-
rambaut
2009-08-31 20:37
#192
Rev.: 2168
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
Sibon.Li@gmail.com
2009-08-31 18:03
#191
Rev.: 2167
-
1 lines of code changed in 1 file:
-
src/dr/app/tools:
NormaliseMeanTreeRate.java (+1 -1)
-
Sibon.Li@gmail.com
2009-08-31 18:01
#190
Rev.: 2166
-
302 lines of code changed in 1 file:
-
src/dr/app/tools:
NormaliseMeanTreeRate.java (+302)
-
dong.w.xie
2009-08-31 16:57
#189
Rev.: 2165
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+3 -3)
-
rambaut
2009-08-29 01:58
#188
Rev.: 2164
-
7 lines of code changed in 4 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+2 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
BranchRatesModelGenerator.java (+1 -1),
Generator.java (+3 -3)
-
rambaut
2009-08-29 01:43
#187
Rev.: 2163
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+6 -7)
-
rambaut
2009-08-29 01:26
#186
Rev.: 2162
-
3 lines of code changed in 2 files:
-
lib:
beagle.jar (changed)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3)
-
dong.w.xie
2009-08-28 17:29
#185
Rev.: 2161
-
23 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+7 -5)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+1)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+9 -7)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+2 -1)
-
dong.w.xie
2009-08-28 15:03
#184
Rev.: 2160
-
0 lines of code changed in 8 files:
-
examples/beauti1.5/starBEAST:
g10.xml (new),
g11.xml (new),
x10.xml (new),
x11.xml (new)
-
dong.w.xie
2009-08-28 15:02
#183
Rev.: 2159
-
7 lines of code changed in 1 file:
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+7 -2)
-
dong.w.xie
2009-08-28 14:36
#182
Rev.: 2158
-
0 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (-3)
-
dong.w.xie
2009-08-28 13:31
#181
Rev.: 2157
-
137 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+48 -24)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+51 -45)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+38 -36)
-
dong.w.xie
2009-08-28 10:40
#180
Rev.: 2156
-
18 lines of code changed in 2 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+10 -10)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+8 -8)
-
dong.w.xie
2009-08-28 10:11
#179
Rev.: 2155
-
31 lines of code changed in 3 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+10 -10)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+11)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+10 -12)
-
jheled
2009-08-28 06:12
#178
Rev.: 2154
-
12 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
TN93.java (+12 -4)
-
dong.w.xie
2009-08-27 17:24
#177
Rev.: 2153
-
89 lines of code changed in 10 files:
-
src/dr/app/beauti:
BeautiFrame.java (+4 -36)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+6 -3),
InitialTreeGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+42 -3),
ClockModelOptions.java (+21 -18),
Parameter.java (+5 -1)
-
src/dr/app/beauti/priorsPanel:
PriorTableModel.java (+2 -4),
PriorsPanel.java (+5 -7)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (-6)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+2 -1)
-
jheled
2009-08-27 15:29
#176
Rev.: 2152
-
4 lines of code changed in 1 file:
-
src/dr/inference/markovchain:
MarkovChain.java (+4)
-
Sibon.Li@gmail.com
2009-08-27 15:23
#175
Rev.: 2151
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1)
-
Sibon.Li@gmail.com
2009-08-27 15:15
#174
Rev.: 2150
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -4)
-
dong.w.xie
2009-08-27 13:38
#173
Rev.: 2149
-
63 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5 -2)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+37 -44)
-
src/dr/app/beauti/enumTypes:
FixRateType.java (+4 -4)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+17)
-
dong.w.xie
2009-08-27 13:37
#172
Rev.: 2148
-
4 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1),
release_parsers.properties (+1)
-
src/dr/evomodel/substmodel:
TN93.java (+2 -2)
-
dong.w.xie
2009-08-27 10:47
#171
Rev.: 2147
-
13 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
PartitionTreeModel.java (+12)
-
dong.w.xie
2009-08-27 10:29
#170
Rev.: 2146
-
24 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+24 -8)
-
rambaut
2009-08-27 00:14
#169
Rev.: 2145
-
5 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastMain.java (+1 -1)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+4 -4)
-
dong.w.xie
2009-08-26 18:13
#168
Rev.: 2144
-
141 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+53 -12)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+69 -5)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+11 -16)
-
src/dr/evomodel/substmodel:
NucModelType.java (+5 -1),
TN93.java (+3 -3)
-
dong.w.xie
2009-08-26 17:52
#167
Rev.: 2143
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+4 -3)
-
alexei.drummond
2009-08-26 17:11
#166
Rev.: 2142
-
17 lines of code changed in 2 files:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+1 -2),
Parameter.java (+16)
-
Sibon.Li@gmail.com
2009-08-26 17:07
#165
Rev.: 2141
-
40 lines of code changed in 2 files:
-
src/dr/evomodel/tree:
TreeLogger.java (+35 -2)
-
src/dr/evomodelxml:
TreeLoggerParser.java (+5 -1)
-
alexei.drummond
2009-08-26 16:56
#164
Rev.: 2140
-
708 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+66 -65)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+276 -223),
PartitionData.java (+25 -30)
-
src/dr/evolution/alignment:
SimpleAlignment.java (+288 -266)
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+53 -53)
-
dong.w.xie
2009-08-26 12:56
#163
Rev.: 2139
-
10 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+10)
-
philippe.lemey@gmail.com
2009-08-25 17:06
#162
Rev.: 2138
-
368 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+368 -427)
-
dong.w.xie
2009-08-25 16:32
#161
Rev.: 2137
-
119 lines of code changed in 9 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+34 -14)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
InitialTreeGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+53 -21),
PartitionTreeModel.java (-32)
-
