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rambaut
2010-12-23 00:42
#32
Rev.: 3768
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362 lines of code changed in 2 files:
-
src/dr/app/tools:
TimeSlicer.java (+292 -95)
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src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+70 -114)
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rambaut
2010-12-22 11:38
#31
Rev.: 3767
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16 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+16)
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rambaut
2010-12-22 11:31
#30
Rev.: 3766
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41 lines of code changed in 1 file:
-
src/dr/app/tools:
AntigenicPlotter.java (+41 -41)
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rambaut
2010-12-22 11:23
#29
Rev.: 3765
-
350 lines of code changed in 2 files:
-
src/dr/app/tools:
AntigenicPlotter.java (+148 -31),
TimeSlicer.java (+202 -128)
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rambaut
2010-12-22 00:20
#28
Rev.: 3764
-
5 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+5 -1)
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rambaut
2010-12-22 00:04
#27
Rev.: 3763
-
9 lines of code changed in 4 files:
-
src/dr/app/phylogeography/tools:
TreeKMLGenerator.java (+4 -5)
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src/dr/app/phylogeography/tools/kml:
Settings.java (+3 -3)
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src/dr/app/tools:
TimeSlicer.java (+2 -2)
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rambaut
2010-12-21 22:48
#26
Rev.: 3762
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2 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+2 -2)
-
philippe.lemey@gmail.com
2010-12-21 09:34
#25
Rev.: 3761
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1 lines of code changed in 1 file:
-
src/dr/geo:
KernelDensityEstimator2D.java (+1 -1)
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rambaut
2010-12-17 10:49
#24
Rev.: 3760
-
131 lines of code changed in 2 files:
-
src/dr/app/beast:
development_parsers.properties (+1)
-
src/dr/evomodel/branchratemodel:
PassageBranchRateModel.java (new 130)
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dong.w.xie
2010-12-15 16:57
#23
Rev.: 3759
-
5 lines of code changed in 5 files:
-
src/dr/evomodel/speciation:
ModelAveragingSpeciationLikelihood.java (+2 -1)
-
src/dr/evomodel/speciation/ModelAveragingResearch:
ModelAveragingIndexSpeciationLikelihood.java (+2 -1)
-
src/dr/inference/model:
Bounds.java (new)
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dong.w.xie
2010-12-15 15:58
#22
Rev.: 3758
-
8 lines of code changed in 5 files:
-
src/dr/evomodel/speciation:
ModelAveragingSpeciationLikelihood.java (+2 -2)
-
src/dr/evomodelxml/speciation:
ModelAveragingSpeciationLikelihoodParser.java (+1 -1)
-
src/test/dr/evomodel/operators:
UniformIntegerOperatorTest.java (+5 -5)
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dong.w.xie
2010-12-15 14:49
#21
Rev.: 3757
-
757 lines of code changed in 6 files:
-
src/dr/evomodel/speciation/ModelAveragingResearch:
MAIndexResearch.java (new 193),
MAIndexResearchLog.java (new 196),
ModelAveragingIndexSpeciationLikelihood.java (+205),
ModelAveragingIndexSpeciationLikelihoodParser.java (new 58)
-
src/dr/evomodelxml/speciation:
ModelAveragingSpeciationLikelihoodParser.java (+103)
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src/dr/inference/trace:
LogFileTraces.java (+2 -2)
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dong.w.xie
2010-12-15 14:46
#20
Rev.: 3756
-
92 lines of code changed in 6 files:
-
src/dr/app/beast:
development_parsers.properties (+1 -1)
-
src/dr/evomodel/speciation:
ModelAveragingSpeciationLikelihood.java (+73 -15)
-
src/dr/inference/model:
Bounds.java (+5 -1)
-
src/dr/inference/operators:
RandomWalkIntegerOperator.java (+7 -7),
UniformIntegerOperator.java (new)
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rambaut
2010-12-15 03:49
#19
Rev.: 3755
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+1 -1)
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rambaut
2010-12-14 04:15
#18
Rev.: 3754
-
0 lines of code changed in 22 files:
-
src/dr/app/phylogeography:
Phylogeography.java (del)
-
src/dr/app/phylogeography/builder:
AbstractBuilder.java (del),
BuildException.java (del),
Builder.java (del),
BuilderFactory.java (del),
ContinuousDiffusionTreeBuilder.java (del),
DiscreteDiffusionTreeBuilder.java (del),
DiscreteTreeBuilder.java (del)
-
src/dr/app/phylogeography/generator:
Generator.java (del),
KMLGenerator.java (del),
Utils.java (del)
-
src/dr/app/phylogeography/structure:
Container.java (del),
Coordinates.java (del),
GeoItem.java (del),
Group.java (del),
Item.java (del),
Layer.java (del),
Line.java (del),
Place.java (del),
Polygon.java (del),
Style.java (del),
TimeLine.java (del)
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rambaut
2010-12-14 04:12
#17
Rev.: 3753
-
1 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+1 -1)
-
rambaut
2010-12-14 03:07
#16
Rev.: 3752
-
2 lines of code changed in 1 file:
