-
alexei.drummond
2010-09-29 21:34
#90
Rev.: 3587
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+2 -2)
-
alexei.drummond
2010-09-29 19:02
#89
Rev.: 3586
-
1 lines of code changed in 1 file:
-
src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (+1 -1)
-
alexei.drummond
2010-09-29 18:56
#88
Rev.: 3585
-
41 lines of code changed in 2 files:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+32 -6)
-
src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+9 -2)
-
msuchard
2010-09-28 13:45
#87
Rev.: 3584
-
29 lines of code changed in 2 files:
-
src/dr/app/tools:
LogCombiner.java (+23 -7),
LogCombinerDialog.java (+6)
-
msuchard
2010-09-28 09:02
#86
Rev.: 3583
-
59 lines of code changed in 2 files:
-
src/dr/evoxml:
UPGMATreeParser.java (new)
-
msuchard
2010-09-28 06:44
#85
Rev.: 3582
-
2 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/parsers:
GeneralSubstitutionModelParser.java (+1 -1)
-
src/dr/evomodelxml/substmodel:
GeneralSubstitutionModelParser.java (+1 -1)
-
jheled
2010-09-27 17:57
#84
Rev.: 3580
-
2 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
VDdemographicFunction.java (+2 -2)
-
dong.w.xie
2010-09-27 13:49
#83
Rev.: 3578
-
578 lines of code changed in 7 files:
-
src/test/dr/app/beauti:
BeautiTester.java (new),
BeautiTesterConfig.java (+498)
-
src/test/dr/beauti:
BeautiTester.java (del),
BeautiTesterConfig.java (del)
-
src/test/dr/integration:
GTRParameterEstimationTest.java (+10 -7)
-
dong.w.xie
2010-09-27 12:03
#82
Rev.: 3577
-
6 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
VDdemographicFunction.java (+6 -9)
-
alexei.drummond
2010-09-27 11:44
#81
-
396 lines of code changed in 4 files:
-
src/dr/evomodel/coalescent:
VDdemographicFunction.java (+97 -70)
-
src/dr/evomodel/speciation:
SpeciesTreeModel.java (+244 -241)
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+7 -4)
-
rambaut
2010-09-27 11:01
#80
Rev.: 3574
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
SpeciesTreeModel.java (+1 -1)
-
msuchard
2010-09-27 09:25
#79
Rev.: 3573
-
23 lines of code changed in 1 file:
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+23 -5)
-
akaruiws
2010-09-25 18:02
#78
Rev.: 3572
-
117 lines of code changed in 3 files:
-
src/dr/evomodel/substmodel:
NewMicrosatelliteModel.java (+63 -15)
-
src/dr/evomodelxml/substmodel:
NewMicrosatelliteModelParser.java (new 54)
-
alexander.alekseyenko
2010-09-25 04:58
#77
Rev.: 3571
-
343 lines of code changed in 6 files:
-
examples/release:
testMSSD.xml (new 2)
-
examples/unrelease:
testMVPolyaLikelihood.xml (new 93)
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/inferencexml/operators:
DeltaMixOperatorParser.java (+2 -2)
-
src/dr/math/distributions:
MultivariatePolyaDistributionLikelihood.java (+245)
-
jheled
2010-09-24 13:14
#76
Rev.: 3570
-
18 lines of code changed in 8 files:
-
src/dr/evomodelxml/operators:
ExchangeOperatorParser.java (+3),
SubtreeSlideOperatorParser.java (new)
-
src/dr/inference/distribution:
MixedDistributionLikelihood.java (new)
-
src/dr/inferencexml/distribution:
MixedDistributionLikelihoodParser.java (new)
-
src/dr/inferencexml/operators:
UniformOperatorParser.java (+4)
-
dong.w.xie
2010-09-24 10:41
#75
Rev.: 3569
-
103 lines of code changed in 3 files:
-
build.xml (+2 -1)
-
