-
rambaut
2013-03-30 10:00
#93
Rev.: 5555
-
32 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+32 -37)
-
julia.pal.r@gmail.com
2013-03-29 13:12
#92
Rev.: 5554
-
90 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+90 -9)
-
julia.pal.r@gmail.com
2013-03-29 05:26
#91
Rev.: 5553
-
44 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GPSkytrackAnalysis.java (+1),
GaussianProcessSkytrackLikelihood.java (+41 -38)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+2)
-
fbielejec
2013-03-28 23:48
#90
Rev.: 5552
-
208 lines of code changed in 5 files:
-
src/dr/app/bss:
BeagleSequenceSimulatorConsoleApp.java (+203 -86),
MainFrame.java (+1 -1),
PartitionData.java (+1 -1),
README.textile (+1),
Utils.java (+2 -2)
-
dong.w.xie@gmail.com
2013-03-28 11:48
#89
Rev.: 5551
-
26 lines of code changed in 2 files:
-
src/dr/app/seqgen:
SeqGen.java (+26 -15)
-
alexei.drummond
2013-03-28 11:02
#88
Rev.: 5550
-
5 lines of code changed in 1 file:
-
src/dr/app/seqgen:
SeqGen.java (+5 -3)
-
fbielejec
2013-03-28 02:55
#87
-
203 lines of code changed in 7 files:
-
src/dr/app/beagle/tools/parsers:
PartitionParser.java (+2 -2)
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+7 -3),
BeagleSequenceSimulatorConsoleApp.java (+187),
MainFrame.java (+1 -69),
PartitionData.java (+3 -3),
README.textile (+3)
-
philippe.lemey@gmail.com
2013-03-28 01:22
#86
Rev.: 5547
-
1 lines of code changed in 2 files:
-
src/dr/evomodel/transmission:
TransmissionStatistic.java (new)
-
philippe.lemey@gmail.com
2013-03-28 00:56
#85
Rev.: 5546
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/transmission:
TransmissionStatistic.java (+1 -1)
-
msuchard
2013-03-27 06:44
#84
Rev.: 5545
-
1 lines of code changed in 2 files:
-
src/dr/inference/model:
DiagonalMatrix.java (new)
-
msuchard
2013-03-27 03:48
#83
Rev.: 5544
-
857 lines of code changed in 5 files:
-
src/dr/inference/model:
DiagonalMatrix.java (+58 -25)
-
src/dr/math/distributions:
WishartDistribution.java (+31 -5)
-
src/dr/math/matrixAlgebra:
LUPDecomposition.java (+278 -268),
Matrix.java (new)
-
msuchard
2013-03-27 03:29
#82
Rev.: 5543
-
15 lines of code changed in 4 files:
-
src/dr/inference/model:
Variable.java (new)
-
src/dr/inference/operators:
RandomWalkOperator.java (new)
-
julia.pal.r@gmail.com
2013-03-26 06:36
#81
Rev.: 5542
-
23 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GPSkytrackAnalysis.java (+20 -18)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+3 -2)
-
rambaut
2013-03-26 05:04
#80
Rev.: 5541
-
67 lines of code changed in 1 file:
-
src/dr/evomodelxml/tree:
TreeLoggerParser.java (+67 -31)
-
fbielejec
2013-03-26 03:34
#79
Rev.: 5540
-
0 lines of code changed in 1 file:
-
src/dr/app/bss/icons:
bubble-blue.png (new)
-
fbielejec
2013-03-26 02:24
#78
Rev.: 5539
-
24 lines of code changed in 7 files:
-
src/dr/app/bss:
JTableButtonCellRenderer.java (new),
PartitionDataList.java (+4 -2),
README.textile (+2 -2),
TreesPanel.java (+2),
TreesTableModel.java (+11 -22),
Utils.java (+3 -9)
-
fbielejec
2013-03-26 01:43
#77
Rev.: 5538
-
135 lines of code changed in 17 files:
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+1 -1),
BranchSubstitutionModelEditor.java (-10),
ClockRateModelEditor.java (+1 -2),
