2 files:
-
src/dr/evomodelxml/treelikelihood:
TreeTraitParserUtilities.java (+14 -11)
-
src/dr/inference/model:
Parameter.java (+5)
-
dong.w.xie
2010-08-25 11:39
#82
Rev.: 3442
-
29 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+29 -37)
-
dong.w.xie
2010-08-25 10:57
#81
Rev.: 3441
-
0 lines of code changed in 1 file:
-
rambaut
2010-08-25 07:05
#80
-
8 lines of code changed in 2 files:
-
msuchard
2010-08-25 06:52
#79
Rev.: 3438
-
224 lines of code changed in 7 files:
-
src/dr/app/beagle/evomodel/operators:
TipStateSwapOperator.java (+81)
-
src/dr/app/beagle/evomodel/parsers:
TipStateSwapOperatorParser.java (+45)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+9 -3),
BeagleTreeLikelihood.java (+20)
-
src/dr/app/beast:
beagle_parsers.properties (+3)
-
src/dr/evomodel/operators:
TipStateSwapOperator.java (+66 -68)
-
msuchard
2010-08-25 06:50
#78
Rev.: 3437
-
2 lines of code changed in 1 file:
-
src/dr/app/util:
Arguments.java (+2 -1)
-
mandevsgill
2010-08-25 05:21
#77
Rev.: 3436
-
742 lines of code changed in 4 files:
-
src/dr/evolution/coalescent:
TreeIntervals.java (+3 -1)
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (+307 -66)
-
src/dr/evomodel/coalescent/operators:
GMRFMultiocusSkyrideBlockUpdateOperator.java (+422)
-
src/dr/evomodelxml/coalescent/operators:
GMRFSkyrideBlockUpdateOperatorParser.java (+10)
-
rambaut
2010-08-25 01:21
#76
Rev.: 3435
-
2 lines of code changed in 1 file:
-
src/dr/app/util:
Arguments.java (+2 -1)
-
rambaut
2010-08-25 00:37
#75
Rev.: 3434
-
10 lines of code changed in 4 files:
-
src/dr/util:
ErrorLogHandler.java (+5 -2),
MessageLogHandler.java (new)
-
rambaut
2010-08-25 00:26
#74
Rev.: 3433
-
8 lines of code changed in 1 file:
-
rambaut
2010-08-24 23:39
#73
Rev.: 3432
-
103 lines of code changed in 8 files:
-
release/Mac/lib:
libquaqua.jnilib (changed),
quaqua.jar (changed)
-
src/dr/app/beauti/enumTypes:
PriorType.java (+12 -1)
-
src/dr/app/beauti/options:
PartitionClockModel.java (+14 -19),
PartitionOptions.java (+6)
-
src/dr/app/beauti/priorsPanel:
DefaultPriorDialog.java (+36 -19),
PriorDialog.java (+15 -15),
PriorsPanel.java (+20 -5)
-
rambaut
2010-08-24 21:07
#72
Rev.: 3431
-
7 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastParser.java (+5 -7)
-
src/dr/evomodel/coalescent:
BayesianSkylineLikelihood.java (+2 -19),
DemographicLogger.java (del),
DemographicReconstructor.java (del)
-
rambaut
2010-08-24 21:01
#71
Rev.: 3430
-
0 lines of code changed in 1 file:
-
src/dr/app/beast:
release_parsers.properties (-2)
-
dong.w.xie
2010-08-24 10:37
#70
Rev.: 3429
-
3 lines of code changed in 1 file:
-
src/dr/app/beast:
development_parsers.properties (+3 -3)
-
dong.w.xie
2010-08-23 17:42
#69
Rev.: 3428
-
279 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+279 -275)
-
dong.w.xie
2010-08-23 11:22
#68
Rev.: 3427
-
3 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastMain.java (+1 -1)
-
src/dr/xml:
XMLParser.java (+2 -2)
-
rambaut
2010-08-23 08:01
#67
Rev.: 3426
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -1)
-
rambaut
2010-08-22 21:07
#66
Rev.: 3425
-
56 lines of code changed in 7 files:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+9 -4)
-
src/dr/app/beauti/options:
Parameter.java (+6 -2),
PartitionClockModel.java (+23 -23)
-
src/dr/app/beauti/priorsPanel:
DefaultPriorDialog.java (+3 -3),
PriorTableModel.java (new),
PriorsPanel.java (+13 -3)
-
rambaut
2010-08-22 20:50
#65
Rev.: 3424
-
25 lines of code changed in 7 files:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+5 -5)
-
src/dr/app/beauti/generator:
ParameterPriorGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
ModelOptions.java (+1 -1),
Parameter.java (+8),
PartitionClockModel.java (+1 -1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+4 -4),
PriorsPanel.java (+5 -5)
-
msuchard
2010-08-22 08:39
#64
Rev.: 3423
-
37 lines of code changed in 5 files:
-
lib:
beagle.jar (changed)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (-1),
PartialsRescalingScheme.java (+1)
-
src/dr/inference/operators:
