-
alexei.drummond
2008-07-31 01:34
#87
Rev.: 1075
-
2 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1),
BeautiTester.java (+1 -1)
-
alexei.drummond
2008-07-31 01:25
#86
Rev.: 1074
-
40 lines of code changed in 1 file:
-
src/dr/app/beauti:
NexusApplicationImporter.java (+40 -33)
-
alexei.drummond
2008-07-30 23:41
#85
Rev.: 1073
-
36 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -4),
PartitionModelGenerator.java (+31 -43)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1)
-
alexei.drummond
2008-07-30 23:10
#84
Rev.: 1072
-
8 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -4)
-
alexei.drummond
2008-07-30 22:59
#83
Rev.: 1071
-
46 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -3),
BeautiTester.java (+3 -3),
NexusApplicationImporter.java (+32 -15)
-
src/dr/app/beauti/options:
OperatorType.java (+5 -5)
-
alexei.drummond
2008-07-30 20:50
#82
Rev.: 1070
-
191 lines of code changed in 6 files:
-
src/dr/app/beauti:
ModelsPanel.java (new 140)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
PartitionModelGenerator.java (+23 -35)
-
src/dr/app/beauti/options:
Operator.java (+3 -1),
Parameter.java (+1),
PartitionModel.java (+23 -3)
-
alexei.drummond
2008-07-30 19:40
#81
Rev.: 1069
-
22 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiTester.java (+22 -18)
-
alexei.drummond
2008-07-30 19:17
#80
Rev.: 1068
-
122 lines of code changed in 7 files:
-
src/dr/app/beauti:
ModelsPanel.java (+2 -2)
-
src/dr/app/beauti/options:
AAModelType.java (del),
AminoAcidModelType.java (+45),
ModelOptions.java (-2),
PartitionModel.java (+65 -107)
-
src/dr/app/tools:
BeastOptions.java (+2 -2)
-
src/dr/evomodel/substmodel:
EmpiricalAminoAcidModel.java (+8 -8)
-
rambaut
2008-07-30 09:30
#79
Rev.: 1067
-
459 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiTester.java (+453 -363)
-
src/dr/app/beauti/options:
BeautiOptions.java (+6 -2)
-
alexei.drummond
2008-07-30 05:30
#78
Rev.: 1066
-
261 lines of code changed in 11 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1),
DataPanel.java (+13 -8),
ModelsPanel.java (+58 -37)
-
src/dr/app/beauti/generator:
BeastGenerator.java (-1),
PartitionModelGenerator.java (+18 -26)
-
src/dr/app/beauti/options:
AAModelType.java (new 45),
ModelOptions.java (+4 -11),
Operator.java (+2 -18),
PartitionModel.java (+3 -9)
-
src/dr/app/tools:
BeastOptions.java (+3 -31)
-
src/dr/evomodel/substmodel:
EmpiricalAminoAcidModel.java (+114 -111)
-
alexei.drummond
2008-07-30 02:17
#77
Rev.: 1065
-
71 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+2),
ModelsPanel.java (+19 -10)
-
src/dr/app/beauti/generator:
PartitionModelGenerator.java (+10 -8)
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -2),
FrequencyPolicy.java (+19),
ModelOptions.java (-4),
PartitionModel.java (+14 -10)
-
rambaut
2008-07-29 23:44
#76
Rev.: 1064
-
836 lines of code changed in 10 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1),
DataPanel.java (+2 -2),
ModelsPanel.java (+1 -1),
NexusApplicationImporter.java (+1 -1),
PriorsPanel.java (new 451)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -4),
PartitionModelGenerator.java (+26 -57),
TreeLikelihoodGenerator.java (+12 -11)
-
src/dr/app/beauti/options:
Parameter.java (+5 -4),
PartitionModel.java (+333 -182)
-
rambaut
2008-07-29 21:52
#75
Rev.: 1063
-
128 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
PartitionModelGenerator.java (+125 -88)
-
src/dr/app/beauti/options:
PartitionModel.java (+3 -2)
-
alexei.drummond
2008-07-29 21:37
#74
Rev.: 1062
-
21 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+8 -5),