src/test/dr/evolution:
FilteredTreeTraitTest.java (new 101)
-
src/test/dr/evomodel:
FilteredTreeTraitTest.java (del)
-
dong.w.xie
2010-09-24 10:38
#74
Rev.: 3568
-
269 lines of code changed in 2 files:
-
src/test/dr/evomodel/substmodel:
TimeIrreversibleTest.java (+269)
-
src/test/dr/integration:
TimeIrreversibleTest.java (del)
-
alexander.alekseyenko
2010-09-24 04:20
#73
Rev.: 3567
-
249 lines of code changed in 10 files:
-
examples/incorrect:
testLewisMk.xml (del),
testMSSD.xml (del),
testPathSampling.xml (del)
-
examples/release:
testIBDweights.xml (del),
testLewisMk.xml (new 25),
testMSSD.xml (+208)
-
examples/unrelease:
testIBDweights.xml (new),
testPathSampling.xml (new 2)
-
src/dr/app/beagle/evomodel/parsers:
GeneralSubstitutionModelParser.java (+8 -5)
-
src/dr/evomodelxml/substmodel:
GeneralSubstitutionModelParser.java (+6 -3)
-
alexander.alekseyenko
2010-09-24 04:19
#72
Rev.: 3566
-
216 lines of code changed in 3 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/inference/operators:
DeltaMixOperator.java (new 132)
-
src/dr/inferencexml/operators:
DeltaMixOperatorParser.java (+83)
-
akaruiws
2010-09-23 20:13
#71
-
121 lines of code changed in 3 files:
-
src/dr/app/seqgen:
GeoDiffusionSimulator.java (+112)
-
dong.w.xie
2010-09-23 16:18
#70
Rev.: 3563
-
3 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+3 -3)
-
dong.w.xie
2010-09-22 12:54
#69
Rev.: 3561
-
10 lines of code changed in 5 files:
-
build.xml (+1 -1)
-
release/common/icons:
TreeStat.icns (new),
TreeStat.ico (new),
TreeStat.png (new)
-
src/dr/app/treestat:
TreeStatApp.java (+9 -2)
-
philippe.lemey@gmail.com
2010-09-18 01:11
#68
Rev.: 3556
-
16 lines of code changed in 1 file:
-
src/dr/app/tools:
TreeAnnotator.java (+16 -6)
-
dong.w.xie
2010-09-17 12:23
#67
Rev.: 3555
-
94 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+6 -4)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+88 -86)
-
dong.w.xie
2010-09-15 16:50
#66
Rev.: 3549
-
0 lines of code changed in 1 file:
-
release/Windows:
BEAUTi_launch4j.xml (del)
-
dong.w.xie
2010-09-15 16:28
#65
Rev.: 3547
-
26 lines of code changed in 6 files:
-
build.xml (+5 -4),
build_BEAST_Backup_2009_10_27.xml (+1 -1),
scripts (del)
-
release/Windows:
BEAUti_launch4j.xml (+16)
-
src/dr/app/beast:
development_parsers.properties (+1 -1)
-
src/dr/app/treestat:
TreeStatApp.java (+3 -5)
-
dong.w.xie
2010-09-15 11:48
#64
Rev.: 3542
-
12 lines of code changed in 2 files:
-
release/common:
VERSION HISTORY.txt (+11 -4)
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
-
dong.w.xie
2010-09-15 10:45
#63
Rev.: 3541
-
27 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
TMRCAStatisticsGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -2)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+5 -5)
-
src/dr/evomodelxml/tree:
TMRCAStatisticParser.java (+19 -4)
-
msuchard
2010-09-15 07:58
#62
Rev.: 3540
-
7 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+7 -3)
-
dong.w.xie
2010-09-14 18:11
#61
Rev.: 3539
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/traitspanel:
GuessTraitDialog.java (+2 -3)
-
dong.w.xie
2010-09-14 11:03
#60
Rev.: 3538
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3 -2)
-
rambaut
2010-09-13 22:26
#59
Rev.: 3537
-
130 lines of code changed in 3 files:
-
src/dr/app/beast:
release_parsers.properties (+1 -1)
-
src/dr/evomodel/continuous:
DiffusionRateStatistic.java (+129),
TreeDispersionStatistic.java (del)
-
rambaut
2010-09-13 22:13
#58
Rev.: 3536
-
2 lines of code changed in 1 file:
-
release/common:
VERSION HISTORY.txt (+2 -1)
-
philippe.lemey@gmail.com
2010-09-13 22:00
#57
-
0 lines of code changed in 4 files:
-
examples/release/Phylogeography/continuous:
RacRABV_LogNRRW.xml (new),
RacRABV_homogeneous.xml (new)
-
rambaut
2010-09-13 21:47
#56
Rev.: 3532
-
2 lines of code changed in 1 file:
-
release/common:
VERSION HISTORY.txt (+2 -1)
-
philippe.lemey@gmail.com
2010-09-13 21:47
#55
Rev.: 3533
-
0 lines of code changed in 2 files:
-
examples/release/Phylogeography/continuous:
RacRABV_gammaRRW.xml (changed)
-
dong.w.xie
2010-09-13 15:47
#54
Rev.: 3531
-
16 lines of code changed in 3 files:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+11 -6)
-
src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+3 -3)
-
src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (+2 -1)
-
dong.w.xie
2010-09-13 11:58
#53
Rev.: 3530
-
4 lines of code changed in 1 file:
-
src/dr/app/tracer/analysis:
BayesFactorsFrame.java (+4 -3)
-
dong.w.xie
2010-09-13 10:51
#52
Rev.: 3529
-
3 lines of code changed in 1 file:
-
src/dr/app/tracer/analysis:
BayesFactorsFrame.java (+3 -2)
-
msuchard
2010-09-13 07:07
#51
Rev.: 3528
-
113 lines of code changed in 3 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/evomodel/coalescent:
GMRFIntervalHeightsStatistic.java (new 64)
-
src/dr/evomodelxml/coalescent:
GMRFIntervalHeightsStatisticParser.java (new 48)
-
rambaut
2010-09-11 08:41
#50
Rev.: 3527
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+6)
-
rambaut
2010-09-11 01:58
#49
Rev.: 3526
-
76 lines of code changed in 3 files:
-
release/common:
VERSION HISTORY.txt (+68 -96)
-
src/dr/evolution/tree:
MutableTree.java (+4 -1)
-
src/dr/evomodel/tree:
TreeModel.java (+4)
-
msuchard
2010-09-11 00:27
#48
Rev.: 3525
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
rambaut
2010-09-10 21:12
#47
Rev.: 3524
-
21 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
TreeDispersionStatistic.java (new 21)
-
dong.w.xie
2010-09-10 17:15
#46
Rev.: 3523
-
19 lines of code changed in 1 file:
-
release/common:
VERSION HISTORY.txt (+19 -7)
-
dong.w.xie
2010-09-10 16:55
#45
Rev.: 3522
-
8 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+8 -5)
-
dong.w.xie
2010-09-10 16:29
#44
Rev.: 3521
-
2 lines of code changed in 3 files:
-
release/common:
VERSION HISTORY.txt (+1 -1)
-
src/dr/app/treestat/statistics:
B1Statistic.java (+1 -1)
-
rambaut
2010-09-10 03:17
#43
Rev.: 3520
-
5 lines of code changed in 3 files:
-
src/dr/evomodel/continuous:
IntegratedMultivariateTraitLikelihood.java (+1 -1)
-
src/dr/evomodel/operators:
TipTraitSwapOperator.java (+4 -2)
-
rambaut
2010-09-10 03:01
#42
Rev.: 3519
-
32 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
TreeDispersionStatistic.java (+32 -21)
-
rambaut
2010-09-10 02:54
#41
Rev.: 3518
-
126 lines of code changed in 3 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/evomodel/continuous:
IntegratedMultivariateTraitLikelihood.java (+12)
-
src/dr/evomodel/operators:
TipTraitSwapOperator.java (+113)
-
rambaut
