-
dong.w.xie
2011-03-31 17:52
#74
Rev.: 3910
-
65 lines of code changed in 3 files:
-
release/common:
README.txt (+5 -5),
VERSION HISTORY.txt (+59 -2)
-
src/dr/app/beast:
BeastVersion.java (+1 -3)
-
dong.w.xie
2011-03-31 16:53
#73
Rev.: 3909
-
37 lines of code changed in 8 files:
-
src/dr/app/beauti/generator:
LogGenerator.java (+1 -1),
PatternListGenerator.java (+6),
SubstitutionModelGenerator.java (+2 -2),
TreeLikelihoodGenerator.java (+17 -3),
TreeModelGenerator.java (+1 -1),
TreePriorGenerator.java (+3 -3)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+1)
-
src/dr/evolution/io:
MicroSatImporter.java (+6)
-
dong.w.xie
2011-03-31 13:07
#72
Rev.: 3908
-
171 lines of code changed in 23 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+1 -1),
OldClockModelsPanel.java (+1 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -11)
-
src/dr/app/beauti/generator:
LogGenerator.java (+4 -1),
OperatorsGenerator.java (+30 -28),
PatternListGenerator.java (+2 -1),
SubstitutionModelGenerator.java (+32 -6),
TreeLikelihoodGenerator.java (+5 -2),
TreeModelGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -3),
ClockModelGroup.java (+11 -1),
ClockModelOptions.java (+1 -1),
ModelOptions.java (+3 -3),
PartitionClockModel.java (+2 -2),
PartitionClockModelTreeModelLink.java (+53 -36),
PartitionOptions.java (+1 -1),
PartitionTreeModel.java (+3 -3)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+2 -2)
-
src/dr/app/beauti/types:
OperatorType.java (+1)
-
src/dr/inferencexml/operators:
MicrosatUpDownOperatorParser.java (+3 -3),
UpDownOperatorParser.java (new)
-
dong.w.xie
2011-03-30 16:45
#71
Rev.: 3907
-
240 lines of code changed in 15 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+9 -6),
PatternListGenerator.java (+4 -3),
SubstitutionModelGenerator.java (+82 -3),
TreeLikelihoodGenerator.java (+43 -29),
TreeModelGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+14),
ModelOptions.java (+6),
PartitionSubstitutionModel.java (+64 -6),
PartitionTreeModel.java (+3)
-
src/dr/app/beauti/types:
MicroSatModelType.java (+4 -3)
-
src/dr/evolution/io:
MicroSatImporter.java (+3 -3)
-
src/dr/evomodelxml/treelikelihood:
MicrosatelliteSamplerTreeLikelihoodParser.java (+5 -4)
-
src/dr/evoxml:
MicrosatelliteParser.java (+2 -2)
-
dong.w.xie
2011-03-29 15:53
#70
Rev.: 3906
-
35 lines of code changed in 4 files:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+9),
PartitionOptions.java (+3 -1),
PartitionTreePrior.java (+13 -8),
TreeModelOptions.java (+10 -1)
-
dong.w.xie
2011-03-28 17:06
#69
Rev.: 3905
-
368 lines of code changed in 15 files:
-
src/dr/app/beauti/clockModelsPanel:
OldClockModelsPanel.java (+7 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+5)
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+14),
PatternListGenerator.java (+2 -1),
TreeModelGenerator.java (+31 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+29),
PartitionOptions.java (+3),
PartitionSubstitutionModel.java (+58 -22),
PartitionTreeModel.java (+14)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+98 -38),
SiteModelsPanel.java (+1)
-
src/dr/app/beauti/types:
MicroSatModelType.java (+43 -8),
OperatorType.java (+1)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+53 -72)
-
src/dr/evolution/io:
MicroSatImporter.java (+9 -4)
-
akaruiws
2011-03-28 10:28
#68
Rev.: 3904
-
8 lines of code changed in 1 file:
-
src/dr/evolution/datatype:
Microsatellite.java (+8)
-
denise.kuehnert@gmail.com
2011-03-25 17:45
#67
Rev.: 3903
-
60 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
BirthDeathSerialSkylineModel.java (+60 -47)
-
dong.w.xie
2011-03-25 16:23
#66
Rev.: 3902
-
152 lines of code changed in 10 files:
-
src/dr/app/beauti/generator:
ParameterPriorGenerator.java (+11 -1)
-
src/dr/app/beauti/options:
ModelOptions.java (+5),
Parameter.java (+10 -2),
PartitionOptions.java (+5 -2),
PartitionTreePrior.java (+22 -16)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+32 -2)
-
src/dr/app/beauti/types:
PriorScaleType.java (+1),
PriorType.java (+15 -1)
-
src/dr/evomodelxml/speciation:
BirthDeathSerialSamplingModelParser.java (+2 -2)
-
src/dr/inferencexml/distribution:
PriorParsers.java (+49)
-
denise.kuehnert@gmail.com
2011-03-25 14:31
#65
Rev.: 3901
-
231 lines of code changed in 1 file:
-
src/dr/math/distributions:
BetaDistribution.java (+231)
-
dong.w.xie
2011-03-25 12:10
#64
Rev.: 3900
-
482 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
TreePriorGenerator.java (+359 -348)
-
src/dr/app/beauti/options:
PartitionOptions.java (+4 -4),
PartitionTreePrior.java (+83 -4)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+35 -16)
-
src/dr/app/beauti/types:
TreePriorType.java (+1 -1)
-
dong.w.xie
2011-03-24 15:55
#63
Rev.: 3899
-
159 lines of code changed in 8 files:
-
src/dr/app/beauti/generator:
Generator.java (+4),
TreePriorGenerator.java (+110 -53)
-
src/dr/app/beauti/options:
PartitionOptions.java (+1 -1)
-
src/dr/app/beauti/types:
TreePriorType.java (+3)
-
src/dr/evomodelxml/speciation:
BirthDeathModelParser.java (+14 -7),
BirthDeathSerialSamplingModelParser.java (+16 -7)
-
src/test/dr/evomodel/speciation:
BirthDeathSSLikelihoodTest.java (+11 -4)
-
jheled
2011-03-24 13:20
#62
Rev.: 3898
-
57 lines of code changed in 6 files:
-
src/dr/inference/model:
RPNcalculatorStatistic.java (+7 -2),
RPNexpressionCalculator.java (new)
-
src/dr/inferencexml/model:
RPNcalculatorStatisticParser.java (new)
-
dong.w.xie
2011-03-24 09:41
#61
Rev.: 3897
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
PatternListGenerator.java (+3 -3)
-
dong.w.xie
2011-03-23 17:16
#60
Rev.: 3896
-
223 lines of code changed in 17 files:
-
src/dr/app/beast:
development_parsers.properties (-3),
release_parsers.properties (+2)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2),
PartitionClockModelPanel.java (+5 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+39 -3),
PartitionClockModel.java (+2 -5),
PartitionClockModelTreeModelLink.java (+1),
PartitionOptions.java (+142 -6),
PartitionSubstitutionModel.java (+1),
PartitionTreeModel.java (+17 -15),
PartitionTreePrior.java (+2 -1),
PriorOptions.java (+4 -4)
-
src/dr/app/beauti/siteModelsPanel:
CreateModelDialog.java (new)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (new)
-
dong.w.xie
2011-03-23 12:16
#59
Rev.: 3895
-
25 lines of code changed in 5 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ClockModelOptions.java (+7 -3)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+6 -2)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+1 -1),
TreesPanel.java (+10 -9)
-
dong.w.xie
2011-03-23 11:24
#58
Rev.: 3894
-
107 lines of code changed in 7 files:
-
src/dr/app/beauti/clockModelsPanel:
OldClockModelsPanel.java (+22 -20)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+1 -1)
-
src/dr/app/beauti/options:
ClockModelGroup.java (+4 -2),
ClockModelOptions.java (+1),
PartitionClockModel.java (+70 -29),
PriorOptions.java (+3 -3)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+6)
-
dong.w.xie
2011-03-22 16:15
#57
Rev.: 3893
-
126 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
Generator.java (+52 -42),
PatternListGenerator.java (+69 -65),
SubstitutionModelGenerator.java (+4 -6),
TreeLikelihoodGenerator.java (+1 -3)
-
dong.w.xie
2011-03-22 12:52
#56
Rev.: 3892
-
154 lines of code changed in 11 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+7 -2)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+3 -3)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -1),