src/dr/app/beauti/priorsPanel:
PriorsPanel.java (+12 -4)
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+8 -12)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+2 -3)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+8 -4)
-
dong.w.xie
2009-08-25 14:29
#160
Rev.: 2136
-
9 lines of code changed in 4 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+3)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
InitialTreeGenerator.java (+1 -1)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+4)
-
dong.w.xie
2009-08-25 13:51
#159
Rev.: 2135
-
44 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+2 -1)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+42 -59)
-
dong.w.xie
2009-08-25 13:12
#158
Rev.: 2134
-
53 lines of code changed in 4 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+43 -1),
ClockModelOptions.java (+1 -1),
ModelOptions.java (-15),
PartitionData.java (+9 -7)
-
dong.w.xie
2009-08-25 11:24
#157
Rev.: 2133
-
51 lines of code changed in 6 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -3)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2 -2)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+3 -3),
PartitionClockModel.java (+35),
STARBEASTOptions.java (+6 -2)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+2 -11)
-
dong.w.xie
2009-08-25 10:57
#156
Rev.: 2132
-
233 lines of code changed in 14 files:
-
src/dr/app/beauti:
BeautiFrame.java (+8 -7)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+1 -1)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+12 -12),
InitialTreeGenerator.java (+1 -1),
OperatorsGenerator.java (+3 -3),
STARBEASTGenerator.java (+8 -8),
TreePriorGenerator.java (+2 -2)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+9 -121),
ClockModelOptions.java (+1 -1),
PartitionTreeModel.java (+1 -1),
STARBEASTOptions.java (+179)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+2 -2),
TreesPanel.java (+4 -4)
-
dong.w.xie
2009-08-25 10:25
#155
Rev.: 2131
-
54 lines of code changed in 16 files:
-
src/dr/app/beauti/generator:
Generator.java (+3 -2),
SubstitutionModelGenerator.java (+6 -6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -6),
ClockModelOptions.java (-7),
ModelOptions.java (+1 -1),
PartitionClockModel.java (+1 -1),
PartitionClockModelTreeModelLink.java (+1 -1),
PartitionData.java (+1 -1),
PartitionOptions.java (+35),
PartitionSubstitutionModel.java (+1 -1),
PartitionTreeModel.java (+1 -1),
PartitionTreePrior.java (+1 -1),
PriorOptions.java (-5),
SubstitutionModelOptions.java (-7),
TreeModelOptions.java (+1 -6)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+1 -8)
-
rambaut
2009-08-24 18:50
#154
Rev.: 2130
-
420 lines of code changed in 2 files:
-
src/dr/app/tools:
LogCombiner.java (+2 -4),
TimeSlicer.java (+418 -242)
-
dong.w.xie
2009-08-24 18:25
#153
Rev.: 2129
-
294 lines of code changed in 16 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2 -4)
-
src/dr/app/beauti/enumTypes:
FixRateType.java (+5 -4)
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+8 -8),
TreePriorGenerator.java (+12 -9)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+91 -8),
ModelOptions.java (+18 -1),
PartitionClockModel.java (+6 -21),
PartitionClockModelTreeModelLink.java (+3 -7),
PartitionData.java (+10 -8),
PartitionTreeModel.java (+46 -36),
PriorOptions.java (+46 -52),
TreeModelOptions.java (+13 -28)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+1 -1)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+11),
TreesPanel.java (+1 -1)
-
src/dr/math:
MathUtils.java (+21)
-
dong.w.xie
2009-08-24 10:57
#152
Rev.: 2128
-
53 lines of code changed in 4 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+12),
ModelOptions.java (+4),
PartitionData.java (+21 -1)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+16)
-
dong.w.xie
2009-08-21 17:14
#151
Rev.: 2127
-
355 lines of code changed in 10 files:
-
src/dr/app/beauti/generator:
Generator.java (+22 -22),
InitialTreeGenerator.java (+1 -1),
TreePriorGenerator.java (+4 -4)
-
src/dr/app/beauti/options:
BeautiOptions.java (+138 -130),
ClockModelOptions.java (+8),
PartitionData.java (+10 -4),
PartitionTreeModel.java (+53 -7),
PriorOptions.java (+88 -108),
TreeModelOptions.java (+27 -1)
-
src/dr/app/beauti/util:
CommandLineBeauti.java (+4 -4)
-
dong.w.xie
2009-08-21 14:29
#150
Rev.: 2126
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
TraitGuesser.java (+4 -4)
-
dong.w.xie
2009-08-21 11:52
#149
Rev.: 2125
-
105 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
PriorOptions.java (+105 -105)
-
dong.w.xie
2009-08-21 11:50
#148
Rev.: 2124
-
413 lines of code changed in 16 files:
-
src/dr/app/beauti/enumTypes:
AminoAcidModelType.java (del),
NucModelType.java (del)
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (+2 -3),
PriorOptions.java (+210),
TreeModelOptions.java (+83)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+5 -4)
-
src/dr/app/beauti/util:
NexusApplicationImporter.java (+1 -1)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+2 -2)
-
src/dr/evomodel/substmodel:
AminoAcidModelType.java (+68),
EmpiricalAminoAcidModel.java (-1),
HKY.java (+1 -1),
NucModelType.java (+36)
-
src/dr/evomodelxml:
HKYParser.java (+1 -1)
-
src/test/dr/beauti:
BeautiTesterConfig.java (+2 -2)
-
src/test/dr/integration:
GTRParameterEstimationTest.java (+1 -2)
-
dong.w.xie
2009-08-21 11:01
#147
Rev.: 2123
-
779 lines of code changed in 72 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+4 -3)
-
src/dr/app/beauti/components:
SequenceErrorModelComponentGenerator.java (+1),
SequenceErrorModelComponentOptions.java (+3),
SequenceErrorType.java (del),
TipDateSamplingComponentGenerator.java (+1),
TipDateSamplingComponentOptions.java (+3),
TipDateSamplingType.java (del)
-
src/dr/app/beauti/enumTypes:
AminoAcidModelType.java (new 68),
ClockType.java (+52),
FixRateType.java (+45),
FrequencyPolicyType.java (new 44),
NucModelType.java (new 36),
OperatorType.java (+69),
PriorScaleType.java (new 34),
PriorType.java (+135),
RelativeRatesType.java (new 43),