ColumnResizer.java (new),
JTableButtonCellRenderer.java (-1),
MainFrame.java (+77 -215),
PartitionDataList.java (+3 -5),
PartitionTableModel.java (-11),
PartitionsPanel.java (+1 -14),
README.textile (+1 -1),
SimulationPanel.java (+5 -131),
TaxaTableModel.java (new),
TreesPanel.java (+29 -10),
TreesTableModel.java (+9 -23),
XMLGenerator.java (-2)
-
fbielejec
2013-03-25 22:44
#76
Rev.: 5537
-
51 lines of code changed in 4 files:
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+11 -9),
MainFrame.java (+1 -1),
TreesTableModel.java (+22 -7),
Utils.java (+17)
-
fbielejec
2013-03-25 11:37
#75
Rev.: 5536
-
48 lines of code changed in 7 files:
-
src/dr/app/bss:
MainFrame.java (+17 -18),
PartitionData.java (+1 -3),
PartitionDataList.java (+1 -6),
README.textile (+1 -1),
TreePanel.java (del),
TreesPanel.java (-25),
TreesTableModel.java (+28 -6)
-
fbielejec
2013-03-25 09:14
#74
Rev.: 5535
-
33 lines of code changed in 5 files:
-
src/dr/app/bss:
PartitionDataList.java (+1 -1),
TaxaPanel.java (-1),
TreesPanel.java (+2),
TreesTableModel.java (+30 -5)
-
fbielejec
2013-03-25 08:43
#73
Rev.: 5534
-
225 lines of code changed in 8 files:
-
src/dr/app/bss:
MainFrame.java (+2 -2),
PartitionDataList.java (+2 -2),
TaxaPanel.java (+8),
TaxaTableModel.java (+45 -21),
TreePanel.java (new 52),
TreesPanel.java (+51 -67),
TreesTableModel.java (+39 -29),
Utils.java (+26 -9)
-
fbielejec
2013-03-25 04:18
#72
Rev.: 5533
-
174 lines of code changed in 7 files:
-
src/dr/app/bss:
JTableButtonCellRenderer.java (+42 -6),
MainFrame.java (+4 -6),
PartitionsPanel.java (+5 -108),
TreePanel.java (+3 -2),
TreesPanel.java (+27 -27),
TreesTableModel.java (+92 -15),
Utils.java (+1)
-
baele.guy@gmail.com
2013-03-24 01:04
#71
Rev.: 5532
-
63 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeModel.java (+63)
-
julia.pal.r@gmail.com
2013-03-23 09:39
#70
Rev.: 5531
-
24 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GPSkytrackAnalysis.java (+24 -107)
-
julia.pal.r@gmail.com
2013-03-23 07:40
#69
Rev.: 5530
-
148 lines of code changed in 6 files:
-
src/dr/evomodel/coalescent:
GPSkytrackAnalysis.java (+85 -61)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+59)
-
src/dr/evomodelxml/coalescent:
GPSkytrackAnalysisParser.java (+1 -1)
-
src/dr/evomodelxml/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperatorParser.java (new)
-
julia.pal.r@gmail.com
2013-03-23 04:33
#68
Rev.: 5529
-
495 lines of code changed in 7 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/coalescent:
GPSkytrackAnalysis.java (+361),
GaussianProcessSkytrackLikelihood.java (+16 -13)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+1 -1)
-
src/dr/evomodelxml/coalescent:
GPSkytrackAnalysisParser.java (+100),
GaussianProcessSkytrackLikelihoodParser.java (new)
-
fbielejec
2013-03-23 04:03
#67
Rev.: 5528
-
97 lines of code changed in 7 files:
-
src/dr/app/bss:
MainFrame.java (-1),
PartitionDataList.java (+2 -1),
PartitionTableModel.java (+10 -10),
PartitionsPanel.java (+2 -2),
TreesPanel.java (+21 -19),
TreesTableModel.java (+54 -38),
Utils.java (+8)
-
fbielejec
2013-03-23 03:20
#66
Rev.: 5527
-
111 lines of code changed in 7 files:
-
src/dr/app/bss:
MainFrame.java (+3),
PartitionTableModel.java (+2 -1),