ClockModelOptions.java (+31 -28),
PartitionClockModel.java (+7 -2),
PartitionSubstitutionModel.java (+7 -1),
PartitionTreeModel.java (+33 -27),
PriorOptions.java (+8 -7)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+7 -3)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+34 -31),
TreesPanel.java (+6)
-
dong.w.xie
2011-03-22 10:11
#55
Rev.: 3891
-
10 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+10 -10)
-
dong.w.xie
2011-03-22 09:38
#54
Rev.: 3890
-
13 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+13 -6)
-
dong.w.xie
2011-03-22 09:25
#53
Rev.: 3889
-
15 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
PatternListGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
PartitionClockModel.java (+6 -6),
PartitionOptions.java (+4 -4)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+3 -2)
-
dong.w.xie
2011-03-21 17:18
#52
Rev.: 3888
-
66 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+12),
PartitionClockModelTreeModelLink.java (+42 -29),
PriorOptions.java (+12 -6)
-
dong.w.xie
2011-03-21 11:23
#51
Rev.: 3887
-
50 lines of code changed in 8 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+7 -4),
TipDateSamplingComponentOptions.java (+4 -4)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+1 -1),
ModelOptions.java (+2 -2),
PartitionClockModelTreeModelLink.java (+4 -2),
PartitionSubstitutionModel.java (+23 -23),
PartitionTreePrior.java (+7 -7),
STARBEASTOptions.java (+2 -2)
-
dong.w.xie
2011-03-21 10:46
#50
Rev.: 3886
-
56 lines of code changed in 8 files:
-
src/dr/app/beauti/generator:
Generator.java (+10 -11),
InitialTreeGenerator.java (+2 -2),
ParameterPriorGenerator.java (+4 -4)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -4),
Parameter.java (+20 -4)
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+3 -3),
PriorDialog.java (+9 -9)
-
src/dr/app/beauti/types:
PriorType.java (+6 -6)
-
msuchard
2011-03-21 07:57
#49
Rev.: 3885
-
11 lines of code changed in 1 file:
-
src/dr/inference/markovjumps:
SubordinatedProcess.java (+11 -8)
-
msuchard
2011-03-21 07:36
#48
Rev.: 3884
-
7 lines of code changed in 1 file:
-
src/dr/evomodelxml/branchratemodel:
ArbitraryBranchRatesParser.java (+7 -1)
-
philippe.lemey@gmail.com
2011-03-19 07:51
#47
Rev.: 3883
-
4 lines of code changed in 2 files:
-
src/dr/app/tools:
TimeSlicer.java (+4 -4)
-
philippe.lemey@gmail.com
2011-03-18 22:34
#46
Rev.: 3882
-
34 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+34 -6)
-
dong.w.xie
2011-03-18 17:53
#45
Rev.: 3881
-
209 lines of code changed in 13 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+6 -7),
OldClockModelsPanel.java (+6 -7)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+10 -7),
InitialTreeGenerator.java (+6 -6),
LogGenerator.java (+22 -20),
OperatorsGenerator.java (+4 -4)
-
src/dr/app/beauti/options:
BeautiOptions.java (+10),
ClockModelOptions.java (+109 -92),
Operator.java (+11 -1),
PartitionClockModel.java (+3 -3),
PartitionTreeModel.java (+2 -1),
PriorOptions.java (+13 -11)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+7 -2)
-
dong.w.xie
2011-03-17 16:03
#44
Rev.: 3880
-
147 lines of code changed in 6 files:
-
src/dr/app/beauti/clockModelsPanel:
OldClockModelsPanel.java (+113 -45)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ClockModelOptions.java (+9 -8)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+3 -1)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+5 -2)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+16 -12)
-
msuchard
2011-03-17 11:27
#43
Rev.: 3879
-
3 lines of code changed in 1 file:
-
src/dr/inference/model:
BayesianStochasticSearchVariableSelection.java (+3 -2)
-
msuchard
2011-03-17 10:51
#42
Rev.: 3878