RandomWalkOperator.java (+23 -13)
-
src/dr/inferencexml/operators:
RandomWalkOperatorParser.java (+13 -2)
-
rambaut
2010-08-21 04:14
#63
Rev.: 3422
-
85 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
PartitionClockModel.java (+85 -85)
-
rambaut
2010-08-21 03:53
#62
Rev.: 3421
-
39 lines of code changed in 7 files:
-
build.xml (+3 -20)
-
release/Mac/lib:
libquaqua.jnilib (changed),
libquaqua64.jnilib (changed),
quaqua-filechooser-only.jar (changed),
quaqua.jar (changed)
-
src/dr/app/beauti:
BeautiApp.java (+33 -12)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+3 -12)
-
rambaut
2010-08-21 01:26
#61
Rev.: 3420
-
73 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+73 -32)
-
rambaut
2010-08-20 22:13
#60
Rev.: 3419
-
16 lines of code changed in 12 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -4),
Generator.java (+1 -1),
InitialTreeGenerator.java (+1 -1),
SubstitutionModelGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+1 -1),
TraitData.java (+1 -1)
-
src/dr/app/beauti/priorsPanel:
RealNumberField.java (new 1)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+1 -1)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+1 -1),
PartitionTreePriorPanel.java (+1 -1)
-
rambaut
2010-08-20 21:58
#59
Rev.: 3418
-
60 lines of code changed in 2 files:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+12 -3),
SpecialNumberPanel.java (+48 -17)
-
rambaut
2010-08-20 21:23
#58
Rev.: 3417
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+5 -1)
-
rambaut
2010-08-20 21:13
#57
Rev.: 3416
-
58 lines of code changed in 9 files:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+8 -9)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+27 -24),
PriorOptionsPanel.java (+2 -1)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+6 -6),
SiteModelsPanel.java (+4 -2)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+2 -1),
PartitionTreePriorPanel.java (+2 -1),
SpeciesTreesPanel.java (+2 -1),
TreesPanel.java (+5 -3)
-
rambaut
2010-08-20 18:49
#56
Rev.: 3415
-
580 lines of code changed in 1 file:
-
examples:
benchmark2.xml (+580)
-
rambaut
2010-08-20 04:13
#55
Rev.: 3414
-
283 lines of code changed in 7 files:
-
src/dr/app/beast:
BeastMain.java (+181 -167)
-
src/dr/evomodel/treelikelihood:
NativeNucleotideLikelihoodCore.java (-3)
-
src/dr/evomodelxml:
CSVExporterParser.java (new)
-
src/dr/util:
FileHelpers.java (new)
-
src/dr/xml:
XMLParser.java (+12 -1)
-
rambaut
2010-08-19 22:46
#54
Rev.: 3413
-
1 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+1)
-
rambaut
2010-08-19 21:34
#53
Rev.: 3412
-
165 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+165 -155)
-
rambaut
2010-08-19 21:31
#52
Rev.: 3411
-
46 lines of code changed in 11 files:
-
src/dr/app/beast:
BeastDialog.java (+7),
BeastMain.java (+5 -1)
-
src/dr/evomodel/tree:
TreeSummary.java (+3 -1)
-
src/dr/evomodelxml/coalescent:
DemographicLoggerParser.java (del)
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+2)
-
src/dr/inference/loggers:
MCLogger.java (+5 -27)
-
src/dr/inferencexml/loggers:
LoggerParser.java (+3 -28),
MLLoggerParser.java (new)
-
src/dr/xml:
XMLParser.java (+20 -1)
-
rambaut
2010-08-19 20:56
#51
Rev.: 3410
-
1 lines of code changed in 1 file:
-
src/dr/inferencexml/loggers:
LoggerParser.java (+1 -1)
-
rambaut
2010-08-19 20:54
#50
Rev.: 3409
-
8 lines of code changed in 1 file:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+8 -8)
-
rambaut
2010-08-19 20:50
#49
Rev.: 3408
-
17 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastMain.java (+7 -1)
-
src/dr/inferencexml/loggers:
LoggerParser.java (+10 -2)
-
dong.w.xie
2010-08-19 17:15
#48
Rev.: 3407
-
0 lines of code changed in 42 files:
-
examples/beauti1.5:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del),
codon (del)
-
examples/beauti1.5/Gopher data:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del),
gopher_mapping.txt (del)
-
examples/beauti1.5/Virus Practical/FPV:
FPV.nex (del),
FPV.xml (del),
FPV1.xml (del)
-
examples/beauti1.5/Virus Practical/Flu:
Flu.nex (del),
Flu.xml (del)
-
examples/beauti1.5/Virus Practical/RSVA:
RSVA.nex (del),
RSVA.xml (del),
RSVA1.xml (del)
-
examples/beauti1.5/starBEAST:
YuleMultiLoci.xml (del),
YuleSingleLocus.xml (del),
birthDeathMultiLoci.xml (del),
brithDeathSingleLocus.xml (del),
g10.xml (del),
g11.xml (del),
x10.xml (del),
x11.xml (del)
-
examples/beauti1.5/treePrior+clockModel:
BayesianSkyline+unccorelatedExp.xml (del),
GMRFBayesianSkyride+strict .xml (del),
Yule+unccorelatedExp.xml (del),
birthDeath+unccorelatedLn.xml (del),
birthDeath+uncorrelatedLn.xml (del),
constant+uncorrelatedExp.xml (del),
expansionDoubling+strict.xml.xml (del),
exponentialDoubling+strict.xml (del),
extendedBayesianSkyline+uncorrelatedLn.xml (del),
logisticDoubling+uncorrelatedLn.xml (del)
-
dong.w.xie
2010-08-19 17:10
#47
Rev.: 3406
-
7 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+7 -4)
-
dong.w.xie
2010-08-19 11:17
#46
Rev.: 3405
-
30 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
LogGenerator.java (+2 -1)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+11)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2)
-
src/dr/inferencexml/loggers:
LoggerParser.java (+15)
-
rambaut
2010-08-18 23:24
#45
Rev.: 3404
-
279 lines of code changed in 13 files:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+4)
-
src/dr/app/beauti/generator:
AlignmentGenerator.java (+2 -2),
BeastGenerator.java (+111 -110),
BranchRatesModelGenerator.java (+1 -1),
GeneralTraitGenerator.java (+10 -7),
SubstitutionModelGenerator.java (+19 -17),
TreePriorGenerator.java (+72 -70)
-
src/dr/app/beauti/options:
DateGuesser.java (+9 -4),
PartitionTreePrior.java (+10 -10),
TraitGuesser.java (+7 -2)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+16 -15)
-
src/dr/app/beauti/util:
XMLWriter.java (+18 -9)
-
rambaut
2010-08-18 13:00
#44
Rev.: 3403
-
45 lines of code changed in 2 files:
-
src/dr/app/beauti/options:
PartitionClockModel.java (+3 -6)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+42 -26)
-
dong.w.xie
2010-08-17 16:23
#43
Rev.: 3402
-
76 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10),
InitialTreeGenerator.java (+7 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
PartitionTreeModel.java (+2 -2)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+32 -11)
-
src/dr/evolution/util:
Units.java (+24 -11)
-
dong.w.xie
2010-08-17 12:01
#42
Rev.: 3401
-
134 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeautiFrame.java (+8 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+4 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+109 -2),
Generator.java (+5)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+8 -7)
-
msuchard
2010-08-17 04:54
#41
Rev.: 3400
-
118 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+3)
-
src/dr/evomodel/operators:
FunkyPriorMixerOperator.java (+115 -31)
-
rambaut
2010-08-16 20:47
#40
Rev.: 3399
-
15 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+10 -1)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+5 -2)
-
rambaut
2010-08-16 20:35
#39
Rev.: 3398
-
58 lines of code changed in 2 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+17 -37)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+41 -10)
-
dong.w.xie
2010-08-16 17:56
#38
Rev.: 3397
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+6 -1)
-
dong.w.xie
2010-08-16 17:53
#37
Rev.: 3396
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+4)
-
dong.w.xie
2010-08-16 17:34
#36
Rev.: 3395
-
9 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
Generator.java (+2 -2)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+7 -5)
-
dong.w.xie
2010-08-16 17:07
#35
Rev.: 3394
-
34 lines of code changed in 2 files:
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+18 -4),
PriorDialog.java (+16 -5)
-
dong.w.xie
2010-08-16 11:19
#34
Rev.: 3393
-
4 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
NativeNucleotideLikelihoodCore.java (+4 -1)
-
alexei.drummond
2010-08-13 16:52
#33
-
4 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
-
dong.w.xie