2010-09-09 23:49
#40
Rev.: 3517
-
173 lines of code changed in 1 file:
-
src/dr/app/util:
Utils.java (+173)
-
rambaut
2010-09-09 23:38
#39
Rev.: 3516
-
1 lines of code changed in 2 files:
-
src/dr/app/phylogeography/spread/layerspanel:
LayersPanel.java (+1)
-
rambaut
2010-09-09 23:33
#38
Rev.: 3515
-
4 lines of code changed in 7 files:
-
lib:
jam.jar (changed)
-
src/dr/app/phylogeography/spread:
SpreadFrame.java (+1)
-
src/dr/app/util:
Arguments.java (+1 -1),
OSType.java (new),
Utils.java (+1 -1)
-
rambaut
2010-09-09 23:27
#37
Rev.: 3514
-
77 lines of code changed in 36 files:
-
src/dr/app/gui:
DeleteActionResponder.java (+1 -1),
FileDrop.java (+1 -1),
MultiLineTableCellContent.java (del),
MultiLineTableCellRenderer.java (del),
SelectAllActionResponder.java (+1 -1)
-
src/dr/app/gui/components:
ColorWellButton.java (new),
JVerticalLabel.java (+1 -1),
RealNumberField.java (+1 -1),
WholeNumberField.java (+1 -1)
-
src/dr/app/gui/table:
MultiLineTableCellContent.java (new 16),
MultiLineTableCellRenderer.java (new 37),
RealNumberCellEditor.java (+2 -2),
TableEditorStopper.java (new),
WholeNumberCellEditor.java (+2 -2)
-
src/dr/app/phylogeography/builder:
Builder.java (+1 -1)
-
src/dr/app/phylogeography/spread:
DeleteActionResponder.java (del),
InputFile.java (new),
SelectAllActionResponder.java (del),
SpreadFrame.java (+2 -1)
-
src/dr/app/phylogeography/spread/inputpanel:
InputPanel.java (new),
ReadsPanel.java (del),
SourcesPanel.java (del),
SourcesSettingsDialog.java (del)
-
src/dr/app/phylogeography/spread/layerspanel:
LayersPanel.java (+1 -1)
-
src/dr/app/tools:
RateIndicatorBF.java (new 5)
-
rambaut
2010-09-09 23:01
#36
-
569 lines of code changed in 18 files:
-
src/dr/app/gui:
DeleteActionResponder.java (+12),
FileDrop.java (+8 -8),
MultiLineTableCellContent.java (new 1),
MultiLineTableCellRenderer.java (new 1),
SelectAllActionResponder.java (+9)
-
src/dr/app/gui/components:
ColorWellButton.java (+1 -1),
JVerticalLabel.java (+1 -1),
RealNumberField.java (+1 -1),
WholeNumberField.java (+1 -1)
-
src/dr/app/gui/table:
RealNumberCellEditor.java (+2 -2),
TableEditorStopper.java (+1 -1),
WholeNumberCellEditor.java (+2 -2)
-
src/dr/app/phylogeography/spread/inputpanel:
ReadsPanel.java (new 53),
SourcesPanel.java (new 295),
SourcesSettingsDialog.java (new 86)
-
src/dr/app/util:
Arguments.java (+80 -80),
OSType.java (+14 -14),
Utils.java (+1 -174)
-
dong.w.xie
2010-09-09 14:25
#35
Rev.: 3511
-
29 lines of code changed in 1 file:
-
src/dr/app/tracer/application:
TracerFrame.java (+29 -14)
-
dong.w.xie
2010-09-09 12:38
#34
Rev.: 3510
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+2 -2)
-
dong.w.xie
2010-09-09 11:45
#33
Rev.: 3509
-
55 lines of code changed in 3 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+35 -4)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+19 -2)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+1)
-
msuchard
2010-09-09 04:22
#32
Rev.: 3508
-
64 lines of code changed in 6 files:
-
src/dr/inference/distribution:
GeneralizedLinearModel.java (new)
-
src/dr/inference/operators:
MultivariateNormalOperator.java (new)
-
src/dr/inferencexml/distribution:
GeneralizedLinearModelParser.java (new)
-
dong.w.xie
2010-09-08 11:02
#31
Rev.: 3507
-
4 lines of code changed in 1 file:
-
release/common:
VERSION HISTORY.txt (+4 -1)
-
msuchard
2010-09-08 10:34
#30
Rev.: 3506
-
61 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+3 -3)
-
src/dr/evolution/coalescent:
TreeIntervals.java (+27)
-
src/dr/evomodel/coalescent:
GMRFMultilocusSkyrideLikelihood.java (+31 -37)
-
akaruiws
2010-09-08 10:06
#29
Rev.: 3505
-
11 lines of code changed in 3 files:
-
src/dr/evomodel/substmodel:
NewMicrosatelliteModel.java (+7 -2)
-
src/dr/math:
ModifiedBesselFirstKind.java (new)
-
akaruiws
2010-09-08 09:52
#28
Rev.: 3504
-
35 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
NewMicrosatelliteModel.java (+35)
-
akaruiws
2010-09-08 00:43
#27
Rev.: 3503
-
22 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
NewMicrosatelliteModel.java (+22)
-
alexei.drummond
2010-09-07 23:08
#26
Rev.: 3502
-
49 lines of code changed in 1 file:
-
src/dr/math:
ModifiedBesselFirstKind.java (+49)
-
dong.w.xie
2010-09-07 17:32
#25
Rev.: 3501
-
32 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
TMRCAStatisticsGenerator.java (+4 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+3 -1)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+25 -17)
-
dong.w.xie
2010-09-07 16:35
#24
Rev.: 3500
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
STARBEASTGenerator.java (+2 -5)
-
dong.w.xie
2010-09-07 15:19
#23
Rev.: 3499
-
109 lines of code changed in 5 files:
-
build.xml (+30 -4)
-
release/Linux/scripts:
treestat (new 27)
-
release/Mac/scripts:
treestat (new 27)
-
release/Windows:
TreeStat_launch4j.xml (+20)
-
release/Windows/scripts:
treestat.cmd (new 5)
-
dong.w.xie
2010-09-07 11:57
#22
Rev.: 3498
-
23 lines of code changed in 3 files:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+13 -8)
-
src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+8 -8)
-
src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (+2 -1)
-
rambaut
2010-09-07 10:37
#21
Rev.: 3497
-
9503 lines of code changed in 256 files:
-
src/dr/app/beast:
BeastDialog.java (+3 -3),
BeastMC3.java (+1 -1),
BeastMain.java (+2 -2)
-
src/dr/app/beauti:
BeautiApp.java (+1 -1),
BeautiDefaultFileMenuFactory.java (+4 -4),
BeautiFrame.java (+5 -5),
BeautiMacFileMenuFactory.java (+4 -4),
BeautiMenuBarFactory.java (new),
BeautiPanel.java (new)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+7 -9)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+5 -5),
SelectClockDialog.java (new),
SelectModelDialog.java (+1 -1),
SelectTreeDialog.java (new)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+2 -2)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+4 -4)
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+3 -3),
PriorDialog.java (+3 -5),
PriorOptionsPanel.java (+2 -2),
PriorsPanel.java (+4 -4),
RealNumberField.java (del),
SpecialNumberPanel.java (+1)
-
src/dr/app/beauti/siteModelsPanel:
CreateModelDialog.java (+1 -1),
PartitionModelPanel.java (+2 -2),
SiteModelsPanel.java (+6 -6)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+14 -14)
-
src/dr/app/beauti/tipdatepanel:
GuessDatesDialog.java (+2 -2),
TipDatesPanel.java (+9 -10)
-
src/dr/app/beauti/traitspanel:
CreateTraitDialog.java (+1 -1),
GuessTraitDialog.java (+5 -5),
TraitsPanel.java (+6 -6)
-
src/dr/app/beauti/treespanel:
GenerateTreeDialog.java (+1 -1),