-
27 lines of code changed in 5 files:
-
src/dr/app/tools:
TreeAnnotator.java (+3 -1)
-
src/dr/geo:
KernelDensityEstimator2D.java (new)
-
src/dr/geo/contouring:
ContourWithSynder.java (new)
-
dong.w.xie
2011-03-16 16:48
#41
Rev.: 3877
-
397 lines of code changed in 11 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+7 -17),
OldClockModelsPanel.java (+56 -41)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+8 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+22 -1),
ClockModelGroup.java (+56),
ClockModelOptions.java (+226 -111),
PartitionClockModel.java (+10)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+5 -4)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+1 -1)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+1 -1)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+5 -6)
-
dong.w.xie
2011-03-16 09:53
#40
Rev.: 3876
-
915 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -6)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (del),
TaxonSetPanel.java (+902)
-
src/dr/app/oldbeauti:
TaxaPanel.java (+7 -4)
-
dong.w.xie
2011-03-15 17:14
#39
Rev.: 3875
-
202 lines of code changed in 3 files:
-
src/dr/app/beauti/clockModelsPanel:
OldClockModelsPanel.java (+159 -10)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ClockModelOptions.java (+42 -1)
-
alexei.drummond
2011-03-15 09:15
#38
Rev.: 3874
-
16 lines of code changed in 2 files:
-
src/dr/evolution/tree:
CountConstrainedRankedHistories.java (+16 -7)
-
alexei.drummond
2011-03-14 22:08
#37
Rev.: 3873
-
228 lines of code changed in 3 files:
-
src/dr/evolution/tree:
CountConstrainedRankedHistories.java (+212 -32),
RankedNode.java (+16 -7)
-
dong.w.xie
2011-03-14 16:27
#36
Rev.: 3872
-
431 lines of code changed in 18 files:
-
src/dr/app/beauti:
BeautiFrame.java (-5)
-
src/dr/app/beauti/generator:
AlignmentGenerator.java (+1 -14),
BeastGenerator.java (+42 -135),
PatternListGenerator.java (+185)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+59 -40)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -2),
PartitionSubstitutionModel.java (+11 -2)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+27)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+4 -6)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+9 -7),
PartitionTreePriorPanel.java (+35 -25),
TreesPanel.java (+11 -8)
-
src/dr/app/beauti/types:
MicroSatModelType.java (+2 -1)
-
src/dr/app/beauti/util:
CommandLineBeauti.java (+1 -1)
-
src/dr/evolution/datatype:
Microsatellite.java (+14 -2)
-
src/dr/evolution/io:
MicroSatImporter.java (+9 -3)
-
src/dr/evoxml:
MicrosatelliteParser.java (+10 -6)
-
alexei.drummond
2011-03-14 15:32
#35
Rev.: 3871
-
231 lines of code changed in 1 file:
-
src/dr/evolution/tree:
CountConstrainedRankedHistories.java (+231)
-
alexei.drummond
2011-03-12 17:59
#34
Rev.: 3870
-
48 lines of code changed in 3 files:
-
src/dr/evolution/tree:
RankedForest.java (new),
RankedNode.java (+19 -12)
-
alexei.drummond
2011-03-12 15:39
#33
Rev.: 3869
-
361 lines of code changed in 2 files:
-
src/dr/evolution/tree:
RankedForest.java (+73 -9),
RankedNode.java (+288 -129)
-
alexei.drummond
2011-03-11 15:39
#32
Rev.: 3868
-
325 lines of code changed in 2 files:
-
src/dr/evolution/tree:
RankedForest.java (+98),
RankedNode.java (+227)
-
dong.w.xie
2011-03-11 14:03
#31
Rev.: 3867
-
57 lines of code changed in 4 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (-20)
-
src/dr/app/beauti/options:
BeautiOptions.java (+18 -10)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+3)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+36 -33)
-
dong.w.xie
2011-03-11 12:03
#30
Rev.: 3866
-
64 lines of code changed in 9 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+12),