SequenceErrorType.java (+23),
StartingTreeType.java (+48),
TipDateSamplingType.java (new 21),
TreePriorType.java (+52)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -1),
BranchRatesModelGenerator.java (+1),
Generator.java (+1 -1),
InitialTreeGenerator.java (+2 -1),
OperatorsGenerator.java (+3 -5),
STARBEASTGenerator.java (+1),
SubstitutionModelGenerator.java (+4 -2),
TreeLikelihoodGenerator.java (+1),
TreeModelGenerator.java (+1 -1),
TreePriorGenerator.java (+2)
-
src/dr/app/beauti/options:
AminoAcidModelType.java (del),
BeautiOptions.java (+4 -7),
ClockModelOptions.java (+4),
ClockType.java (del),
FixRateType.java (del),
FrequencyPolicy.java (del),
ModelOptions.java (+3 -1),
NucModelType.java (del),
Operator.java (+2),
OperatorType.java (del),
Parameter.java (+2 -1),
PartitionClockModel.java (+3 -2),
PartitionClockModelTreeModelLink.java (+5 -1),
PartitionData.java (-1),
PartitionSubstitutionModel.java (+12 -7),
PartitionTreeModel.java (+3 -1),
PartitionTreePrior.java (+4 -1),
PriorScaleType.java (del),
RelativeRatesType.java (del),
StartingTreeType.java (del),
SubstitutionModelOptions.java (+3),
TreePriorType.java (del)
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+1),
PriorDialog.java (+1),
PriorType.java (del)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+5 -5)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+2 -2)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (+2 -2),
PartitionTreeModelPanel.java (+1 -9),
PartitionTreePriorPanel.java (+1 -2),
SpeciesTreesPanel.java (+3 -6),
TreesPanel.java (+2 -11)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+1 -1),
NexusApplicationImporter.java (+2)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+3 -3),
BeautiOptions.java (+1 -1)
-
src/dr/evomodel/substmodel:
EmpiricalAminoAcidModel.java (+1 -1),
HKY.java (+1 -1)
-
src/dr/evomodelxml:
HKYParser.java (+1 -1)
-
src/test/dr/beauti:
BeautiTesterConfig.java (+2)
-
src/test/dr/integration:
GTRParameterEstimationTest.java (+1)
-
dong.w.xie
2009-08-21 10:13
#146
Rev.: 2122
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
PartitionTreeModel.java (+5 -1)
-
alexander.alekseyenko
2009-08-21 09:56
#145
Rev.: 2121
-
7 lines of code changed in 1 file:
-
src/dr/evolution/datatype:
MutationDeathType.java (+7 -4)
-
rambaut
2009-08-20 21:06
#144
Rev.: 2120
-
6 lines of code changed in 1 file:
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+6)
-
dong.w.xie
2009-08-20 17:32
#143
Rev.: 2119
-
14 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -31),
ClockModelOptions.java (+12 -1),
ModelOptions.java (-12)
-
dong.w.xie
2009-08-20 17:22
#142
Rev.: 2118
-
148 lines of code changed in 15 files:
-
src/dr/app/beauti:
BeautiFrame.java (+5 -5)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+7 -7),
InitialTreeGenerator.java (+2 -2),
OperatorsGenerator.java (+6 -6),
STARBEASTGenerator.java (+5 -5),
TreePriorGenerator.java (+7 -7)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -5),
PartitionTreePrior.java (+21 -21),
TreePrior.java (del),
TreePriorType.java (new 52)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (-13)
-
src/dr/app/beauti/treespanel:
OldTreesPanel.java (+12 -12),
PartitionTreePriorPanel.java (+20 -20),
SpeciesTreesPanel.java (+4 -4),
TreesPanel.java (+2 -2)
-
dong.w.xie
2009-08-20 17:06
#141
Rev.: 2117
-
599 lines of code changed in 5 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+17 -382),
ModelOptions.java (+17 -3),
PartitionSubstitutionModel.java (+124 -129)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+440),
CommandLineBeauti.java (+1 -1)
-
dong.w.xie
2009-08-20 16:30
#140
Rev.: 2116
-
143 lines of code changed in 4 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+27 -331),
ClockModelOptions.java (-2),
SubstitutionModelOptions.java (+114)
-
dong.w.xie
2009-08-20 16:16
#139
Rev.: 2115
-
17 lines of code changed in 1 file:
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+17 -5)
-
dong.w.xie
2009-08-20 16:04
#138
Rev.: 2114
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+5 -16)
-
dong.w.xie
2009-08-20 15:57
#137
Rev.: 2113
-
18 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+2 -2)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2 -2)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+1 -1),
OperatorsGenerator.java (+1 -1),
TreePriorGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+7 -13)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+3 -3)
-
dong.w.xie
2009-08-20 15:13
#136
Rev.: 2112
-
270 lines of code changed in 13 files:
-
src/dr/app/beauti:
BeautiFrame.java (+9 -19)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+14 -10)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+11 -32),
InitialTreeGenerator.java (+9 -23),
OperatorsGenerator.java (+8 -7),
STARBEASTGenerator.java (+6 -6),
TreePriorGenerator.java (+3 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+33 -17)
-
src/dr/app/beauti/siteModelsPanel:
SiteModelsPanel.java (+13)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+14 -27),
PartitionTreePriorPanel.java (+66 -49),
SpeciesTreesPanel.java (+3 -3),
TreesPanel.java (+81 -82)
-
msuchard
2009-08-20 12:42
#135
Rev.: 2111
-
2 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/sitemodel:
GammaSiteRateModel.java (+1 -1)
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+1 -1)
-
rambaut
2009-08-20 08:02
#134
Rev.: 2110
-
371 lines of code changed in 1 file:
-
examples:
new_benchmark.xml (+371)
-
rambaut
2009-08-20 07:59
#133
Rev.: 2109
-
6 lines of code changed in 6 files:
-
src/dr/app/misc:
Coevolve.java (new)
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+2 -1)
-
src/dr/evomodel/MSSD:
ALSTreeLikelihood.java (+1 -1)
-
src/dr/evomodel/treelikelihood:
EpochTreeLikelihood.java (+1 -1),
NodePosteriorTreeLikelihood.java (+1 -1)
-
msuchard
2009-08-20 06:17
#132
Rev.: 2108
-
7 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+7 -3)
-
msuchard
2009-08-20 06:14
#131
Rev.: 2107
-
13 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