-
build_phylogeography.xml (+2 -8)
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rambaut
2010-12-14 02:43
#15
Rev.: 3751
-
1330 lines of code changed in 58 files:
-
build_phylogeography.xml (+2)
-
src/dr/app/phylogeography/spread:
CreateBuilderDialog.java (del),
DataPanel.java (del),
DefaultFileMenuFactory.java (del),
DeleteActionResponder.java (del),
EditBuilderDialog.java (del),
InputFile.java (del),
InputFileSettingsDialog.java (del),
InputPanel.java (del),
LayerBuilderDialog.java (del),
LayersPanel.java (del),
Location.java (del),
MacFileMenuFactory.java (del),
MultiLineTableCellContent.java (del),
MultiLineTableCellRenderer.java (del),
OutputPanel.java (del),
SelectAllActionResponder.java (del),
SelectBuilderDialog.java (del),
SpreadApp.java (del),
SpreadDocument.java (del),
SpreadFrame.java (del),
SpreadMenuBarFactory.java (del),
TimelinePanel.java (del)
-
src/dr/app/phylogeography/spread/images:
gear.png (del),
small_trees.png (del),
tree.png (del),
trees.png (del)
-
src/dr/app/phylogeography/spread/inputpanel:
InputFileSettingsDialog.java (del),
InputPanel.java (del),
ReadsPanel.java (del),
SourcesPanel.java (del),
SourcesSettingsDialog.java (del)
-
src/dr/app/phylogeography/spread/layerspanel:
CreateBuilderDialog.java (del),
DefaultFileMenuFactory.java (del),
EditBuilderDialog.java (del),
LayersPanel.java (del)
-
src/dr/app/phylogeography/spread/renderpanel:
RenderPanel.java (del)
-
src/dr/app/treespace:
InputFile.java (+156),
Location.java (del),
MacFileMenuFactory.java (+105),
OutputPanel.java (del),
SpreadApp.java (del),
SpreadDocument.java (del),
SpreadFrame.java (del),
SpreadMenuBarFactory.java (del),
TimelinePanel.java (new 39),
TreeSpaceApp.java (+119),
TreeSpaceDocument.java (+56),
TreeSpaceFrame.java (+418),
TreeSpaceMenuBarFactory.java (new 30),
layerspanel (del)
-
src/dr/app/treespace/inputpanel:
InputFileSettingsDialog.java (new),
InputPanel.java (+299)
-
src/dr/app/treespace/renderpanel:
RenderPanel.java (new)
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dong.w.xie
2010-12-13 16:49
#14
Rev.: 3748
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/types:
PriorType.java (+2 -2)
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dong.w.xie
2010-12-13 16:38
#13
Rev.: 3747
-
21 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -5),
PriorOptions.java (+12 -12)
-
src/dr/app/beauti/types:
PriorType.java (+4 -4)
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rambaut
2010-12-10 04:43
#12
Rev.: 3746
-
109 lines of code changed in 5 files:
-
src/dr/app/tools:
AntigenicPlotter.java (+8 -3)
-
src/dr/evomodel/continuous:
AbstractMultivariateTraitLikelihood.java (+8 -4),
AntigenicTraitLikelihood.java (+90 -49)
-
src/dr/evomodel/operators:
PrecisionMatrixGibbsOperator.java (+2 -1)
-
src/dr/inference/model:
MatrixParameter.java (+1 -1)
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rambaut
2010-12-08 04:47
#11
Rev.: 3745
-
101 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+101 -55)
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rambaut
2010-12-08 01:04
#10
Rev.: 3744
-
13 lines of code changed in 4 files:
-
src/dr/geo:
KernelDensityEstimator2D.java (+6 -6)
-
src/dr/geo/contouring:
ContourWithR.java (new),
ContourWithSynder.java (+3 -3)
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rambaut
2010-12-08 01:03
#9
Rev.: 3743
-
90 lines of code changed in 2 files:
-
src/dr/app/tools:
AntigenicPlotter.java (+12 -12)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+78 -4)
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rambaut
2010-12-07 04:15
#8
Rev.: 3742
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+1)
-
rambaut
2010-12-07 03:58
#7
Rev.: 3741
-
66 lines of code changed in 3 files:
-
src/dr/app/tools:
AntigenicPlotter.java (+25 -25)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+41 -2)
-
src/dr/inference/model:
CompoundParameter.java (-1)
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rambaut
2010-12-06 01:07
#6
Rev.: 3740
-
384 lines of code changed in 2 files:
-
src/dr/app/tools:
AntigenicPlotter.java (+365)
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+19 -1)
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rambaut
2010-12-05 12:38
#5
Rev.: 3739
-
6 lines of code changed in 2 files:
-
src/dr/app/phylogeography/tools:
TreeKMLGenerator.java (+2 -2)
-
src/dr/app/phylogeography/tools/kml:
Settings.java (+4 -4)
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rambaut
2010-12-05 12:37
#4
Rev.: 3738
-
96 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+96 -10)
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rambaut
2010-12-04 03:19
#3
Rev.: 3737
-
78 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+78 -31)
-
rambaut
2010-12-04 02:15
#2
Rev.: 3736
-
56 lines of code changed in 1 file:
-
src/dr/evomodel/continuous:
AntigenicTraitLikelihood.java (+56 -36)
-
dong.w.xie
2010-12-01 12:08
#1
Rev.: 3734
-
98 lines of code changed in 3 files:
-
src/dr/inference/operators:
RandomWalkIntegerOperator.java (+5 -2),
UniformIntegerOperator.java (+13 -4)
-
src/test/dr/evomodel/operators:
UniformIntegerOperatorTest.java (+80)