PartitionsPanel.java (+33 -10),
TaxaPanel.java (+20 -20),
TaxaTableModel.java (+6 -3),
TreesPanel.java (+41 -8),
TreesTableModel.java (+6 -4)
-
fbielejec
2013-03-23 02:24
#65
-
498 lines of code changed in 12 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (-1)
-
src/dr/app/bss:
JTableButtonCellEditor.java (new 65),
JTableButtonCellRenderer.java (+34),
JTableButtonMouseListener.java (new 35),
MainFrame.java (+5 -2),
PartitionData.java (-1),
PartitionDataList.java (+3),
PartitionTableModel.java (+1 -1),
PartitionsPanel.java (+104 -109),
README.textile (+1 -3),
TreesPanel.java (+128),
TreesTableModel.java (+122)
-
fbielejec
2013-03-23 00:04
#64
Rev.: 5524
-
91 lines of code changed in 6 files:
-
src/dr/app/bss:
MainFrame.java (+1 -4),
PartitionData.java (+77 -41),
PartitionDataList.java (+3 -2),
README.textile (-1),
Utils.java (+3 -1),
XMLGenerator.java (+7)
-
fbielejec
2013-03-22 20:36
#63
Rev.: 5523
-
5 lines of code changed in 2 files:
-
src/dr/evolution/util:
Taxon.java (new)
-
fbielejec
2013-03-22 09:07
#62
Rev.: 5522
-
189 lines of code changed in 7 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+163 -258)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (new),
PartitionParser.java (+1 -1)
-
src/dr/app/bss:
MainFrame.java (+18 -10),
README.textile (+2 -5),
XMLGenerator.java (+4 -6)
-
fbielejec
2013-03-22 00:33
#61
Rev.: 5521
-
148 lines of code changed in 9 files:
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+1 -19),
Partition.java (+1 -2)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (-2)
-
src/dr/app/bss:
MainFrame.java (+1 -2),
PartitionData.java (+4),
PartitionDataList.java (+1 -2),
SimulationPanel.java (+7 -7),
Utils.java (+12 -3),
XMLGenerator.java (+121 -168)
-
fbielejec
2013-03-22 00:10
#60
-
50 lines of code changed in 7 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+3 -1)
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+12 -4)
-
src/dr/app/beagle/tools/parsers:
BeagleSequenceSimulatorParser.java (+18 -20)
-
src/dr/app/bss:
MainFrame.java (+6 -2),
XMLGenerator.java (+5 -4)
-
src/dr/app/tools:
LogCombiner.java (+6)
-
fbielejec
2013-03-21 23:45
#59
Rev.: 5518
-
150 lines of code changed in 3 files:
-
src/dr/app/bss:
README.textile (+2 -7),
Utils.java (+137 -155),
XMLGenerator.java (+11 -5)
-
julia.pal.r@gmail.com
2013-03-21 05:55
#58
Rev.: 5517
-
49 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+10 -3)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+28 -3)
-
src/dr/evomodelxml/coalescent:
GaussianProcessSkytrackLikelihoodParser.java (+11 -1)
-
fbielejec
2013-03-21 03:46
#57
Rev.: 5516
-
16 lines of code changed in 3 files:
-
src/dr/app/bss:
PartitionData.java (+1 -1),
Utils.java (+11 -2),
XMLGenerator.java (+4 -2)
-
fbielejec
2013-03-21 03:25
#56
Rev.: 5515
-
106 lines of code changed in 2 files:
-
src/dr/app/bss:
README.textile (+1 -1),
XMLGenerator.java (+105 -45)
-
fbielejec
2013-03-21 02:50
#55
Rev.: 5514
-
81 lines of code changed in 3 files:
-
src/dr/app/bss:
README.textile (+3 -2),
SiteRateModelEditor.java (+1 -1),
XMLGenerator.java (+77 -8)
-
fbielejec
2013-03-21 01:25
#54
Rev.: 5513
-
50 lines of code changed in 2 files:
-
src/dr/app/bss:
PartitionData.java (+43 -4),
README.textile (+7 -1)
-