TreeLikelihood.java (+13 -2)
-
msuchard
2009-08-20 04:44
#130
Rev.: 2106
-
53 lines of code changed in 5 files:
-
src/dr/app/beagle/evomodel/parsers:
AncestralStateTreeLikelihoodParser.java (+10 -3),
TreeLikelihoodParser.java (+12 -4)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+2 -2),
BeagleTreeLikelihood.java (+20 -3),
PartialsRescalingScheme.java (+9)
-
msuchard
2009-08-19 16:56
#129
Rev.: 2105
-
15 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+15 -17)
-
dong.w.xie
2009-08-19 14:50
#128
Rev.: 2104
-
72 lines of code changed in 5 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+4 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -7),
ClockModelOptions.java (+35 -1),
FixRateType.java (new 4),
PartitionClockModel.java (+24 -6)
-
msuchard
2009-08-19 06:31
#127
Rev.: 2103
-
2 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+1 -1)
-
src/dr/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+1 -1)
-
msuchard
2009-08-19 06:28
#126
Rev.: 2102
-
57 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+6 -4)
-
src/dr/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+6 -4)
-
src/dr/inference/model:
BayesianStochasticSearchVariableSelection.java (+45 -2)
-
msuchard
2009-08-18 21:30
#125
Rev.: 2101
-
19 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+4 -10)
-
src/dr/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+5 -11)
-
src/dr/inference/model:
BayesianStochasticSearchVariableSelection.java (+10)
-
Sibon.Li@gmail.com
2009-08-18 17:57
#124
Rev.: 2100
-
1 lines of code changed in 2 files:
-
src/test/dr/distibutions:
NormalDistributionTest.java (+1 -1)
-
Sibon.Li@gmail.com
2009-08-18 17:53
#123
Rev.: 2099
-
5 lines of code changed in 4 files:
-
src/dr/math/distributions:
InverseGaussianDistribution.java (new),
LogNormalDistribution.java (+2 -1),
NormalDistribution.java (+1 -1)
-
dong.w.xie
2009-08-18 16:36
#122
Rev.: 2098
-
52 lines of code changed in 7 files:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -1)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+12 -3)
-
src/dr/app/beauti/datapanel:
DataPanel.java (+2)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+29 -1),
PartitionClockModel.java (+3 -3),
PartitionClockModelTreeModelLink.java (+1 -1)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+2 -5)
-
dong.w.xie
2009-08-18 14:08
#121
Rev.: 2097
-
127 lines of code changed in 10 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+2 -2),
TipDateSamplingComponentOptions.java (+2 -2)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -5),
ModelOptions.java (+14 -14),
Parameter.java (+7 -7),
PartitionClockModel.java (+4 -4),
PartitionClockModelTreeModelLink.java (+5 -5),
PartitionSubstitutionModel.java (+31 -31),
PartitionTreePrior.java (+20 -20),
PriorScaleType.java (new 37)
-
dong.w.xie
2009-08-18 12:11
#120
Rev.: 2096
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1)
-
dong.w.xie
2009-08-18 12:04
#119
Rev.: 2095
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -1)
-
dong.w.xie
2009-08-18 11:57
#118
Rev.: 2094
-
47 lines of code changed in 5 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+14 -14)
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+5 -2)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+17),
PartitionClockModel.java (+9 -18),
PartitionClockModelTreeModelLink.java (+2 -2)
-
jheled
2009-08-18 11:18
#117
Rev.: 2093
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+3 -1)
-
msuchard
2009-08-18 06:52
#116
Rev.: 2092
-
164 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/substmodel:
GeneralSubstitutionModel.java (+1 -1),
SVSGeneralSubstitutionModel.java (+80 -1)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+1 -1)
-
src/dr/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+82 -21)
-
dong.w.xie
2009-08-17 17:33
#115
Rev.: 2091
-
174 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+26 -487),
BranchRatesModelGenerator.java (+73 -1),
OperatorsGenerator.java (+23 -17)
-
src/dr/app/beauti/options:
BeautiOptions.java (+8 -5),
ClockModelOptions.java (+1 -1),
RelativeRatesType.java (new 43)
-
msuchard
2009-08-17 17:12
#114
Rev.: 2090
-
26 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+4),
PartialsRescalingScheme.java (+22)
-
jheled
2009-08-17 16:57
#113
Rev.: 2089
-
8 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+1 -1)
-
src/dr/inference/distribution:
CachedDistributionLikelihood.java (+1 -1)
-
src/dr/inferencexml:
CachedDistributionLikelihoodParser.java (+6 -6)
-
jheled
2009-08-17 16:56
#112
Rev.: 2088
-
2 lines of code changed in 1 file:
-
src/dr/evolution/io:
NexusImporter.java (+2 -1)
-
dong.w.xie
2009-08-17 16:27
#111
Rev.: 2087
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+1)
-
dong.w.xie
2009-08-17 13:07
#110
Rev.: 2086
-
28 lines of code changed in 5 files:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+6 -8)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -1),
ModelOptions.java (+9),
OperatorType.java (new 1),
PartitionClockModelTreeModelLink.java (+1 -4)
-
dong.w.xie
2009-08-17 12:55
#109
Rev.: 2085
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -3)
-
dong.w.xie
2009-08-17 12:06
#108
Rev.: 2084
-
50 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+15 -3),
BranchRatesModelGenerator.java (+28)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+7 -2)
-
msuchard
2009-08-17 09:02
#107
Rev.: 2083
-
38 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/parsers:
AncestralStateTreeLikelihoodParser.java (+11 -4),
TreeLikelihoodParser.java (+7 -2)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+3 -1),
BeagleTreeLikelihood.java (+17 -9)
-
msuchard
2009-08-16 15:16
#106
Rev.: 2082
-
24 lines of code changed in 4 files:
-
src/dr/evomodel/sitemodel:
GammaSiteModel.java (+6)
-
src/dr/evomodel/substmodel:
FrequencyModel.java (+6),
SVSGeneralSubstitutionModel.java (+6)
-
src/dr/evomodel/treelikelihood:
AncestralStateTreeLikelihood.java (+6)
-
msuchard
2009-08-16 14:35
#105
Rev.: 2081
-
376 lines of code changed in 4 files:
-