PartitionModelGenerator.java (+13 -13)
-
alexei.drummond
2008-07-29 21:15
#73
Rev.: 1061
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
DataPartition.java (+1 -4)
-
rambaut
2008-07-29 12:55
#72
Rev.: 1060
-
28 lines of code changed in 3 files:
-
src/dr/app/beauti:
DataPanel.java (+1 -1)
-
src/dr/app/beauti/options:
DataPartition.java (+12 -1),
PartitionModel.java (+15 -15)
-
alexei.drummond
2008-07-29 12:43
#71
Rev.: 1059
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
DataPartition.java (+1 -4)
-
rambaut
2008-07-29 12:33
#70
Rev.: 1058
-
326 lines of code changed in 8 files:
-
src/dr/app/beauti:
ModelsPanel.java (+27 -27),
NexusApplicationImporter.java (+12 -12)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+67 -43),
PartitionModelGenerator.java (+53 -53),
TreeLikelihoodGenerator.java (+26 -45)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
DataPartition.java (-12),
PartitionModel.java (+140 -38)
-
rambaut
2008-07-29 11:04
#69
Rev.: 1057
-
66 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -1),
PartitionModelGenerator.java (+11 -11)
-
src/dr/app/beauti/options:
BeautiOptions.java (+25 -7),
DataPartition.java (+5),
ModelOptions.java (+1 -1),
PartitionModel.java (+22 -1)
-
rambaut
2008-07-29 10:11
#68
Rev.: 1056
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1)
-
rambaut
2008-07-29 10:03
#67
Rev.: 1055
-
7 lines of code changed in 2 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -8),
PartitionModel.java (-1)
-
rambaut
2008-07-29 04:13
#66
Rev.: 1054
-
293 lines of code changed in 7 files:
-
examples:
testRelaxedClock.xml (+30 -18)
-
src/dr/app/beauti:
ModelsPanel.java (+12 -16)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+20 -4),
PartitionModelGenerator.java (+46 -21)
-
src/dr/app/beauti/options:
BeautiOptions.java (+47 -7),
PartitionModel.java (+26 -24)
-
src/dr/evolution/coalescent:
ExponentialGrowth.java (+112 -99)
-
alexei.drummond
2008-07-29 02:22
#65
Rev.: 1053
-
36 lines of code changed in 3 files:
-
src/dr/app/beauti:
ModelsPanel.java (+21 -15)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+4 -8)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -5)
-
alexei.drummond
2008-07-28 09:58
#64
Rev.: 1052
-
34 lines of code changed in 6 files:
-
src/dr/app/beauti:
ModelsPanel.java (+9 -26),
PanelUtils.java (new 2)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+4 -4)
-
src/dr/app/beauti/options:
BeautiOptions.java (+13 -9),
ClockType.java (+4 -5),
PartitionModel.java (+2 -2)
-
alexei.drummond
2008-07-28 09:11
#63
Rev.: 1051
-
73 lines of code changed in 10 files:
-
src/dr/app/beauti:
ModelsPanel.java (+5 -43),
PriorsPanel.java (+1 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+9 -9),
BranchRatesModelGenerator.java (+5 -5),
TreeLikelihoodGenerator.java (+2 -5),
TreeModelGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+25 -42),
ClockType.java (+23),
ModelOptions.java (-5),
TreePrior.java (+1 -5)
-
alexei.drummond
2008-07-28 08:32
#62
Rev.: 1050
-
14 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+14 -15)
-
rambaut
2008-07-27 11:00
#61
Rev.: 1049
-
20 lines of code changed in 3 files:
-
src/dr/app/beauti:
CreateModelDialog.java (new 1),
DataPanel.java (+17 -5),
SelectModelDialog.java (new 2)
-
rambaut
2008-07-27 10:35
#60
Rev.: 1048
-
54 lines of code changed in 3 files:
-
src/dr/app/beauti:
DataPanel.java (+12 -18),
PriorsPanel.java (+21 -43)
-
src/dr/app/beauti/options:
TreePrior.java (+21 -1)
-
alexei.drummond
2008-07-27 09:59
#59
Rev.: 1047
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
TreeLikelihoodGenerator.java (+2 -3)
