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    fbielejec
    2012-09-28 21:06
    #22
    Rev.: 5178
  
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    133 lines of code changed in 1 file: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+133 -249)
      
 
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    msuchard
    2012-09-27 21:22
    #21
    Rev.: 5177
  
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    104 lines of code changed in 3 files: 
      - 
        src/dr/app/beast:
        development_parsers.properties (+1)
      
- 
        src/dr/evomodelxml:
        LeafTraitExtractorParser.java (new 89)
      
- 
        src/dr/geo:
        GeoSpatialDistribution.java (+14 -10)
      
 
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    tbcbedford@gmail.com
    2012-09-27 00:36
    #20
    Rev.: 5176
  
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    2 lines of code changed in 1 file: 
      - 
        src/dr/evomodel/antigenic:
        AntigenicLikelihood.java (+2 -1)
      
 
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    fbielejec
    2012-09-24 21:54
    #19
    Rev.: 5175
  
- 
    
    162 lines of code changed in 1 file: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+162 -45)
      
 
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    rambaut
    2012-09-19 03:38
    #18
    Rev.: 5174
  
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    0 lines of code changed in 2 files: 
      - 
        src/dr/evomodelxml/coalescent:
        CoalescentSimulatorParser.java (-2)
      
 
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    fbielejec
    2012-09-19 00:53
    #17
    Rev.: 5173
  
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    58 lines of code changed in 4 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+52 -30),
        Partition.java (+1 -1)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+3 -2),
        PartitionParser.java (+2 -2)
      
 
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    fbielejec
    2012-09-18 21:55
    #16
    Rev.: 5172
  
- 
    
    169 lines of code changed in 4 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+138 -10),
        Partition.java (+2)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+29 -2),
        PartitionParser.java (-4)
      
 
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    fbielejec
    2012-09-18 19:31
    #15
    Rev.: 5171
  
- 
    
    38 lines of code changed in 4 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+7 -5),
        Partition.java (+5 -12)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+18 -6),
        PartitionParser.java (+8 -17)
      
 
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    Sibon.Li@gmail.com
    2012-09-18 19:14
    #14
    Rev.: 5170
  
- 
    
    2 lines of code changed in 4 files: 
      - 
        src/dr/inference/markovchain:
        MarkovChainDelegate.java (+1 -1)
      
- 
        src/dr/inference/mcmc:
        MCMC.java (new)
      
 
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    Sibon.Li@gmail.com
    2012-09-18 17:42
    #13
    Rev.: 5169
  
- 
    
    153 lines of code changed in 1 file: 
      - 
        src/dr/app/tracer/application:
        InstantiableTracerApp.java (+153)
      
 
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    fbielejec
    2012-09-18 02:30
    #12
    Rev.: 5168
  
- 
    
    20 lines of code changed in 2 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+3 -2)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+17 -5)
      
 
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    fbielejec
    2012-09-18 02:13
    #11
    Rev.: 5167
  
- 
    
    166 lines of code changed in 6 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+9 -9),
        Partition.java (+4)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+8 -86),
        PartitionParser.java (+142 -2)
      
- 
        src/dr/app/beast:
        beagle_parsers.properties (+3),
        development_parsers.properties (-1)
      
 
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    fbielejec
    2012-09-18 00:44
    #10
    Rev.: 5166
  
- 
    
    72 lines of code changed in 4 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (-1),
        Partition.java (+65)
      
- 
        src/dr/app/beagle/tools/parsers:
        PartitionParser.java (+7)
      
- 
        src/dr/app/bss:
        Partition.java (del)
      
 
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    fbielejec
    2012-09-18 00:14
    #9
    Rev.: 5165
  
- 
    
    118 lines of code changed in 2 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+110 -38)
      
- 
        src/dr/app/bss:
        Partition.java (new 8)
      
 
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    fbielejec
    2012-09-17 20:11
    #8
    Rev.: 5164
  
- 
    
    59 lines of code changed in 1 file: 
      - 
        src/dr/app/bss:
        Partition.java (+59)
      