msuchard
2013-03-20 12:29
#53
Rev.: 5512
-
154 lines of code changed in 9 files:
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (+80 -5),
MultivariateNormalDistributionModel.java (+2 -27)
-
src/dr/inference/operators:
AdaptableVarianceMultivariateNormalOperator.java (+9 -4)
-
src/dr/inferencexml/distribution:
MultivariateNormalDistributionModelParser.java (+2 -50)
-
src/dr/inferencexml/model:
CompoundLikelihoodParser.java (+3 -2)
-
src/dr/util:
Transform.java (+58 -12)
-
fbielejec
2013-03-20 10:28
#52
Rev.: 5511
-
74 lines of code changed in 2 files:
-
src/dr/app/bss:
PartitionData.java (+73 -60),
README.textile (+1 -2)
-
baele.guy@gmail.com
2013-03-19 21:31
#51
Rev.: 5510
-
5 lines of code changed in 1 file:
-
src/dr/inference/operators:
AdaptableVarianceMultivariateNormalOperator.java (+5 -4)
-
msuchard
2013-03-19 18:02
#50
Rev.: 5509
-
363 lines of code changed in 9 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/inference/distribution:
MultivariateNormalDistributionModel.java (+23 -3)
-
src/dr/inference/model:
MatrixParameter.java (new)
-
src/dr/inference/operators:
AdaptableVarianceMultivariateNormalOperator.java (+147 -256)
-
src/dr/inferencexml/distribution:
MultivariateNormalDistributionModelParser.java (+25 -2)
-
src/dr/math/distributions:
MultivariateNormalDistribution.java (new)
-
src/dr/util:
Transform.java (+114 -4)
-
fbielejec
2013-03-19 11:29
#49
Rev.: 5508
-
87 lines of code changed in 6 files:
-
src/dr/app/bss:
MainFrame.java (+58 -13),
PartitionsPanel.java (-2),
SimulationPanel.java (+9 -9),
TaxaPanel.java (+2 -113),
TreePanel.java (-31),
Utils.java (+18)
-
fbielejec
2013-03-19 09:56
#48
Rev.: 5507
-
309 lines of code changed in 6 files:
-
src/dr/app/bss:
PartitionDataList.java (+3 -3),
PartitionTableModel.java (+71 -71),
README.textile (+1),
SimulationPanel.java (+6 -6),
TaxaPanel.java (+110 -110),
TaxaTableModel.java (+118)
-
fbielejec
2013-03-19 09:04
#47
Rev.: 5506
-
169 lines of code changed in 9 files:
-
src/dr/app/bss:
FrequencyModelEditor.java (+1 -1),
MainFrame.java (+2 -5),
PartitionTableModel.java (+46 -50),
PartitionsPanel.java (+69 -102),
README.textile (-1),
SimulationPanel.java (+4),
TaxaPanel.java (+23 -21),
TreePanel.java (+5 -1),
Utils.java (+19 -6)
-
julia.pal.r@gmail.com
2013-03-19 05:49
#46
Rev.: 5505
-
126 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+126 -5)
-
julia.pal.r@gmail.com
2013-03-19 03:57
#45
Rev.: 5504
-
19 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+19 -144)
-
fbielejec
2013-03-19 03:34
#44
Rev.: 5503
-
28 lines of code changed in 4 files:
-
src/dr/app/bss:
MainFrame.java (+3 -1),
PartitionsPanel.java (-2),
README.textile (+1 -1),
TaxaPanel.java (+24 -10)
-
fbielejec
2013-03-19 03:07
#43
Rev.: 5502
-
17 lines of code changed in 2 files:
-
src/dr/app/bss:
PartitionsPanel.java (+16 -6),
README.textile (+1 -1)
-
fbielejec
2013-03-19 02:35
#42
Rev.: 5501
-
7 lines of code changed in 1 file:
-
src/dr/app/bss:
PartitionsPanel.java (+7 -42)
-
fbielejec
2013-03-19 02:19
#41
Rev.: 5500
-
49 lines of code changed in 1 file:
-
src/dr/app/bss:
PartitionsPanel.java (+49 -81)
-
fbielejec
2013-03-19 01:48
#40
Rev.: 5499
-
157 lines of code changed in 2 files:
-
src/dr/app/bss:
PartitionTableModel.java (-1),
PartitionsPanel.java (+157 -93)
-
fbielejec
2013-03-19 01:22
#39
Rev.: 5498
-
62 lines of code changed in 4 files:
-
src/dr/app/bss:
BranchSubstitutionModelEditor.java (+2),
PartitionTableModel.java (+52 -16),
PartitionsPanel.java (+1 -1),
Utils.java (+7 -7)
-
fbielejec
2013-03-19 00:41
#38
Rev.: 5497
-
24 lines of code changed in 7 files:
-
src/dr/app/bss:
BranchSubstitutionModelEditor.java (+9 -1),
ClockRateModelEditor.java (+1),
FrequencyModelEditor.java (+1),
PartitionTableModel.java (+2 -2),
PartitionsPanel.java (+2 -2),
SiteRateModelEditor.java (+1),
Utils.java (+8)
-
fbielejec
2013-03-18 22:56
#37
Rev.: 5496
-
44 lines of code changed in 7 files:
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+1 -1),
MainFrame.java (+3 -1),
PartitionData.java (+10 -3),
PartitionTableModel.java (+15),
PartitionsPanel.java (+12 -7),
README.textile (+1 -4),
XMLGenerator.java (+2)
-
fbielejec
2013-03-18 21:11
#36
Rev.: 5495
-
147 lines of code changed in 10 files:
-
src/dr/app/bss:
BranchSubstitutionModelEditor.java (+6 -1),
ClockRateModelEditor.java (+7 -2),
FrequencyModelEditor.java (+6 -1),
MainFrame.java (+13 -11),
PartitionData.java (+52 -67),
PartitionTableModel.java (+9 -1),
PartitionsPanel.java (+38 -11),
README.textile (+1),
SiteRateModelEditor.java (+6 -1),
Utils.java (+9 -1)
-
julia.pal.r@gmail.com
2013-03-17 23:27
#35
Rev.: 5494
-
74 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+16 -3)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+58 -28)
-
julia.pal.r@gmail.com
2013-03-16 06:09
#34
Rev.: 5493
-
13 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+13 -9)
-
julia.pal.r@gmail.com
2013-03-16 04:37
#33
Rev.: 5492
-
49 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+2 -2)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+47 -43)
-
baele.guy@gmail.com
2013-03-16 04:10
#32
Rev.: 5491
-
160 lines of code changed in 1 file:
-
src/dr/inference/operators:
AdaptableVarianceMultivariateNormalOperator.java (+160 -32)
-
julia.pal.r@gmail.com
2013-03-15 15:48
#31
Rev.: 5490
-
376 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+85 -33)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+232 -93)
-
src/dr/evomodelxml/coalescent:
GaussianProcessSkytrackLikelihoodParser.java (+59 -3)
-
fbielejec
2013-03-14 23:50
#30
Rev.: 5489
-
34 lines of code changed in 4 files:
-
src/dr/app/bss:
MainFrame.java (+8 -4),
PartitionData.java (+5 -5),
PartitionTableModel.java (+1 -1),
PartitionsPanel.java (+20 -8)
-
rambaut
2013-03-14 08:34
#29
Rev.: 5488
-
1367 lines of code changed in 17 files:
-
src/dr/app/mapper/application:
LocationsPanel.java (new 714),
MapperApp.java (new),
MapperDefaultFileMenuFactory.java (del),
MapperDocument.java (+132 -7),
MapperFileMenuHandler.java (del),
MapperFrame.java (+214 -16),
MapperMacFileMenuFactory.java (del),
MapperMenuBarFactory.java (del),
MeasurementsPanel.java (+32 -24)
-
src/dr/app/mapper/application/menus:
MapperDefaultFileMenuFactory.java (new 93),
MapperFileMenuHandler.java (new 21),
MapperMacFileMenuFactory.java (new 131),
MapperMenuBarFactory.java (new 28)
-
fbielejec
2013-03-14 03:21
#28
Rev.: 5487
-
104 lines of code changed in 4 files:
-
src/dr/app/bss:
MainFrame.java (+33 -8),