src/dr/app/beagle/evomodel/parsers:
AncestralStateTreeLikelihoodParser.java (+81)
-
src/dr/app/beagle/evomodel/treelikelihood:
AncestralStateBeagleTreeLikelihood.java (+281),
BeagleTreeLikelihood.java (+13 -9)
-
src/dr/app/beast:
beagle_parsers.properties (+1)
-
msuchard
2009-08-16 11:56
#104
Rev.: 2080
-
153 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/parsers:
SVSGeneralSubstitutionModelParser.java (+115)
-
src/dr/app/beagle/evomodel/substmodel:
SVSGeneralSubstitutionModel.java (+37)
-
src/dr/app/beast:
beagle_parsers.properties (+1 -1)
-
msuchard
2009-08-16 10:50
#103
Rev.: 2079
-
128 lines of code changed in 4 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/inference/distribution:
CachedDistributionLikelihood.java (+69)
-
src/dr/inferencexml:
CachedDistributionLikelihoodParser.java (+57),
DistributionLikelihoodParser.java (+1 -1)
-
msuchard
2009-08-16 05:53
#102
Rev.: 2078
-
22 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/sitemodel:
GammaSiteRateModel.java (+3 -1)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+19 -1)
-
msuchard
2009-08-16 05:03
#101
Rev.: 2077
-
11 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+11 -1)
-
msuchard
2009-08-15 13:46
#100
Rev.: 2076
-
10 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/parsers:
GammaSiteModelParser.java (+1 -1)
-
src/dr/app/beagle/evomodel/sitemodel:
GammaSiteRateModel.java (+7 -5)
-
src/dr/inference/markovchain:
MarkovChain.java (+2 -2)
-
rambaut
2009-08-15 12:16
#99
Rev.: 2075
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
rambaut
2009-08-15 12:15
#98
Rev.: 2074
-
1 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+1 -1)
-
msuchard
2009-08-15 11:07
#97
Rev.: 2073
-
110 lines of code changed in 3 files:
-
src/dr/app/beagle/evomodel/parsers:
GeneralSubstitutionModelParser.java (+107)
-
src/dr/app/beagle/evomodel/substmodel:
GeneralSubstitutionModel.java (+2 -73)
-
src/dr/app/beast:
beagle_parsers.properties (+1)
-
dong.w.xie
2009-08-14 17:55
#96
Rev.: 2072
-
391 lines of code changed in 12 files:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+143 -49)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+3 -3),
OperatorsGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+42 -42),
ClockModelOptions.java (+105),
FixRateType.java (+3 -3),
PartitionClockModel.java (+43 -30),
PartitionClockModelTreeModelLink.java (+32 -28)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+6 -2)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+11 -1)
-
src/test/dr/beauti:
BeautiTesterConfig.java (+1 -1)
-
rambaut
2009-08-14 12:09
#95
Rev.: 2071
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
dong.w.xie
2009-08-13 14:03
#94
Rev.: 2070
-
5 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+5 -5)
-
dong.w.xie
2009-08-13 13:27
#93
Rev.: 2069
-
15 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+11 -5)
-
src/dr/app/beauti/options:
BeautiOptions.java (+4 -33)
-
rambaut
2009-08-13 12:40
#92
Rev.: 2068
-
299 lines of code changed in 2 files:
-
examples:
benchmark.xml (new 292)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+7 -1)
-
dong.w.xie
2009-08-13 12:20
#91
Rev.: 2067
-
84 lines of code changed in 7 files:
-
build_BEAST_MCMC.xml (+56 -48)
-
release:
LogAnalyser_launch4j.xml (new 20),
LogCombiner_launch4j.xml (new 4),
TreeAnnotator_launch4j.xml (new 4)
-
release/extra_lib:
NucleotideLikelihoodCore.dll (new),
libNucleotideLikelihoodCore.jnilib (new),
libNucleotideLikelihoodCore.so (new)
-
msuchard
2009-08-13 10:17
#90
Rev.: 2066
-
37 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
AbstractTreeLikelihood.java (+26 -1),
BeagleTreeLikelihood.java (+11 -1)
-
rambaut
2009-08-13 09:45
#89
Rev.: 2065
-
14 lines of code changed in 2 files:
-
src/dr/evomodel/branchratemodel:
ArbitraryBranchRates.java (+1 -1),
DiscretizedBranchRates.java (+13 -9)
-
msuchard
2009-08-13 09:31
#88
Rev.: 2064
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/branchratemodel:
DiscretizedBranchRates.java (+1 -1)
-
rambaut
2009-08-13 02:28
#87
Rev.: 2063
-
29 lines of code changed in 5 files:
-
examples:
benchmark.xml (+4 -1)
-
src/dr/app/beagle/evomodel/treelikelihood:
AbstractTreeLikelihood.java (+6 -1),
BeagleTreeLikelihood.java (+7 -9)
-
src/dr/evomodel/treelikelihood:
AbstractTreeLikelihood.java (+4 -1),
TreeLikelihood.java (+8 -1)
-
rambaut
2009-08-12 23:45
#86
Rev.: 2062
-
58 lines of code changed in 1 file:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+58 -29)
-
rambaut
2009-08-12 22:41
#85
Rev.: 2061
-
1175 lines of code changed in 19 files:
-
src/dr/app/beauti/alignmentviewer:
AlignmentBuffer.java (new 20),
AlignmentBufferListener.java (new 9),
AlignmentPane.java (new 259),
AlignmentViewer.java (new 182),
AminoAcidDecorator.java (new 46),
CellDecorator.java (new 12),
ChemicalAminoAcidDecorator.java (new 79),
ColumnDecorator.java (new 11),
HydropathyAminoAcidDecorator.java (new 52),
NucleotideDecorator.java (new 43),
PlotPane.java (new 84),
RowDecorator.java (new 11),
RulerPane.java (new 106),
StateCellDecorator.java (new 37),
StateDecorator.java (new 11),
TaxonPane.java (new 39),
VolumeAminoAcidDecorator.java (new 60)
-
src/dr/app/beauti/datapanel:
BeautiAlignmentBuffer.java (new 62),
DataPanel.java (+52 -49)
-
dong.w.xie
2009-08-12 17:20
#84
Rev.: 2060
-
1 lines of code changed in 1 file:
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+1 -1)
-
dong.w.xie
2009-08-12 16:57
#83
Rev.: 2059
-
81 lines of code changed in 4 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+17 -9),
ViewAligmentPanel.java (new),
ViewAlignmentDialog.java (del)
-
Sibon.Li@gmail.com
2009-08-12 14:42
#82
Rev.: 2058
-
6 lines of code changed in 2 files:
-
src/test/dr/distibutions:
InverseGaussianDistributionTest.java (new)
-
Sibon.Li@gmail.com
2009-08-12 14:39
#81
Rev.: 2057
-
262 lines of code changed in 2 files:
-
src/dr/math/distributions:
InverseGaussianDistribution.java (+203 -79)
-
src/test/dr/distibutions:
InverseGaussianDistributionTest.java (+59 -21)
-
dong.w.xie
2009-08-12 12:55