-
rambaut
2008-07-27 09:59
#58
Rev.: 1046
-
50 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -4),
DataPanel.java (+42 -4),
ModelsPanel.java (+4)
-
src/dr/app/beauti/options:
PartitionModel.java (+3)
-
alexei.drummond
2008-07-27 09:50
#57
Rev.: 1045
-
115 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+20 -16),
PartitionModelGenerator.java (+46 -22),
TreeLikelihoodGenerator.java (+31 -28)
-
src/dr/app/beauti/options:
DataPartition.java (+14 -3),
PartitionModel.java (+4)
-
alexei.drummond
2008-07-27 08:48
#56
Rev.: 1044
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
Generator.java (+3 -3)
-
alexei.drummond
2008-07-27 08:45
#55
Rev.: 1043
-
34 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+34 -22)
-
alexei.drummond
2008-07-26 22:38
#54
Rev.: 1042
-
971 lines of code changed in 22 files:
-
src/dr/app/beast:
BeastParser.java (+1 -1)
-
src/dr/app/beauti:
DataPanel.java (+13 -10),
ModelsPanel.java (+60 -45),
NexusApplicationImporter.java (+4 -3),
XMLWriter.java (+65 -55)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+50 -52),
BranchRatesModelGenerator.java (+10 -20),
Generator.java (+37 -6),
InitialTreeGenerator.java (+3 -3),
PartitionModelGenerator.java (+52 -79),
TreeLikelihoodGenerator.java (+3 -2),
TreeModelGenerator.java (+2 -1),
TreePriorGenerator.java (+28 -37)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4 -3),
ModelOptions.java (+25 -13),
NucModelType.java (+13),
Operator.java (+14 -8),
PartitionModel.java (+2 -2)
-
src/dr/app/tools:
BeastOptions.java (+16 -15)
-
src/dr/evolution/alignment:
SitePatterns.java (+456 -419)
-
src/dr/evomodel/substmodel:
HKY.java (+54 -94)
-
src/dr/evomodelxml:
HKYParser.java (+59)
-
alexei.drummond
2008-07-26 05:06
#53
Rev.: 1037
-
3608 lines of code changed in 20 files:
-
src/dr/app/beauti:
BeastGenerator.java (del),
BeautiFrame.java (+6 -3),
CommandLineBeauti.java (+5 -2),
NexusApplicationImporter.java (+16 -15),
PriorsPanel.java (+6 -19)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1309),
BranchRatesModelGenerator.java (+225),
Generator.java (+140),
InitialTreeGenerator.java (+173),
PartitionModelGenerator.java (+615),
TreeLikelihoodGenerator.java (+149),
TreeModelGenerator.java (+74),
TreePriorGenerator.java (+569)
-
src/dr/app/beauti/options:
AbstractModelOptions.java (del),
BeautiOptions.java (+80 -65),
ModelOptions.java (+128),
Operator.java (+20 -5),
OperatorType.java (+37),
PartitionModel.java (+46 -50),
TreePrior.java (+10)
-
rambaut
2008-07-25 11:20
#52
Rev.: 1033
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti:
ModelsPanel.java (+4 -3)
-
rambaut
2008-07-25 11:17
#51
Rev.: 1032
-
227 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeautiFrame.java (+33 -17),
ModelsPanel.java (+38 -44),
NexusApplicationImporter.java (+133 -238),
PanelUtils.java (+2 -1)
-
src/dr/app/beauti/options:
DataPartition.java (+21 -3)
-
rambaut
2008-07-25 08:07
#50
Rev.: 1031
-
3673 lines of code changed in 13 files:
-
src/dr/app/beauti:
BeastGenerator.java (new 2874),
BeautiFrame.java (+47 -36),
CreateModelDialog.java (+111),
DataPanel.java (+169 -12),
ModelsPanel.java (+204 -131),
OperatorsPanel.java (+2 -1),
PanelUtils.java (+59),
SamplesPanel.java (+30 -20),
SelectModelDialog.java (+125)
-
src/dr/app/beauti/options:
AbstractModelOptions.java (new 1),
BeautiOptions.java (+13),
DataPartition.java (+4),
PartitionModel.java (+34 -3)
-
alexei.drummond
2008-07-24 10:03
#49
Rev.: 1029
-
22 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+22 -21)
-
alexei.drummond
2008-07-24 10:01
#48
Rev.: 1028
-