PartitionData.java (+67 -52),
PartitionsPanel.java (+1 -2)
-
src/dr/app/bss/test:
Test.java (new 3)
-
fbielejec
2013-03-14 02:57
#27
Rev.: 5486
-
6 lines of code changed in 1 file:
-
src/dr/app/bss:
PartitionData.java (+6 -11)
-
fbielejec
2013-03-14 02:46
#26
Rev.: 5485
-
76 lines of code changed in 8 files:
-
src/dr/app/bss:
MainFrame.java (+4 -4),
PartitionData.java (+8 -1),
PartitionDataList.java (+10 -13),
PartitionsPanel.java (+4 -3),
TreePanel.java (+1 -1),
Utils.java (+41 -1),
XMLGenerator.java (+3 -3)
-
src/dr/app/bss/test:
Test.java (+5 -2)
-
fbielejec
2013-03-14 01:52
#25
Rev.: 5484
-
20 lines of code changed in 4 files:
-
src/dr/app/bss:
MainFrame.java (+1 -1),
PartitionDataList.java (+1 -1),
Utils.java (+1 -1)
-
src/dr/app/bss/test:
Test.java (+17 -6)
-
fbielejec
2013-03-14 00:46
#24
Rev.: 5483
-
89 lines of code changed in 2 files:
-
src/dr/app/bss:
Utils.java (+23 -20)
-
src/dr/app/bss/test:
Test.java (+66)
-
rambaut
2013-03-14 00:00
#23
Rev.: 5482
-
158 lines of code changed in 7 files:
-
src/dr/app/beast:
release_parsers.properties (+1)
-
src/dr/evomodel/branchratemodel:
AttributeBranchRateModel.java (new 73)
-
src/dr/evomodel/tree:
EmpiricalTreeDistributionModel.java (+2 -61)
-
src/dr/evomodelxml:
EmpiricalTreeDistributionModelParser.java (new)
-
src/dr/evomodelxml/branchratemodel:
AttributeBranchRateModelParser.java (new 81)
-
fbielejec
2013-03-13 22:49
#22
Rev.: 5481
-
154 lines of code changed in 5 files:
-
src/dr/app/bss:
MainFrame.java (+21 -3),
PartitionData.java (+3 -1),
PartitionDataList.java (+2 -1),
README.textile (+10 -6),
Utils.java (+118 -64)
-
rambaut
2013-03-13 08:37
#21
Rev.: 5480
-
22 lines of code changed in 1 file:
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+22 -9)
-
julia.pal.r@gmail.com
2013-03-13 05:50
#20
Rev.: 5479
-
33 lines of code changed in 2 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+5 -1)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+28 -20)
-
tbcbedford@gmail.com
2013-03-13 03:49
#19
Rev.: 5478
-
781 lines of code changed in 1 file:
-
src/dr/evomodel/antigenic:
AntigenicLikelihoodSimple.java (+781)
-
rambaut
2013-03-13 00:12
#18
Rev.: 5477
-
3 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
EmpiricalTreeDistributionModel.java (+3 -1)
-
msuchard
2013-03-12 08:53
#17
Rev.: 5476
-
6 lines of code changed in 2 files:
-
src/dr/inferencexml/distribution:
BinomialLikelihoodParser.java (+6 -1)
-
julia.pal.r@gmail.com
2013-03-12 06:39
#16
Rev.: 5475
-
9 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+9 -4)
-
rambaut
2013-03-11 01:12
#15
Rev.: 5474
-
2064 lines of code changed in 18 files:
-
src/dr/app/beauti/options:
DateGuesser.java (+19 -5)
-
src/dr/app/mapper/application:
GeneralPreferencesSection.java (new),
MapperApp.java (+47 -22),
MapperDefaultFileMenuFactory.java (new 23),
MapperDocument.java (+77),
MapperFileMenuHandler.java (new 9),
MapperFrame.java (+210 -736),
MapperFrameOld.java (new 865),
MapperMacFileMenuFactory.java (new 48),
MapperMenuBarFactory.java (new 2),
MeasurementsPanel.java (+236),
StrainsPanel.java (new 437)
-
src/dr/app/mapper/application/images:
Mapper.png (changed)
-
src/dr/app/mapper/application/mapper:
Analysis.java (new 53),