OldTreesPanel.java (+4 -4),
PartitionTreeModelPanel.java (+5 -5),
PartitionTreePriorPanel.java (+17 -17),
SpeciesTreesPanel.java (+7 -7),
TreeDisplayPanel.java (+2 -2),
TreesPanel.java (+61 -61)
-
src/dr/app/coalgen:
DataPanel.java (new),
ModelPanel.java (new),
SimulationsPanel.java (+1 -1)
-
src/dr/app/gui:
ColorFunction.java (new 61)
-
src/dr/app/gui/chart:
AreaPlot.java (+161),
Axis.java (+855),
BlankAxis.java (new 72),
CategoryDensityPlot.java (+188),
ChartException.java (new 37),
ChartLayout.java (new 339),
ChartRuntimeException.java (new 12),
ChartSelector.java (+113),
ChartSetupDialog.java (+185),
DensityEstimatePlot.java (+98),
DiscreteAxis.java (new 100),
DiscreteJChart.java (new 111),
FrequencyPlot.java (+310),
JChart.java (+663),
JChartPanel.java (new 147),
KDENumericalDensityPlot.java (+185),
KDESetupDialog.java (new 190),
LineDistributionPlot.java (+97),
LinePlot.java (+92),
LinearAxis.java (new 59),
LogAxis.java (new 224),
NumericalDensityPlot.java (+156),
PDFPlot.java (+135),
Plot.java (+622),
RegressionPlot.java (+131),
ScatterPlot.java (+191)
-
src/dr/app/gui/components:
ColorWellButton.java (+107),
JVerticalLabel.java (+108),
RealNumberField.java (+245),
WholeNumberField.java (+211)
-
src/dr/app/gui/table:
DateCellEditor.java (+75),
RealNumberCellEditor.java (+46),
TableEditorStopper.java (+87),
TableSorter.java (new 539),
TaxonListTable.java (new 195),
WholeNumberCellEditor.java (+46)
-
src/dr/app/gui/table/images:
sortAscending.png (new),
sortDescending.png (new)
-
src/dr/app/gui/tree:
CoordinateTransform.java (new 52),
JTreeDisplay.java (new 245),
JTreePanel.java (new 191),
NodeDecorator.java (new 46),
NodeHeightBoxPlot.java (new 98),
SquareTreePainter.java (new 539),
TreePainter.java (new 65)
-
src/dr/app/gui/util:
LongTask.java (new 82),
LongTaskMonitor.java (new 69),
SimpleLongTask.java (new 51),
SwingWorker.java (new 157),
TaskListener.java (new 17)
-
src/dr/app/oldbeauti:
BeautiApp.java (+1 -2),
BeautiDefaultFileMenuFactory.java (new),
BeautiFrame.java (+3 -3),
BeautiMacFileMenuFactory.java (new),
BeautiMenuBarFactory.java (new),
DataPanel.java (new),
DiscretePriorDialog.java (new),
MCMCPanel.java (+4 -4),
ModelPanel.java (new),
OperatorsPanel.java (+4 -4),
PriorDialog.java (+3 -3),
PriorsPanel.java (new),
TaxaPanel.java (+4 -4)
-
src/dr/app/pathogen:
PathogenApp.java (+1 -1),
PathogenDefaultFileMenuFactory.java (+4 -4),
PathogenFrame.java (+2 -2),
PathogenMacFileMenuFactory.java (+4 -4),
PathogenMenuBarFactory.java (+5 -5),
SamplesPanel.java (+5 -6),
TreesPanel.java (+4 -4)
-
src/dr/app/phylogeography/builder:
ContinuousDiffusionTreeBuilder.java (+3 -3),
DiscreteDiffusionTreeBuilder.java (new)
-
src/dr/app/phylogeography/spread:
DeleteActionResponder.java (new 13),
OutputPanel.java (+1 -1),
SelectAllActionResponder.java (new 11),
SpreadFrame.java (+38 -13),
TimelinePanel.java (+1 -1)
-
src/dr/app/phylogeography/spread/inputpanel:
InputFileSettingsDialog.java (+3 -4),
InputPanel.java (+31 -12)
-
src/dr/app/phylogeography/spread/layerspanel:
CreateBuilderDialog.java (new),
EditBuilderDialog.java (+1 -1),
LayersPanel.java (+15 -12)
-
src/dr/app/phylogeography/spread/renderpanel:
RenderPanel.java (new 16)
-
src/dr/app/tools:
BranchRatePlotter.java (+4 -4),