#80
Rev.: 2056
-
97 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
ViewAligmentPanel.java (+82),
ViewAlignmentDialog.java (new 15)
-
msuchard
2009-08-12 08:34
#79
Rev.: 2055
-
7 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+7 -2)
-
dong.w.xie
2009-08-11 16:21
#78
Rev.: 2054
-
141 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+22 -5),
ViewAlignmentDialog.java (+119)
-
dong.w.xie
2009-08-11 11:17
#77
Rev.: 2053
-
128 lines of code changed in 12 files:
-
src/dr/app/beauti:
BeautiApp.java (+2 -4),
BeautiMenuBarFactory.java (+3 -1)
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+6)
-
src/dr/app/oldbeauti:
BeautiApp.java (+2 -1),
BeautiMenuBarFactory.java (+3 -1)
-
src/dr/app/pathogen:
PathogenApp.java (+2 -1),
PathogenMenuBarFactory.java (+3 -1)
-
src/dr/app/tracer/application:
TracerApp.java (+2 -1),
TracerMenuBarFactory.java (+3 -1)
-
src/dr/app/treestat:
TreeStatApp.java (+3 -1)
-
src/dr/app/util:
OSType.java (+75),
Utils.java (+24 -24)
-
dong.w.xie
2009-08-11 10:16
#76
Rev.: 2052
-
2 lines of code changed in 32 files:
-
build_BEAST_MCMC.xml (+2)
-
release/Launch4j:
LICENSE.txt (del),
Launch4j.url (del),
launch4j.jar (del),
launch4j.jfpr (del)
-
release/Launch4j/bin:
COPYING (del),
ld.exe (del),
windres.exe (del)
-
release/Launch4j/head:
LICENSE.txt (del)
-
release/Launch4j/lib:
JGoodies.Forms.LICENSE.txt (del),
JGoodies.Looks.LICENSE.txt (del),
Nuvola.Icon.Theme.LICENSE.txt (del),
XStream.LICENSE.txt (del),
commons-beanutils.jar (del),
commons-logging.jar (del),
commons.LICENSE.txt (del),
forms.jar (del),
formsrt.jar (del),
foxtrot.LICENSE.txt (del),
foxtrot.jar (del),
looks.jar (del),
xstream.jar (del)
-
release/Launch4j/manifest:
uac.exe.manifest (del),
xp-themes.exe.manifest (del)
-
release/Launch4j/w32api:
MinGW.LICENSE.txt (del),
libadvapi32.a (del),
libgcc.a (del),
libkernel32.a (del),
libmingw32.a (del),
libmsvcrt.a (del),
libshell32.a (del),
libuser32.a (del)
-
rambaut
2009-08-10 20:40
#75
Rev.: 2051
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
rambaut
2009-08-10 20:37
#74
Rev.: 2050
-
42 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/parsers:
TreeLikelihoodParser.java (+1 -7)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+41 -9)
-
Sibon.Li@gmail.com
2009-08-10 18:03
#73
Rev.: 2049
-
352 lines of code changed in 2 files:
-
src/dr/math/distributions:
NormalDistribution.java (+229)
-
src/test/dr/distibutions:
NormalDistributionTest.java (+123)
-
dong.w.xie
2009-08-10 17:08
#72
Rev.: 2048
-
21 lines of code changed in 1 file:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+21 -7)
-
dong.w.xie
2009-08-10 16:49
#71
Rev.: 2047
-
1267 lines of code changed in 11 files:
-
src/dr/app/beauti:
BeautiFrame.java (+12 -8)
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+329)
-
src/dr/app/beauti/modelsPanel:
ClockModelPanel.java (del),
CreateModelDialog.java (del),
ModelsPanel.java (del),
PartitionModelPanel.java (del)
-
src/dr/app/beauti/siteModelsPanel:
ClockModelPanel.java (del),
CreateModelDialog.java (+104),
ModelsPanel.java (del),
PartitionModelPanel.java (+397),
SiteModelsPanel.java (+425)
-
dong.w.xie
2009-08-10 12:57
#70
Rev.: 2046
-
2 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
PartitionClockModel.java (+1 -1)
-
dong.w.xie
2009-08-10 11:56
#69
Rev.: 2045
-
1731 lines of code changed in 50 files:
-
build_BEAST_MCMC.xml (+91 -38)
-
icons:
beast.icns (del),
beast.ico (del),
beast.png (del),
beauti.icns (del),
beauti.ico (del),
beauti.png (del),
beautidoc.icns (del),
beautidoc.ico (del),
utility.icns (del),
utility.ico (del),
utility.png (del)
-
release:
BEAST_launch4j.xml (new 1),
BEAUTi_launch4j.xml (new 16),
LogCombiner_launch4j.xml (+16),
README.txt (+193),
TreeAnnotator_launch4j.xml (+16),
VERSION HISTORY.txt (+284),
icons (new)
-
release/Launch4j:
LICENSE.txt (new 30),
Launch4j.url (new 2),
launch4j.jar (new),
launch4j.jfpr (new)
-
release/Launch4j/bin:
COPYING (new 340),
ld.exe (new),
windres.exe (new)
-
release/Launch4j/head:
LICENSE.txt (new 23)
-
release/Launch4j/lib:
JGoodies.Forms.LICENSE.txt (new 31),
JGoodies.Looks.LICENSE.txt (new 31),
Nuvola.Icon.Theme.LICENSE.txt (new 504),
XStream.LICENSE.txt (new 27),
commons-beanutils.jar (new),
commons-logging.jar (new),
commons.LICENSE.txt (new 50),
forms.jar (new),
formsrt.jar (new),
foxtrot.LICENSE.txt (new 25),
foxtrot.jar (new),
looks.jar (new),
xstream.jar (new)
-
release/Launch4j/manifest:
uac.exe.manifest (new 12),
xp-themes.exe.manifest (new 14)
-
release/Launch4j/w32api:
MinGW.LICENSE.txt (new 25),
libadvapi32.a (new),
libgcc.a (new),
libkernel32.a (new),
libmingw32.a (new),
libmsvcrt.a (new),
libshell32.a (new),
libuser32.a (new)
-
rambaut
2009-08-07 20:50
#68
Rev.: 2044
-
0 lines of code changed in 13 files:
-
build_development.xml (del),
build_release.xml (del)
-
icons:
beast.icns (new),
beast.ico (new),
beast.png (new),
beauti.icns (new),
beauti.ico (new),
beauti.png (new),
beautidoc.icns (new),
beautidoc.ico (new),
utility.icns (new),
utility.ico (new),
utility.png (new)
-
philippe.lemey@gmail.com
2009-08-07 17:55
#67
Rev.: 2043
-
231 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+231 -14)
-
dong.w.xie
2009-08-07 16:38
#66
Rev.: 2042
-
0 lines of code changed in 27 files:
-
examples/beauti1.6:
26.nex (del),
29.nex (del),
47.nex (del),
53.nex (del),
59.nex (del),
64.nex (del),
72.nex (del),
Darwins-finches.nex (del)
-
examples/beauti1.6/codon:
m1.xml (del),
m2.xml (del),
m3.xml (del),
m4.xml (del),
m5.xml (del),
m6.xml (del)
-
examples/beauti1.6/starBEAST:
g10.xml (del),
g11.xml (del),
x10.xml (del),
x11.xml (del)
-
examples/beauti1.6/treePrior+clockModel:
x1.xml (del),
x2.xml (del),
x3.xml (del),
x4.xml (del),
x5.xml (del),
x6.xml (del),
x7.xml (del),
x8.xml (del),
x9.xml (del)
-
dong.w.xie
2009-08-07 16:35
#65
Rev.: 2041
-
86 lines of code changed in 2 files:
-
build_BEAST_MCMC.xml (+70)
-
release:
BEAST_launch4j.xml (+16)
-
dong.w.xie
2009-08-07 15:45
#64
Rev.: 2040
-
2 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastMain.java (+2 -1)