PartitionClockModel.java (+3 -12),
PartitionClockModelSubstModelLink.java (+5 -5),
PartitionClockModelTreeModelLink.java (+5 -5),
PartitionOptions.java (+20 -1),
PartitionSubstitutionModel.java (+7 -25),
PartitionTreeModel.java (+3 -12),
PartitionTreePrior.java (+3 -13)
-
src/dr/app/beauti/util:
NexusApplicationImporter.java (+6 -5)
-
dong.w.xie
2011-03-11 11:09
#29
Rev.: 3865
-
74 lines of code changed in 4 files:
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+34 -37)
-
src/dr/evolution/io:
MicroSatImporter.java (+39 -22),
PatternImporter.java (new)
-
dong.w.xie
2011-03-10 16:30
#28
Rev.: 3864
-
72 lines of code changed in 5 files:
-
src/dr/app/beauti/clockModelsPanel:
OldClockModelsPanel.java (+14 -19)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+17 -1)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+19 -1)
-
src/dr/app/beauti/types:
MicroSatModelType.java (+20)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+2 -2)
-
dong.w.xie
2011-03-10 12:11
#27
Rev.: 3863
-
259 lines of code changed in 9 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3)
-
src/dr/app/beauti/options:
PartitionTreeModel.java (+4 -6)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+221 -173)
-
src/dr/app/java16compat:
FileNameExtensionFilter.java (del)
-
src/dr/app/tracer/application:
TracerFrame.java (+1 -1)
-
src/dr/app/treespace:
TreeSpaceFrame.java (+1 -3)
-
src/dr/evolution/io:
MicroSatImporter.java (+23 -12),
PatternImporter.java (+3 -2)
-
dong.w.xie
2011-03-09 17:32
#26
Rev.: 3862
-
142 lines of code changed in 3 files:
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+3 -2)
-
src/dr/evolution/io:
MicroSatImporter.java (+120 -7),
PatternImporter.java (+19)
-
alexei.drummond
2011-03-09 10:25
#25
Rev.: 3861
-
55 lines of code changed in 4 files:
-
src/dr/app/seqgen:
SeqGen.java (+43 -32)
-
src/dr/evolution/alignment:
SimpleAlignment.java (+11 -7)
-
src/dr/evolution/sequence:
Sequences.java (new)
-
dong.w.xie
2011-03-08 15:15
#24
Rev.: 3860
-
456 lines of code changed in 29 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+14 -7)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+26 -24)
-
src/dr/app/beauti/generator:
AlignmentGenerator.java (+5 -3),
BeastGenerator.java (+38 -27),
BranchRatesModelGenerator.java (+3 -3),
DiscreteTraitGenerator.java (+3 -3),
InitialTreeGenerator.java (+4 -4),
LogGenerator.java (+1 -1),
SubstitutionModelGenerator.java (+18 -13),
TreeLikelihoodGenerator.java (+13 -10)
-
src/dr/app/beauti/options:
AbstractPartitionData.java (+120),
BeautiOptions.java (+44 -41),
ClockModelOptions.java (+10 -10),
PartitionClockModel.java (+2 -2),
PartitionData.java (+20 -98),
PartitionPattern.java (+53),
PartitionSubstitutionModel.java (+7 -9),
PartitionTreeModel.java (+1 -1),
TraitData.java (+4 -2)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+4 -5)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (new 4)
-
src/dr/app/beauti/treespanel:
GenerateTreeDialog.java (new),
TreesPanel.java (+3 -4)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+23)
-
src/dr/evolution/datatype:
DataType.java (+2),
GeneralDataType.java (+3 -3),
Microsatellite.java (+4 -1)
-
src/dr/evolution/io:
MicroSatImporter.java (+25)
-
philippe.lemey@gmail.com
2011-03-05 01:16
#23
Rev.: 3859
-
4 lines of code changed in 1 file:
-
src/dr/inference/trace:
DnDsPerSiteAnalysis.java (+4 -4)
-
dong.w.xie
2011-03-04 15:40
#22
Rev.: 3858
-
21 lines of code changed in 1 file:
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+21 -15)
-
dong.w.xie
2011-03-04 09:33
#21
Rev.: 3857
-
11 lines of code changed in 1 file:
-
dong.w.xie
2011-03-04 09:31
#20
Rev.: 3856
-
10 lines of code changed in 1 file:
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+10 -3)