LogCombiner.java (+1 -1),
LogCombinerDialog.java (+8 -8),
TreeAnnotator.java (+1 -1),
TreeAnnotatorDialog.java (+3 -3)
-
src/dr/app/tracer/analysis:
BayesFactorsDialog.java (+4 -4),
BayesFactorsFrame.java (+2 -2),
BayesianSkylineDialog.java (+5 -6),
DemographicDialog.java (+5 -6),
DemographicPlotPanel.java (+1 -1),
GMRFSkyrideDialog.java (+5 -8),
LineagesThroughTimeDialog.java (+5 -6),
NewTemporalAnalysisDialog.java (+4 -4),
TemporalAnalysisFrame.java (+2 -2),
TemporalAnalysisPlotPanel.java (+1 -1),
TimeDensityDialog.java (+3 -4),
TraitThroughTimeDialog.java (+5 -6)
-
src/dr/app/tracer/application:
AnalysisMenuFactory.java (+2 -2),
GeneralPreferencesSection.java (new),
TracerApp.java (+1 -1),
TracerDefaultFileMenuFactory.java (new),
TracerFrame.java (+9 -9),
TracerMacFileMenuFactory.java (new),
TracerMenuBarFactory.java (new)
-
src/dr/app/tracer/traces:
BetterDensityPanel.java (+2 -2),
DensityPanel.java (+2 -2),
FilterDialog.java (+1 -1),
FrequencyPanel.java (+2 -2),
IntervalsPanel.java (new),
JIntervalsChart.java (new),
JTraceChart.java (+3 -3),
JointDensityPanel.java (+2 -2),
RawTracePanel.java (+124 -12),
SummaryStatisticsPanel.java (+3 -3),
TableScrollPane.java (+1 -1),
TracePanel.java (+2 -2)
-
src/dr/app/treestat:
CharactersPanel.java (new),
StatisticsPanel.java (+2 -2),
TaxonSetsPanel.java (+2 -2),
TreeStatApp.java (+2 -2),
TreeStatFrame.java (new),
TreeStatPanel.java (+18 -18)
-
src/dr/geo:
GTOPO30Browser.java (+1 -1),
GTOPO30Panel.java (+1 -1),
GTOPO30RandomWalk.java (new),
GTOPO30Tile.java (+1 -1),
InhomogeneousRandomWalk.java (new),
VisualizeKMLNumericalProbs.java (+1 -1)
-
src/dr/gui:
ColorFunction.java (del)
-
src/dr/gui/chart:
AreaPlot.java (del),
Axis.java (del),
BlankAxis.java (del),
CategoryDensityPlot.java (del),
ChartLayout.java (del),
ChartRuntimeException.java (del),
ChartSelector.java (del),
ChartSetupDialog.java (del),
DensityEstimatePlot.java (del),
DensityPlot.java (del),
DiscreteJChart.java (del),
FrequencyPlot.java (del),
JChart.java (del),
JChartPanel.java (del),
KDENumericalDensityPlot.java (del),
KDESetupDialog.java (del),
LineDistributionPlot.java (del),
LinePlot.java (del),
LogAxis.java (del),
NumericalDensityPlot.java (del),
PDFPlot.java (del),
Plot.java (del),
RegressionPlot.java (del),
ScatterPlot.java (del)
-
src/dr/gui/graph:
DefaultGraphModel.java (del),
DefaultVertex.java (del)
-
src/dr/gui/table:
DateCellEditor.java (del),
TableSorter.java (del),
TaxonListTable.java (del)
-
src/dr/gui/table/images:
sortAscending.png (del),
sortDescending.png (del)
-
src/dr/gui/tree:
JTreeDisplay.java (del),
JTreePanel.java (del),
SquareTreePainter.java (del)
-
src/dr/inference/trace:
DensityEstimate.java (+3 -4)
-
dong.w.xie
2010-09-06 18:07
#20
Rev.: 3496
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+1 -1)
-
dong.w.xie
2010-09-06 17:03
#19
Rev.: 3495
-
14 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+14 -2)
-
dong.w.xie
2010-09-06 16:47
#18
Rev.: 3494
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeParameterModel.java (+2 -2)
-
dong.w.xie
2010-09-06 16:42
#17
Rev.: 3493
-
44 lines of code changed in 1 file:
-
release/common:
VERSION HISTORY.txt (+44 -3)
-
dong.w.xie
2010-09-06 15:37
#16
Rev.: 3492
-
24 lines of code changed in 3 files:
-