65 lines of code changed in 5 files:
-
src/dr/app/beauti:
OperatorsPanel.java (+1 -1)
-
src/dr/app/beauti/options:
AbstractModelOptions.java (+1 -1),
BeautiOptions.java (+5),
Operator.java (+16 -3),
PartitionModel.java (+42 -31)
-
rambaut
2008-07-24 04:39
#47
Rev.: 1027
-
13 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1),
ModelsPanel.java (+12 -7)
-
alexei.drummond
2008-07-24 04:37
#46
Rev.: 1026
-
58 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+21 -9),
Parameter.java (+21 -9),
PartitionModel.java (+16 -3)
-
rambaut
2008-07-24 04:23
#45
Rev.: 1025
-
113 lines of code changed in 4 files:
-
src/dr/app/beauti:
DataPanel.java (+2 -3),
ModelsPanel.java (+82 -69)
-
src/dr/app/beauti/options:
BeautiOptions.java (+29),
PartitionModel.java (-26)
-
alexei.drummond
2008-07-24 03:52
#44
Rev.: 1024
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1)
-
rambaut
2008-07-24 03:45
#43
-
3034 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeastGenerator.java (+2874 -2874),
ModelsPanel.java (+19 -29),
NexusApplicationImporter.java (+141 -141)
-
alexei.drummond
2008-07-24 03:44
#42
-
38 lines of code changed in 3 files:
-
src/dr/app/beauti:
SamplesPanel.java (+27 -31)
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -10),
PartitionModel.java (+4)
-
rambaut
2008-07-24 03:36
#41
-
392 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeautiFrame.java (+72 -60),
BeautiTester.java (+316 -313),
CommandLineBeauti.java (+1 -1),
ModelsPanel.java (+2 -2)
-
alexei.drummond
2008-07-24 03:34
#40
Rev.: 1016
-
15 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
DataPartition.java (+15)
-
alexei.drummond
2008-07-24 03:29
#39
-
48 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+33 -24),
DataPartition.java (+11),
PartitionModel.java (+4)
-
alexei.drummond
2008-07-24 03:20
#38
Rev.: 1012
-
91 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
BeautiOptions.java (+91)
-
rambaut
2008-07-24 03:15
#37
Rev.: 1011
-
691 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+11 -11),
ModelPanel.java (del),
ModelsPanel.java (+680)
-
alexei.drummond
2008-07-24 03:10
#36
Rev.: 1010
-
3833 lines of code changed in 36 files:
-
src/dr/app/beauti:
BeastGenerator.java (+23 -19),
BeautiOptions.java (del),
BeautiTester.java (+42 -46),
CommandLineBeauti.java (+12 -10),
DataPanel.java (+21 -24),
DiscretePriorDialog.java (+99 -96),
MCMCPanel.java (+86 -85),
ModelPanel.java (new 345),
NexusApplicationImporter.java (+349 -362),
OperatorsPanel.java (+13 -11),
PartitionsPanel.java (+29 -26),
PriorDialog.java (new 180),
PriorType.java (new 23),
PriorsPanel.java (+4 -2),
SamplesPanel.java (+67 -44),
TaxaPanel.java (+54 -37)
-
src/dr/app/beauti/options:
AbstractModelOptions.java (+152),
BeautiOptions.java (+866),
DataPartition.java (+45),
DateGuesser.java (+156),
Operator.java (+68),
Parameter.java (+181),
PartitionModel.java (+393)
-
src/dr/evomodel/speciation:
SpeciationLikelihood.java (+56 -31)
-
src/dr/evomodel/tree:
TreeHeightStatistic.java (new 40),
TreeModel.java (+9 -46),
TreeModelParser.java (new 291),
TreelengthStatistic.java (new)
-
src/dr/inference/loggers:
ArrayLogFormatter.java (+35 -2),
TabDelimitedFormatter.java (new)
-
src/dr/inference/model:
Parameter.java (+27 -9)
-
src/dr/inference/trace:
AbstractTraceList.java (+39),
ArrayTraceList.java (+93),
LogFileTraces.java (+25 -50),
TraceList.java (+4 -4)
-
rambaut
2008-07-23 11:42
#35
Rev.: 1009
-
2319 lines of code changed in 12 files:
-
src/dr/app/beauti:
BeastGenerator.java (+99 -74),
BeautiFrame.java (+108 -63),
BeautiOptions.java (new 934),