-
alexei.drummond
2011-03-03 21:13
#19
Rev.: 3855
-
59 lines of code changed in 1 file:
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+59 -245)
-
dong.w.xie
2011-03-03 17:13
#18
Rev.: 3854
-
268 lines of code changed in 3 files:
-
src/dr/evomodelxml/tree:
TMRCAStatisticParser.java (+2 -5)
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+266 -25)
-
rambaut
2011-03-03 13:01
#17
Rev.: 3853
-
8 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+1),
MultidimensionalScalingLikelihood.java (+7 -7)
-
alexei.drummond
2011-03-03 12:51
#16
Rev.: 3852
-
24 lines of code changed in 1 file:
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+24 -11)
-
rambaut
2011-03-03 12:35
#15
Rev.: 3851
-
25 lines of code changed in 2 files:
-
src/dr/app/phylogeography/tools:
TreeKMLGenerator.java (+15 -35)
-
src/dr/evomodel/continuous:
MultidimensionalScalingLikelihood.java (+10 -25)
-
dong.w.xie
2011-03-03 12:24
#14
Rev.: 3850
-
181 lines of code changed in 1 file:
-
src/test/dr/calibration:
TestCalibratedYuleModel.java (+181)
-
rambaut
2011-03-03 10:26
#13
Rev.: 3849
-
24 lines of code changed in 2 files:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+23 -6),
MultidimensionalScalingLikelihood.java (+1 -2)
-
rambaut
2011-03-03 07:56
#12
Rev.: 3848
-
100 lines of code changed in 4 files:
-
src/dr/app/phylogeography/tools:
TreeKMLGenerator.java (+6 -2)
-
src/dr/app/tools:
AntigenicPlotter.java (+4)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+34 -16),
MultidimensionalScalingLikelihood.java (+56 -19)
-
msuchard
2011-03-03 05:44
#11
Rev.: 3847
-
306 lines of code changed in 6 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/continuous/plink:
PlinkImporter.java (+235)
-
src/dr/evomodelxml/treelikelihood:
TreeTraitParserUtilities.java (+22 -12)
-
src/dr/inference/distribution:
MultivariateDistributionLikelihood.java (-1)
-
src/dr/util:
CommonCitations.java (+4 -1)
-
src/dr/xml:
XMLParser.java (+44 -15)
-
philippe.lemey@gmail.com
2011-03-02 22:53
#10
Rev.: 3846
-
55 lines of code changed in 1 file:
-
src/dr/inference/trace:
DnDsPerSiteAnalysis.java (+55 -12)
-
msuchard
2011-03-02 14:27
#9
Rev.: 3845
-
1 lines of code changed in 2 files:
-
src/dr/inferencexml/model:
ReciprocalStatisticParser.java (+1 -1)
-
msuchard
2011-03-02 12:15
#8
Rev.: 3844
-
166 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
FLU.java (+166)
-
dong.w.xie
2011-03-02 09:56
#7
Rev.: 3843
-
2 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/parsers:
FrequencyModelParser.java (+1 -1)
-
src/dr/evomodelxml/substmodel:
FrequencyModelParser.java (new)
-
philippe.lemey@gmail.com
2011-03-02 01:16
#6
Rev.: 3842
-
110 lines of code changed in 1 file:
-
src/dr/inference/trace:
DnDsPerSiteAnalysis.java (+110 -16)
-
dong.w.xie
2011-03-01 15:35
#5
Rev.: 3841
-
2 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
TraitData.java (+1 -1)
-
dong.w.xie
2011-03-01 15:17
#4
Rev.: 3840
-
51 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+24 -15)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+7)
-
src/dr/app/beauti/options:
BeautiOptions.java (+13 -4)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+7 -3)
-
dong.w.xie
2011-03-01 14:21
#3
Rev.: 3839
-
14 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+5 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+9 -9)
-
dong.w.xie
2011-03-01 10:49
#2
Rev.: 3838
-
2 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+1 -2)
-
dong.w.xie
2011-03-01 09:43
#1
Rev.: 3837
-
60 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -5)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+20 -19),
STARBEASTGenerator.java (+36 -32)
-
src/dr/app/beauti/options:
TraitData.java (+3 -2)