-
rambaut
2009-08-06 23:44
#63
-
9 lines of code changed in 2 files:
-
lib:
beagle.jar (changed)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+9 -5)
-
dong.w.xie
2009-08-06 16:57
#62
Rev.: 2037
-
6 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+6 -2)
-
msuchard
2009-08-06 14:23
#61
Rev.: 2036
-
1 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+1 -1)
-
dong.w.xie
2009-08-06 14:12
#60
Rev.: 2035
-
16 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+16 -11)
-
jheled
2009-08-06 14:08
#59
Rev.: 2034
-
2 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
SpeciesBindings.java (+2 -1)
-
msuchard
2009-08-06 13:17
#58
Rev.: 2033
-
46 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+46 -26)
-
dong.w.xie
2009-08-06 12:24
#57
Rev.: 2032
-
8 lines of code changed in 2 files:
-
jar_ind_tool.xml (del)
-
src/dr/app/beauti/options:
PartitionClockModelTreeModelLink.java (+8 -8)
-
rambaut
2009-08-06 12:08
#56
Rev.: 2031
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/treelikelihood:
TreeLikelihood.java (+1)
-
msuchard
2009-08-06 08:28
#55
Rev.: 2030
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
jheled
2009-08-06 08:22
#54
Rev.: 2029
-
22 lines of code changed in 10 files:
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+2 -13)
-
src/dr/app/beauti/util:
CommandLineBeauti.java (+7 -8)
-
src/dr/evolution/coalescent:
CoalescentSimulator.java (+2 -2),
ConstantPopulation.java (new)
-
src/dr/evolution/distance:
JukesCantorDistanceMatrix.java (+8 -11)
-
src/dr/evoxml:
DistanceMatrixParser.java (new)
-
src/dr/util:
ErrorLogHandler.java (+1 -1)
-
jheled
2009-08-06 08:22
#53
Rev.: 2028
-
12 lines of code changed in 1 file:
-
src/dr/evomodel/speciation:
SpeciesTreeModel.java (+12 -5)
-
jheled
2009-08-06 08:21
#52
Rev.: 2027
-
1 lines of code changed in 1 file:
-
src/dr/evoxml:
UPGMATreeParser.java (+1 -1)
-
msuchard
2009-08-06 03:05
#51
Rev.: 2026
-
8 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+8 -7)
-
rambaut
2009-08-06 01:56
#50
-
5 lines of code changed in 2 files:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+1 -5)
-
dong.w.xie
2009-08-05 14:03
#49
Rev.: 2023
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+1 -1)
-
alexei.drummond
2009-08-05 13:05
#48
Rev.: 2022
-
39 lines of code changed in 2 files:
-
tracer_release.xml (new 27)
-
src/dr/app/tracer/analysis:
DemographicDialog.java (+12 -4)
-
dong.w.xie
2009-08-05 11:50
#47
Rev.: 2021
-
23 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+23 -32)
-
msuchard
2009-08-05 08:29
#46
Rev.: 2020
-
16 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+16 -14)
-
rambaut
2009-08-05 03:26
#45
Rev.: 2019
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
rambaut
2009-08-05 02:51
#44
Rev.: 2018
-
53 lines of code changed in 1 file:
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+53 -45)
-
dong.w.xie
2009-08-04 15:23
#43
Rev.: 2017
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -2)
-
rambaut
2009-08-04 12:39
#42
Rev.: 2014
-
23 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastMain.java (+3 -7),
BeastVersion.java (+6 -5)
-
src/dr/app/beauti:
BeautiApp.java (+3 -1)
-
src/dr/app/beauti/modelsPanel:
ModelsPanel.java (+4 -4)
-
src/dr/app/oldbeauti:
BeautiApp.java (+7 -11)
-
dong.w.xie
2009-08-04 11:23
#41
Rev.: 2013
-
53 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+53 -12)
-
rambaut
2009-08-04 10:59
#40
Rev.: 2012
-
9 lines of code changed in 1 file:
-
src/dr/app/beauti:
BeautiFrame.java (+9 -10)
-
dong.w.xie
2009-08-04 10:16
#39
Rev.: 2011
-
0 lines of code changed in 9 files:
-
examples/beauti1.6/treePrior+clockModel:
x1.xml (new),
x2.xml (new),
x3.xml (new),
x4.xml (new),
x5.xml (new),
x6.xml (new),
x7.xml (new),
x8.xml (new),
x9.xml (new)
-
rambaut
2009-08-04 04:03
#38
Rev.: 2010
-
13 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+13)
-
rambaut
2009-08-04 03:47
#37
Rev.: 2009
-
4757 lines of code changed in 68 files:
-
build_BEAST_MCMC.xml (+1)
-
src/dr/app/beagle:
parsers (del),
sitemodel (del),
substmodel (del),
treelikelihood (del)
-
src/dr/app/beagle/evomodel/parsers:
CompoundLikelihoodParser.java (+61),
FrequencyModelParser.java (+110),
GTRParser.java (+121),
GY94CodonModelParser.java (+106),
GammaSiteModelParser.java (+113),
HKYParser.java (+59),
MarkovModulatedGY94CodonModelParser.java (+74),
TreeLikelihoodParser.java (+84)
-
src/dr/app/beagle/evomodel/sitemodel:
BranchSiteModel.java (+16),
GammaSiteRateModel.java (+342),
HomogenousBranchSiteModel.java (+63),
SiteRateModel.java (+76)
-
src/dr/app/beagle/evomodel/substmodel:
BaseSubstitutionModel.java (+362),
ColtEigenSystem.java (+54),
DefaultEigenSystem.java (+676),
EigenDecomposition.java (+54),
EigenSystem.java (+38),
FrequencyModel.java (+150),
GTR.java (+181),
GY94CodonModel.java (+388),
GeneralSubstitutionModel.java (+200),
HKY.java (+259),
MarkovModulatedGY94CodonModel.java (+172),
SubstitutionModel.java (+68)
-
src/dr/app/beagle/evomodel/treelikelihood:
AbstractTreeLikelihood.java (+270),
BeagleTreeLikelihood.java (+645)
-
src/dr/app/beast:
beagle_parsers.properties (+8 -8)
-
src/dr/evomodel/beagle/parsers:
CompoundLikelihoodParser.java (del),
FrequencyModelParser.java (del),
GTRParser.java (del),
GY94CodonModelParser.java (del),
GammaSiteModelParser.java (del),
HKYParser.java (del),
MarkovModulatedGY94CodonModelParser.java (del),
TreeLikelihoodParser.java (del)
-
src/dr/evomodel/beagle/sitemodel:
BranchSiteModel.java (del),
GammaSiteRateModel.java (del),
HomogenousBranchSiteModel.java (del),
SiteRateModel.java (del)
-
src/dr/evomodel/beagle/substmodel:
BaseSubstitutionModel.java (del),
ColtEigenSystem.java (del),
DefaultEigenSystem.java (del),
EigenDecomposition.java (del),
EigenSystem.java (del),
FrequencyModel.java (del),
GTR.java (del),
GY94CodonModel.java (del),
GeneralSubstitutionModel.java (del),
HKY.java (del),
MarkovModulatedGY94CodonModel.java (del),
SubstitutionModel.java (del)
-
src/dr/evomodel/beagle/treelikelihood:
AbstractTreeLikelihood.java (del),