AnalysisListener.java (new 36),
MapperPanel.java (new)
-
rambaut
2013-03-07 21:58
#14
Rev.: 5473
-
1 lines of code changed in 2 files:
-
src/dr/evomodel/antigenic:
MultidimensionalScalingLikelihood.java (+1 -2)
-
rambaut
2013-03-07 21:56
#13
Rev.: 5472
-
74 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/tree:
EmpiricalTreeDistributionModel.java (+64 -5)
-
src/dr/evomodelxml:
EmpiricalTreeDistributionModelParser.java (+9 -1)
-
julia.pal.r@gmail.com
2013-03-06 06:39
#12
Rev.: 5471
-
17 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+17 -3)
-
fbielejec
2013-03-05 02:57
#11
Rev.: 5470
-
72 lines of code changed in 5 files:
-
src/dr/app/bss:
DefaultFileMenuFactory.java (+8 -10),
FileMenuHandler.java (new),
MainFrame.java (+60 -32),
README.textile (+1 -1)
-
fbielejec
2013-03-05 02:05
#10
Rev.: 5469
-
48 lines of code changed in 1 file:
-
src/dr/app/bss:
SimpleFileFilter.java (new 48)
-
fbielejec
2013-03-05 02:04
#9
Rev.: 5468
-
162 lines of code changed in 8 files:
-
src/dr/app/beagle/evomodel/parsers:
EpochBranchModelParser.java (+13 -10)
-
src/dr/app/beagle/tools:
BeagleSequenceSimulator.java (+1 -2)
-
src/dr/app/bss:
BeagleSequenceSimulatorApp.java (+4 -3),
DefaultFileMenuFactory.java (+11 -2),
MainFrame.java (+120 -88),
MenuBarFactory.java (+6 -23),
Utils.java (+7)
-
baele.guy@gmail.com
2013-03-04 21:47
#8
Rev.: 5467
-
59 lines of code changed in 1 file:
-
src/dr/inference/operators:
AdaptableVarianceMultivariateNormalOperator.java (+59 -22)
-
msuchard
2013-03-04 16:17
#7
Rev.: 5466
-
36 lines of code changed in 2 files:
-
src/dr/inference/model:
EqualityConstrainedParameter.java (+36 -40)
-
msuchard
2013-03-03 15:46
#6
Rev.: 5465
-
293 lines of code changed in 4 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/inference/model:
EqualityConstrainedParameter.java (+253),
EqualityConstraintModel.java (new)
-
julia.pal.r@gmail.com
2013-03-03 11:11
#5
Rev.: 5464
-
349 lines of code changed in 3 files:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+15 -17)
-
src/dr/evomodel/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperator.java (+333 -358)
-
src/dr/evomodelxml/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperatorParser.java (+1)
-
julia.pal.r@gmail.com
2013-03-02 12:56
#4
Rev.: 5463
-
5 lines of code changed in 1 file:
-
src/dr/evomodelxml/coalescent/operators:
GaussianProcessSkytrackBlockUpdateOperatorParser.java (+5 -5)
-
julia.pal.r@gmail.com
2013-03-02 08:02
#3
Rev.: 5462
-
48 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
GaussianProcessSkytrackLikelihood.java (+48 -40)
-
msuchard
2013-03-01 16:40
#2
Rev.: 5461
-
146 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+4 -1)
-
src/dr/inference/model:
EqualityConstraintModel.java (+142)
-
dong.w.xie@gmail.com
2013-03-01 15:19
#1
Rev.: 5460
-
260 lines of code changed in 22 files:
-
src/dr/app/tracer/application:
TracerApp.java (+1 -1),
TracerFrame.java (+1 -1)
-
src/dr/app/tracer/traces:
FilterAbstractPanel.java (new),
FilterContinuousPanel.java (+5 -4),
FilterDiscretePanel.java (new),
FilterListPanel.java (+109 -51)
-
src/dr/inference/trace:
AbstractTraceList.java (+1 -1),
Filter.java (new),
FilteredTraceList.java (+37 -37),
LogFileTraces.java (new),
Trace.java (+40 -39)