BeautiTester.java (+133 -137),
CommandLineBeauti.java (+170 -158),
DataPanel.java (+22 -529),
ModelPanel.java (+2 -2),
PartitionsPanel.java (+209),
SamplesPanel.java (+628),
TaxaPanel.java (+1 -1)
-
src/dr/app/util:
Utils.java (+12 -12)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+1 -1)
-
rambaut
2008-07-23 04:52
#34
Rev.: 1007
-
553 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeastGenerator.java (+22),
BeautiOptions.java (+12 -3)
-
src/dr/app/tools:
NexusExporter.java (+154 -154)
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+3 -2)
-
src/dr/evomodel/transmission:
TransmissionDemographicModel.java (+354 -354)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+4),
YuleModelParser.java (+4)
-
alexei.drummond
2008-07-22 22:05
#33
Rev.: 1002
-
1405 lines of code changed in 32 files:
-
src/dr/evolution/io:
NewickImporter.java (+177 -174)
-
src/dr/evomodel/coalescent/operators:
GMRFSkyrideBlockUpdateOperator.java (+5 -12)
-
src/dr/evomodel/operators:
BitFlipInSubstitutionModelOperator.java (+137 -150),
ColouredOperator.java (+5 -4),
ColouredSubtreeSlideOperator.java (+5 -12),
FNPR.java (+119 -130),
FixedColouredOperator.java (+5 -4),
RandomWalkOnMapOperator.java (+133 -147),
SubtreeSlideOperator.java (+7 -10)
-
src/dr/inference/loggers:
ArrayLogFormatter.java (+39),
LogFormatter.java (+12 -19),
TabDelimitedFormatter.java (+43 -42)
-
src/dr/inference/markovchain:
MarkovChain.java (+277 -277)
-
src/dr/inference/mcmc:
MCMC.java (+2 -2)
-
src/dr/inference/mcmcmc:
MCMCMC.java (+8 -6)
-
src/dr/inference/operators:
AbstractCoercableOperator.java (+17),
CenteredScaleOperator.java (+5 -18),
CoercableMCMCOperator.java (new),
CoercionMode.java (new 23),
DeltaExchangeOperator.java (+6 -17),
JointOperator.java (+6 -6),
LNVarianceOperator.java (+51 -60),
MCMCOperator.java (+3 -3),
MVOUCovarianceOperator.java (+136 -151),
MultivariateNormalOperator.java (+4 -18),
RandomWalkOperator.java (+131 -142),
ScaleOperator.java (+6 -13),
SimpleMCMCOperator.java (+4 -4),
UpDownOperator.java (+7 -17)
-
alexei.drummond
2008-07-22 03:50
#32
Rev.: 999
-
29 lines of code changed in 4 files:
-
examples/treePriors:
testYuleModel.xml (+1 -7)
-
src/dr/app/beauti:
BeastGenerator.java (+2 -25)
-
src/dr/inference/trace:
TraceAnalysisParser.java (+2 -2)
-
src/test/dr/evomodel/substmodel:
HKYTest.java (+24 -21)
-
alexei.drummond
2008-07-22 03:08
#31
Rev.: 998
-
84 lines of code changed in 2 files:
-
src/dr/app/beauti:
BeastGenerator.java (+11 -13),
BeautiOptions.java (+73 -75)
-
alexei.drummond
2008-07-22 03:03
#30
Rev.: 997
-
113 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastParser.java (+2 -3)
-
src/dr/evomodel/speciation:
BirthDeathGernhard08Model.java (-46),
YuleModel.java (-47)
-
src/dr/evomodelxml:
BirthDeathModelParser.java (+58),
YuleModelParser.java (+53)
-
jheled
2008-07-17 21:33
#29
Rev.: 996
-
2 lines of code changed in 1 file:
-
src/dr/inference/operators:
UpDownOperator.java (+2 -2)
-
jheled
2008-07-17 20:50
#28
Rev.: 995
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeLogger.java (+2 -1)
-
jheled
2008-07-17 20:42
#27
Rev.: 994
-
18 lines of code changed in 2 files:
-
src/dr/evomodel/tree:
TreeLogger.java (+15 -13)
-
src/dr/evomodelxml:
TreeLoggerParser.java (+3 -1)
-
alexei.drummond
2008-07-17 20:30
#26
Rev.: 993
-
137 lines of code changed in 2 files:
-
build_release.xml (+135 -133)
-
src/dr/app/beauti:
BeautiDefaultFileMenuFactory.java (+2 -2)
-
alexei.drummond
2008-07-15 05:25
#25
Rev.: 992
-
2066 lines of code changed in 5 files:
-
src/dr/evolution/io:
NexusImporter.java (+925 -940)
-