src/dr/evomodel/speciation:
BirthDeathSerialSamplingModel.java (+17 -11)
-
src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+6 -5)
-
src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (+1 -1)
-
dong.w.xie
2010-09-06 15:33
#15
Rev.: 3491
-
18 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5 -6)
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+13 -3)
-
philippe.lemey@gmail.com
2010-09-04 07:57
#14
Rev.: 3490
-
46 lines of code changed in 1 file:
-
src/dr/inference/operators:
MultivariateNormalOperator.java (+46 -12)
-
philippe.lemey@gmail.com
2010-09-04 07:55
#13
Rev.: 3489
-
1 lines of code changed in 1 file:
-
src/dr/app/beast:
development_parsers.properties (+1 -1)
-
msuchard
2010-09-04 04:08
#12
Rev.: 3488
-
79 lines of code changed in 9 files:
-
src/dr/evomodel/coalescent:
CovariateGMRFSkylineLikelihood.java (new),
GMRFFixedGridLikelihood.java (+2 -2),
GMRFMultilocusSkyrideLikelihood.java (+48 -124),
GMRFSkyrideLikelihood.java (+21 -24),
GMRFTestLikelihood.java (new)
-
src/dr/evomodelxml/coalescent:
GMRFSkyrideLikelihoodParser.java (+6 -1)
-
msuchard
2010-09-04 04:04
#11
Rev.: 3487
-
1310 lines of code changed in 7 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
NewScalingBeagleTreeLikelihood.java (+1165)
-
src/dr/evomodel/operators:
FunkyPriorMixerOperator.java (new)
-
src/dr/evomodel/speciation:
TaxonRichnessBirthDeathModel.java (new 22)
-
src/dr/evomodelxml/operators:
FunkyPriorMixerOperatorParser.java (+3 -1)
-
src/dr/evomodelxml/speciation:
TaxonRichnessBirthDeathModelParser.java (new 70)
-
dong.w.xie
2010-09-03 14:36
#10
Rev.: 3486
-
3 lines of code changed in 1 file:
-
src/dr/inferencexml/model:
SumStatisticParser.java (+3 -1)
-
dong.w.xie
2010-09-03 14:29
#9
Rev.: 3485
-
169 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+1 -1),
GeneralTraitGenerator.java (new 144),
LogGenerator.java (+9 -2),
TreeLikelihoodGenerator.java (+5 -1),
TreeModelGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+8 -8)
-
dong.w.xie
2010-09-03 14:02
#8
Rev.: 3484
-
54 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+50 -12)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4)
-
dong.w.xie
2010-09-02 11:57
#7
Rev.: 3483
-
13 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+10 -1)
-
rambaut
2010-09-02 04:07
#6
Rev.: 3482
-
28 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+28 -24)
-
rambaut
2010-09-02 03:37
#5
Rev.: 3481
-
18 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+18 -18)
-
rambaut
2010-09-02 02:22
#4
Rev.: 3480
-
40 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GMRFSkyrideLikelihood.java (+12 -6)
-
src/dr/evomodel/treelikelihood:
SequenceErrorModel.java (+26)
-
src/test/dr/evomodel/treelikelihood:
PMDTestProblem.java (+2 -2)
-
rambaut
2010-09-02 01:35
#3
Rev.: 3479
-
120 lines of code changed in 3 files:
-
src/dr/evomodel/treelikelihood:
SequenceErrorModel.java (+111 -56)
-
src/dr/evomodelxml/treelikelihood:
SequenceErrorModelParser.java (new)
-
dong.w.xie
2010-09-01 16:56
#2
Rev.: 3478
-
7 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4)
-
rambaut
2010-09-01 10:45
#1
Rev.: 3477
-
9 lines of code changed in 3 files:
-
src/dr/app/beauti/traitspanel:
TraitsPanel.java (+8 -3)
-
src/dr/evoxml:
AlignmentParser.java (+1 -1)