BeagleTreeLikelihood.java (del)
-
src/dr/evomodel/newtreelikelihood:
GPULikelihoodCore.java (+1 -1),
LikelihoodCoreFactory.java (+1 -1),
NativeLikelihoodCore.java (+1 -1),
ThreadedGPULikelihoodCore.java (+1 -1),
TreeLikelihood.java (new)
-
src/dr/inference/model:
LikelihoodBenchmarker.java (+1 -1)
-
rambaut
2009-08-04 03:37
#36
Rev.: 2008
-
2 lines of code changed in 1 file:
-
src/dr/inference/model:
CompoundLikelihood.java (+2 -2)
-
philippe.lemey@gmail.com
2009-08-04 01:08
#35
Rev.: 2007
-
0 lines of code changed in 1 file:
-
src/dr/app/tools:
RateIndicatorToKML.java (new)
-
rambaut
2009-08-04 00:16
#34
Rev.: 2006
-
21 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+14 -10)
-
src/dr/app/beauti/modelsPanel:
ModelsPanel.java (+4 -4)
-
src/dr/app/util:
Utils.java (+3 -2)
-
rambaut
2009-08-03 22:37
#33
Rev.: 2005
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/util:
BeastImporter.java (+1 -7)
-
rambaut
2009-08-03 21:24
#32
Rev.: 2004
-
22 lines of code changed in 2 files:
-
src/dr/app/beast:
BeastMain.java (+13 -1)
-
src/dr/inference/model:
CompoundLikelihood.java (+9 -1)
-
dong.w.xie
2009-08-03 16:59
#31
Rev.: 2003
-
1 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
-
dong.w.xie
2009-08-03 15:35
#30
Rev.: 2001
-
1873 lines of code changed in 10 files:
-
examples/beauti1.6/starBEAST:
g10.xml (+863 -8),
g11.xml (new),
x10.xml (new),
x11.xml (+56 -18)
-
src/dr/app/beauti/generator:
STARBEASTGenerator.java (+6 -1),
TreePriorGenerator.java (+4)
-
dong.w.xie
2009-08-03 14:45
#29
Rev.: 2000
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+1 -1)
-
dong.w.xie
2009-08-03 11:08
#28
Rev.: 1999
-
28 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
STARBEASTGenerator.java (+28 -18)
-
dong.w.xie
2009-08-03 11:06
#27
Rev.: 1998
-
14 lines of code changed in 2 files:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+3 -1)
-
src/dr/app/beauti/treespanel:
TreesPanel.java (+11 -10)
-
rambaut
2009-08-03 05:05
#26
Rev.: 1997
-
51 lines of code changed in 2 files:
-
src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (new)
-
rambaut
2009-08-02 23:13
#25
Rev.: 1996
-
94 lines of code changed in 1 file:
-
src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (+94 -81)
-
rambaut
2009-08-02 21:57
#24
Rev.: 1995
-
87 lines of code changed in 2 files:
-
lib:
beagle.jar (changed)
-
src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (+87 -44)
-
philippe.lemey@gmail.com
2009-08-02 05:13
#23
Rev.: 1994
-
4 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+4 -4)
-
msuchard
2009-08-02 04:06
#22
Rev.: 1993
-
2 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastVersion.java (+2 -2)
-
rambaut
2009-08-01 23:49
#21
Rev.: 1992
-
94 lines of code changed in 6 files:
-
src/dr/app/beast:
BeastMain.java (+14 -46),
BeastRemote.java (-1),
BeastVersion.java (+55 -3)
-
src/dr/app/beauti:
BeautiApp.java (+6 -10)
-
src/dr/app/pathogen:
PathogenApp.java (+15 -6)
-
src/dr/util:
Version.java (+4)
-
akaruiws
2009-08-01 19:57
#20
Rev.: 1991
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+1 -7)
-
akaruiws
2009-08-01 19:51
#19
Rev.: 1990
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
AsymmetricQuadraticModel.java (+1 -1)
-
akaruiws
2009-08-01 19:44
#18
Rev.: 1989
-
1 lines of code changed in 1 file:
-
src/dr/evomodelxml:
AsymQuadModelParser.java (+1 -3)
-
akaruiws
2009-08-01 19:35
#17
Rev.: 1988
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
AsymmetricQuadraticModel.java (+1 -2)
-
akaruiws
2009-08-01 19:33
#16
Rev.: 1987
-
8 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+8 -1)
-
akaruiws
2009-08-01 19:22
#15
Rev.: 1986
-
0 lines of code changed in 1 file:
-
src/dr/evomodelxml:
AsymQuadModelParser.java (-1)
-
akaruiws
2009-08-01 19:17
#14
-
333 lines of code changed in 2 files:
-
src/dr/evomodelxml:
AsymQuadModelParser.java (+105)
-
src/test/dr/evomodel/substmodel:
AsymQuadTest.java (+228)
-
akaruiws
2009-08-01 19:15
#13
Rev.: 1983
-
170 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
AsymmetricQuadraticModel.java (+170)
-
akaruiws
2009-08-01 19:13
#12
Rev.: 1982
-
51 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
OnePhaseModel.java (+51)
-
akaruiws
2009-08-01 19:11
#11
Rev.: 1981
-
120 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+120)
-
akaruiws
2009-08-01 18:56
#10
Rev.: 1980
-
22 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+22 -15)
-
akaruiws
2009-08-01 18:27
#9
Rev.: 1979
-
3 lines of code changed in 1 file:
-
src/dr/evoxml:
DistanceMatrixParser.java (+3 -1)
-
akaruiws
2009-08-01 18:22
#8
Rev.: 1978
-
35 lines of code changed in 1 file:
-
src/dr/evolution/distance:
SMMDistanceMatrix.java (new 35)
-
akaruiws
2009-08-01 18:17
#7
Rev.: 1977
-
5 lines of code changed in 1 file:
-
src/dr/evoxml:
DistanceMatrixParser.java (+5 -1)
-
akaruiws
2009-08-01 18:16
#6
Rev.: 1976
-
99 lines of code changed in 1 file:
-
src/dr/evoxml:
MicrosatellitePatternParser.java (+99)
-
akaruiws
2009-08-01 17:57
#5
Rev.: 1975
-
51 lines of code changed in 1 file:
-
src/dr/evoxml:
MicrosatelliteParser.java (+51)
-
akaruiws
2009-08-01 17:52
#4
Rev.: 1974
-
245 lines of code changed in 1 file:
-
src/dr/evolution/datatype:
Microsatellite.java (+245)
-
msuchard
2009-08-01 06:12
#3
Rev.: 1973
-
19 lines of code changed in 1 file:
-
src/dr/evomodel/branchratemodel:
TraitBranchRateModel.java (+19 -7)
-
rambaut
2009-08-01 04:03
#2
Rev.: 1972
-
97 lines of code changed in 3 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/app/tools:
LogCombiner.java (+42 -19)
-
src/dr/evomodel/branchratemodel:
TraitBranchRateModel.java (+54 -18)
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rambaut
2009-08-01 01:52
#1
Rev.: 1971
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3 lines of code changed in 2 files:
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src/dr/app/beast:
beagle_parsers.properties (+1 -1)
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src/dr/evomodel/beagle/treelikelihood:
BeagleTreeLikelihood.java (+2 -2)