src/dr/evolution/tree:
Tree.java (+840 -838)
-
src/dr/evoxml:
NewickParser.java (+10 -4)
-
src/dr/inference/model:
CompoundParameter.java (+182 -178),
MatrixParameter.java (+109 -109)
-
alexei.drummond
2008-07-14 19:10
#24
Rev.: 991
-
81 lines of code changed in 3 files:
-
src/dr/evomodelxml:
TreeLoggerParser.java (+1 -1)
-
src/dr/inference/loggers:
Columns.java (+1 -1)
-
src/dr/xml:
Report.java (+79 -68)
-
bloomquist
2008-07-14 10:06
#23
Rev.: 990
-
216 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+216 -216)
-
alexei.drummond
2008-07-12 01:49
#22
Rev.: 989
-
2347 lines of code changed in 36 files:
-
src/dr/evolution/distance:
DistanceMatrix.java (+186 -284)
-
src/dr/evomodel/branchratemodel:
RateEpochBranchRateModel.java (+161 -165)
-
src/dr/evomodel/clock:
NDLikelihood.java (+2 -4)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+2 -4),
PopSizeStatistic.java (+49 -46)
-
src/dr/evomodel/continuous:
BivariateDiscreteDiffusionModel.java (+133 -137)
-
src/dr/evomodel/operators:
SubtreeSlideOperator.java (+1 -4),
TreeBitMoveOperator.java (-2)
-
src/dr/evomodel/sitemodel:
CategoryParameterStatistic.java (new)
-
src/dr/evomodel/tree:
CompatibilityStatistic.java (+130 -119),
ExternalLengthStatistic.java (+57 -50),
MRCATraitStatistic.java (+29 -21),
MonophylyStatistic.java (+107 -96),
ParsimonyStateStatistic.java (+90 -82),
ParsimonyStatistic.java (+73 -66),
RateCovarianceStatistic.java (+62 -54),
RateStatistic.java (+63 -56),
SpeciesTreeStatistic.java (+101 -94),
TMRCAStatistic.java (+1 -6),
TreeMetricStatistic.java (+1 -6),
TreeModelParser.java (+1 -5),
TreeShapeStatistic.java (+95 -79),
TreelengthStatistic.java (+47 -41)
-
src/dr/evomodel/treelikelihood:
AncestralState.java (+74 -71),
AncestralStateTreeLikelihood.java (+2 -3)
-
src/dr/evoxml:
UPGMATreeParser.java (+88 -85)
-
src/dr/exporters:
CSVExporter.java (new)
-
src/dr/inference/distribution:
ExponentialDistributionModel.java (+146 -119),
MultivariateDistributionLikelihood.java (+257 -261)
-
src/dr/inference/model:
LogarithmStatistic.java (+61 -63),
TestStatistic.java (+170 -150)
-
src/dr/inference/operators:
JointOperator.java (+151 -164),
UpDownOperator.java (+2 -4)
-
src/dr/inference/trace:
EBSPAnalysis.java (+3 -6)
-
alexei.drummond
2008-07-12 01:14
#21
Rev.: 988
-
1530 lines of code changed in 24 files:
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+184 -187)
-
src/dr/evomodel/coalescent/operators:
GMRFSkyrideBlockUpdateOperator.java (+2 -6)
-
src/dr/evomodel/operators:
ExchangeOperator.java (+80 -81),
InternalTraitGibbsOperator.java (+84 -86),
NNI.java (+121 -132)
-
src/dr/evomodel/sitemodel:
CategoryParameterStatistic.java (+78 -69)
-
src/dr/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+134 -137)
-
src/dr/evomodel/tree:
GMRFFixedGridImportanceSampler.java (new 81),
GMRFSkyrideFixedGridLogger.java (+4 -14),
TreeTraceAnalysisParser.java (+4 -16)
-
src/dr/evomodelxml:
TreeLoggerParser.java (+1 -4)
-
src/dr/evoxml:
AscertainedSitePatternsParser.java (+54 -53),
PatternsParser.java (+18 -19),
SitePatternsParser.java (+2 -6)
-
src/dr/inference/loggers:
Columns.java (+78 -88),
MLLogger.java (+2 -6)
-
src/dr/inference/markovchain:
ConvergenceListenerParser.java (new 37)
-
src/dr/inference/model:
CompoundLikelihood.java (+178 -162)
-
src/dr/inference/operators:
RegressionGibbsOperator.java (+124 -124),
ScaleOperator.java (+4 -16),
UniformIntegerOperator.java (+2 -4)
-
src/dr/inference/trace:
LogFileTraceExporter.java (+1 -4),
MarginalLikelihoodAnalysis.java (+255 -265),
TraceAnalysisParser.java (+2 -5)
-
alexei.drummond