2010-08-13 15:50
#32
Rev.: 3390
-
46 lines of code changed in 5 files:
-
src/dr/app/beauti/options:
PartitionTreeModel.java (+5)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+1 -15)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+21 -4)
-
src/dr/app/beauti/util:
TextUtil.java (+19 -2)
-
dong.w.xie
2010-08-13 14:41
#31
Rev.: 3389
-
15 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
STARBEASTOptions.java (+11 -8)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+3)
-
src/dr/app/beauti/util:
TextUtil.java (+1 -1)
-
dong.w.xie
2010-08-13 14:04
#30
Rev.: 3388
-
68 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+15 -15)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -8)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (-1)
-
src/dr/app/beauti/util:
TextUtil.java (+42)
-
mandevsgill
2010-08-13 11:53
#29
Rev.: 3387
-
0 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (-2)
-
msuchard
2010-08-13 11:30
#28
Rev.: 3386
-
451 lines of code changed in 3 files:
-
src/dr/evolution/coalescent:
TreeIntervals.java (+271 -247)
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (+169 -1),
GMRFSkyrideLikelihood.java (+11 -11)
-
dong.w.xie
2010-08-12 16:57
#27
Rev.: 3385
-
32 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+18 -12)
-
src/dr/app/beauti/options:
TraitData.java (+4 -1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+6 -6)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+4 -4)
-
dong.w.xie
2010-08-12 15:41
#26
Rev.: 3384
-
9 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+9 -8)
-
dong.w.xie
2010-08-12 12:47
#25
Rev.: 3383
-
20 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -3)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -10)
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -8)
-
src/dr/app/beauti/priorsPanel:
DefaultPriorDialog.java (+1 -1),
PriorDialog.java (+3 -3),
PriorOptionsPanel.java (-1),
PriorsPanel.java (+1 -3)
-
dong.w.xie
2010-08-12 10:55
#24
Rev.: 3382
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+5 -9)
-
dong.w.xie
2010-08-11 17:32
#23
Rev.: 3381
-
97 lines of code changed in 8 files:
-
src/dr/app/beauti:
BeautiFrame.java (+29 -17)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+26 -16)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+5 -7)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+10 -12)
-
src/dr/app/beauti/priorsPanel:
DefaultPriorDialog.java (+2 -1),
PriorsPanel.java (+13 -22)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+7 -4)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+5 -8)
-
msuchard
2010-08-11 13:11
#22
Rev.: 3380
-
191 lines of code changed in 2 files:
-
src/dr/evomodel/operators:
FunkyPriorMixerOperator.java (+125)
-
src/dr/evomodelxml/operators:
FunkyPriorMixerOperatorParser.java (+66)
-
msuchard
2010-08-11 08:12
#21
Rev.: 3379
-
27 lines of code changed in 3 files:
-
src/dr/inference/operators:
UniformOperator.java (+11 -2)
-
src/dr/inferencexml/operators:
UniformOperatorParser.java (+16 -1)
-
dong.w.xie
2010-08-10 12:09
#20
Rev.: 3378
-
50 lines of code changed in 7 files:
-
src/dr/app/beauti/enumTypes:
ClockType.java (new)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ModelOptions.java (+6),
PartitionClockModel.java (+3 -3),
PartitionOptions.java (+7),
PartitionSubstitutionModel.java (+31 -31)
-
dong.w.xie
2010-08-09 17:33
#19
Rev.: 3377
-
63 lines of code changed in 4 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+12 -29)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+1 -3)
-
src/dr/app/beauti/options:
STARBEASTOptions.java (+18)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+32 -2)
-
dong.w.xie
2010-08-09 12:02
#18
Rev.: 3376
-
45 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+2 -2)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -3)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+41 -34)
-
akaruiws
2010-08-09 11:49
#17
Rev.: 3375
-
130 lines of code changed in 2 files:
-
src/dr/inference/model:
OneOnX3Prior.java (new 63)
-
src/dr/inferencexml/model:
OneOnX3PriorParser.java (new 67)
-
dong.w.xie
2010-08-06 12:38
#16
Rev.: 3371
-
30 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+25 -18)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -1)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+2 -2)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+1)
-
dong.w.xie
2010-08-06 11:25
#15
Rev.: 3370
-
61 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+13 -7)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+29 -5),
TraitsPanel.java (+16 -7)
-
rambaut
2010-08-06 04:08
#14
Rev.: 3369
-
1 lines of code changed in 1 file:
-
src/dr/inference/model:
CompoundLikelihood.java (+1 -1)
-
philippe.lemey@gmail.com
2010-08-05 18:35
#13
Rev.: 3368
-
5 lines of code changed in 6 files:
-
examples/Phylogeography/continuous:
RacRABV_LogNRRW.xml (new),
RacRABV_cauchyRRW.xml (new),
RacRABV_gammaRRW.xml (new)
-
dong.w.xie
2010-08-05 16:33
#12
Rev.: 3367
-
9 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5 -3)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+4 -1)
-
dong.w.xie
2010-08-05 11:48
#11
Rev.: 3366
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+1 -1)
-
rambaut
2010-08-05 04:21
#10
Rev.: 3365
-
24 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
SVSComplexSubstitutionModel.java (+8 -3),
SVSGeneralSubstitutionModel.java (+8 -2)
-
src/dr/evomodel/substmodel:
SVSComplexSubstitutionModel.java (+8 -5)
-
rambaut
2010-08-05 04:13
#9
Rev.: 3364
-
673 lines of code changed in 32 files:
-
src/dr/app/beauti:
BeautiFrame.java (+34 -136),
BeautiMacFileMenuFactory.java (+1 -1)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+1 -2)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+103 -130)
-
src/dr/app/beauti/enumTypes:
ClockType.java (+2 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+77 -185),
BranchRatesModelGenerator.java (+33 -32),
GeneralTraitGenerator.java (+3 -3),
Generator.java (+4 -9),
InitialTreeGenerator.java (+1 -1),
LogGenerator.java (+14 -23),
OperatorsGenerator.java (+6 -6),
STARBEASTGenerator.java (+13 -13),
TreeLikelihoodGenerator.java (+1 -6),
TreePriorGenerator.java (+2 -2)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+30 -13),
ClockModelOptions.java (+1 -1),
PartitionClockModelTreeModelLink.java (+1 -3),
PartitionTreeModel.java (+1 -1),
STARBEASTOptions.java (+21 -25),
TraitData.java (+2 -14),
TraitGuesser.java (+34 -65)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+1 -1),
SiteModelsPanel.java (+3 -2)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+8 -8),
GuessTraitDialog.java (+20 -31),
TraitsPanel.java (+35 -19)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+2 -3),
PartitionTreePriorPanel.java (+5 -5),
TreesPanel.java (+34 -100)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+179 -54)
-
dong.w.xie
2010-08-04 18:36
#8
Rev.: 3363
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3 -3)
-
dong.w.xie
2010-08-04 18:30
#7
Rev.: 3362
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3)
-
dong.w.xie
2010-08-04 18:17
#6
Rev.: 3361
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+1 -1)
-
dong.w.xie
2010-08-04 18:00
#5
Rev.: 3360
-
15 lines of code changed in 1 file:
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+15 -15)
-
dong.w.xie
2010-08-03 15:35
#4
Rev.: 3359
-
23 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+4 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+19)
-
dong.w.xie
2010-08-03 12:11
#3
Rev.: 3358
-
170 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+159 -70),
Generator.java (+6 -1)
-
dong.w.xie
2010-08-03 11:29
#2
Rev.: 3357
-
57 lines of code changed in 6 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2 -1)
-
src/dr/app/beauti/enumTypes:
ClockType.java (+2 -2)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+32 -33),
LogGenerator.java (+12 -3),
TreeLikelihoodGenerator.java (+6 -1)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+3 -1)
-
rambaut
2010-08-01 11:18
#1
Rev.: 3356
-
1 lines of code changed in 2 files:
-
src/dr/app/seqgen:
RecomboGen.java (+1 -1)