2008-07-10 21:59
#20
Rev.: 987
-
3503 lines of code changed in 34 files:
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+856 -860)
-
src/dr/evomodel/branchratemodel:
RandomLocalClockModel.java (+2 -5)
-
src/dr/evomodel/clock:
ACLikelihood.java (+1 -3)
-
src/dr/evomodel/coalescent:
CoalescentSimulator.java (+5 -7),
VariableDemographicModel.java (+37 -37)
-
src/dr/evomodel/coalescent/operators:
BayesianSkylineGibbsOperator.java (+4 -18),
GMRFSkyrideBlockUpdateOperator.java (+311 -322)
-
src/dr/evomodel/coalescent/structure:
ColourSamplerModel.java (+51 -56)
-
src/dr/evomodel/continuous:
MultivariateTraitLikelihood.java (+398 -409)
-
src/dr/evomodel/operators:
ColouredSubtreeSlideOperator.java (+2 -10),
SubtreeSlideOperator.java (+294 -301)
-
src/dr/evomodel/substmodel:
FrequencyModel.java (+126 -124)
-
src/dr/evomodel/tree:
TMRCAStatistic.java (+77 -67),
TreeModelParser.java (+17 -66),
TreeTraceAnalysisParser.java (+4 -8)
-
src/dr/evomodel/treelikelihood:
AdvancedTreeLikelihood.java (+90 -69),
AncestralStateTreeLikelihood.java (+164 -174),
ExperimentalTreeLikelihood.java (+63 -47),
TreeLikelihood.java (+67 -56)
-
src/dr/evomodelxml:
TreeLoggerParser.java (+3 -8)
-
src/dr/evoxml:
NewickParser.java (+25 -25),
SimpleTreeParser.java (+20 -19)
-
src/dr/inference/distribution:
ExponentialMarkovModel.java (+140 -128),
LogNormalDistributionModel.java (+1 -7)
-
src/dr/inference/mcmc:
MCMC.java (+381 -389),
MCMCOptions.java (+25 -13)
-
src/dr/inference/model:
CompoundSymmetricMatrix.java (+1 -3),
DesignMatrix.java (+54 -59),
DifferenceStatistic.java (+57 -43),
OrnsteinUhlenbeckPriorLikelihood.java (+33 -33),
ProductStatistic.java (+25 -18),
Statistic.java (+105 -86),
SumStatistic.java (+29 -19)
-
src/dr/xml:
XMLObject.java (+35 -16)
-
jheled
2008-07-10 18:27
#19
Rev.: 986
-
19 lines of code changed in 5 files:
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+1 -1),
TreeLogger.java (+1 -1)
-
src/dr/evomodelxml:
LoggerParser.java (+1 -1)
-
src/dr/inference/loggers:
MCLogger.java (+15 -10),
MLLogger.java (+1 -1)
-
alexei.drummond
2008-07-10 04:26
#18
Rev.: 985
-
2541 lines of code changed in 14 files:
-
src/dr/app/beast:
BeastParser.java (+269 -280)
-
src/dr/app/beauti:
BeastGenerator.java (+127 -125)
-
src/dr/app/tools:
BeastOptions.java (+1174 -1148)
-
src/dr/evomodel/tree:
GMRFSkyrideFixedGridLogger.java (+235 -243),
TreeLogger.java (-200)
-
src/dr/evomodelxml:
BinarySubstitutionModelParser.java (+61),
LoggerParser.java (+197),
TreeLoggerParser.java (+200)
-
src/dr/evoxml:
BinarySubstitutionModelParser.java (del)
-
src/dr/exporters:
CSVExporter.java (+69 -60)
-
src/dr/inference/loggers:
MCLogger.java (-193),
MLLogger.java (+118 -135)
-
src/dr/inference/trace:
EBSPAnalysis.java (+73 -75),
LogFileTraceExporter.java (+18 -23)
-
alexei.drummond
2008-07-10 01:14
#17
Rev.: 984
-
37 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
OldAbstractCoalescentLikelihood.java (+37 -42)
-
jheled
2008-07-10 00:15
#16
Rev.: 983
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent:
VariableSkylineLikelihood.java (+2 -2)
-
alexei.drummond
2008-07-10 00:08
#15
Rev.: 982
-
4 lines of code changed in 1 file:
-
src/dr/evomodel/coalescent/operators:
SampleNonActiveGibbsOperator.java (+4 -4)
-
jheled
2008-07-09 23:31
#14
Rev.: 981
-
34 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeastGenerator.java (+14 -14)
-
src/dr/app/tools:
BeastOptions.java (+8 -8)
-
src/dr/evomodel/coalescent:
BayesianSkylineLikelihood.java (+2 -2),
OldAbstractCoalescentLikelihood.java (+8 -8),
SkylineLikelihood.java (+2 -2)
-
jheled
2008-07-09 23:00
#13
Rev.: 980
-
132 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
TreeMetricStatistic.java (+132 -140)
-
jheled
2008-07-09 22:56
#12
Rev.: 979
-
89 lines of code changed in 3 files:
-
src/dr/evolution/coalescent:
MultiLociTreeSet.java (new 20)
-
src/dr/evomodel/coalescent:
CoalescentLikelihood.java (+68 -24),
OldAbstractCoalescentLikelihood.java (+1 -3)
-
alexei.drummond
2008-07-07 22:26
#11
Rev.: 978
-
1 lines of code changed in 1 file:
-
src/dr/evoxml:
SitePatternsParser.java (+1 -1)
-
alexei.drummond
2008-07-07 22:21
#10
-
31 lines of code changed in 2 files:
-
src/dr/evoxml:
SitePatternsParser.java (+29 -24)
-
bloomquist
2008-07-05 05:35
#9
Rev.: 975
-
85 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/evolution/util:
RandomTaxaSample.java (+83)
-
rambaut
2008-07-05 03:13
#8
Rev.: 974
-
405 lines of code changed in 1 file:
-
src/dr/xml:
XMLObject.java (+405 -401)
-
alexei.drummond
2008-07-04 03:55
#7
Rev.: 973
-
109 lines of code changed in 1 file:
-
src/dr/app/beauti:
PriorsPanel.java (+109 -115)
-
Sibon.Li@gmail.com
2008-07-02 16:06
#6
Rev.: 972
-
386 lines of code changed in 1 file:
-
examples:
testLikelihood.xml (+386 -5)
-
rambaut
2008-07-02 02:30
#5
Rev.: 971
-
1 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
-
rambaut
2008-07-02 02:28
#4
Rev.: 970
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
TreeLikelihood.java (+2)
-
rambaut
2008-07-02 02:25
#3
Rev.: 969
-
751 lines of code changed in 13 files:
-
src/dr/app/misc:
Coevolve.java (+1 -1)
-
src/dr/evomodel/MSSD:
ALSTreeLikelihood.java (+1 -1)
-
src/dr/evomodel/treelikelihood:
ALSTreeLikelihood.java (new 8),
AbstractLikelihoodCore.java (+294 -293),
AdvancedTreeLikelihood.java (+1 -1),
AncestralStateTreeLikelihood.java (+1 -1),
ArbitraryPrecisionLikelihoodCore.java (+2 -2),
ExperimentalTreeLikelihood.java (+37 -46),
LikelihoodCore.java (+2 -2),
PurifyingGammaTreeLikelihood.java (+1 -1),
PurifyingTreeLikelihood.java (+2 -2),
TipsTreeLikelihood.java (new 4),
TreeLikelihood.java (+397 -431)
-
rambaut
2008-07-01 23:19
#2
Rev.: 968
-
870 lines of code changed in 15 files:
-
src/dr/evomodel/treelikelihood:
AbstractLikelihoodCore.java (+341 -301),
AdvancedTreeLikelihood.java (+2 -2),
AminoAcidLikelihoodCore.java (+59 -61),
ArbitraryPrecisionLikelihoodCore.java (+5 -10),
CodonLikelihoodCore.java (del),
ExperimentalTreeLikelihood.java (-2),
GeneralLikelihoodCore.java (new),
LikelihoodCore.java (+2 -2),
NativeAminoAcidLikelihoodCore.java (+17 -21),
NativeNucleotideLikelihoodCore.java (+1 -3),
NucleotideLikelihoodCore.java (new),
TreeLikelihood.java (+441 -402)
-
rambaut
2008-07-01 03:23
#1
Rev.: 967
-
566 lines of code changed in 21 files:
-
src/dr/app/beast:
BeastParser.java (+1)
-
src/dr/app/misc:
Coevolve.java (+1 -1)
-
src/dr/evomodel/MSSD:
ALSTreeLikelihood.java (+3 -8)
-
src/dr/evomodel/treelikelihood:
ALSTreeLikelihood.java (+3 -8),
AbstractLikelihoodCore.java (+23 -87),
AdvancedTreeLikelihood.java (+2 -2),
AminoAcidLikelihoodCore.java (+1 -2),
AncestralStateTreeLikelihood.java (+1 -5),
ArbitraryPrecisionLikelihoodCore.java (+41 -21),
CodonLikelihoodCore.java (new 11),
ExperimentalTreeLikelihood.java (+36 -21),
GeneralLikelihoodCore.java (+1 -3),
LikelihoodCore.java (+10 -8),
NativeAminoAcidLikelihoodCore.java (+2 -2),
NativeNucleotideLikelihoodCore.java (+2 -3),
NucleotideLikelihoodCore.java (+1 -3),
PurifyingGammaTreeLikelihood.java (+2 -2),
PurifyingTreeLikelihood.java (+3 -4),
TipsTreeLikelihood.java (+4 -4),
TreeLikelihood.java (+41 -15)
-
src/dr/math:
BigDecimalUtils.java (new 377)