 
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    fbielejec
    2012-09-17 20:10
    #7
    Rev.: 5163
  
- 
    
    368 lines of code changed in 3 files: 
      - 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (+345 -339)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (+12 -9)
      
- 
        src/dr/app/bss:
        BeagleSequenceSimulatorFrame.java (+11 -8)
      
 
- 
    graham853@gmail.com
    2012-09-15 02:40
    #6
    Rev.: 5162
  
- 
    
    523 lines of code changed in 14 files: 
      - 
        src/dr/evolution/tree:
        SlidableTree.java (+5 -6)
      
- 
        src/dr/evomodel/operators:
        AlloppChangeNumHybridizations.java (+82 -25),
        AlloppNetworkNodeSlide.java (+1 -1),
        AlloppSequenceReassignment.java (+1)
      
- 
        src/dr/evomodel/speciation:
        AlloppDiploidHistory.java (+79 -24),
        AlloppLeggedTree.java (+3 -4),
        AlloppMulLabTree.java (+22),
        AlloppSpeciesBindings.java (+5 -11),
        AlloppSpeciesNetworkModel.java (+153 -28),
        PopsIOSpeciesTreeModel.java (+154 -102)
      
- 
        src/test/dr/evomodel/speciation:
        AlloppSpeciesNetworkModelTEST.java (+18 -1)
      
 
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    rambaut
    2012-09-13 08:04
    #5
    Rev.: 5155
  
- 
    
    1 lines of code changed in 1 file: 
      - 
        src/dr/inference/model:
        CompoundLikelihood.java (+1 -1)
      
 
- 
    msuchard
    2012-09-12 10:00
    #4
  
- 
    
    267 lines of code changed in 7 files: 
      - 
        src/dr/app/beast:
        release_parsers.properties (+1)
      
- 
        src/dr/evomodel/branchratemodel:
        ArbitraryBranchRates.java (+17 -7)
      
- 
        src/dr/evomodelxml/branchratemodel:
        ArbitraryBranchRatesParser.java (+32 -1)
      
- 
        src/dr/inference/distribution:
        SkewNormalDistributionModel.java (new 152)
      
- 
        src/dr/inferencexml/distribution:
        SkewNormalDistributionModelParser.java (new 65)
      
 
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    fbielejec
    2012-09-11 19:41
    #3
    Rev.: 5151
  
- 
    
    45 lines of code changed in 4 files: 
      - 
        src/dr/app/beagle/evomodel/sitemodel:
        EpochBranchSubstitutionModel.java (+36 -28)
      
- 
        src/dr/app/bss:
        BeagleSequenceSimulatorApp.java (+8 -6),
        BeagleSequenceSimulatorData.java (-3),
        ExceptionHandler.java (+1 -1)
      
 
- 
    fbielejec
    2012-09-07 02:06
    #2
    Rev.: 5150
  
- 
    
    135 lines of code changed in 6 files: 
      - 
        build_bss.xml (+125 -136)
      
- 
        src/dr/app/beagle/evomodel/parsers:
        BeagleSubstitutionEpochModelParser.java (-2),
        GammaSiteModelParser.java (+9 -4)
      
- 
        src/dr/app/beagle/tools:
        BeagleSequenceSimulator.java (-23)
      
- 
        src/dr/app/beagle/tools/parsers:
        BeagleSequenceSimulatorParser.java (-4)
      
- 
        src/dr/app/beast:
        beagle_parsers.properties (+1)
      
 
- 
    graham853@gmail.com
    2012-09-02 04:49
    #1
    Rev.: 5149
  
- 
    
    3294 lines of code changed in 39 files: 
      - 
        src/dr/app/beast:
        development_parsers.properties (+3)
      
- 
        src/dr/evomodel/operators:
        AlloppChangeNumHybridizations.java (+237),
        AlloppHybPopSizesScale.java (new 52),
        AlloppMoveLegs.java (+1 -1),
        AlloppNetworkNodeSlide.java (+84 -79)
      
- 
        src/dr/evomodel/speciation:
        AlloppDiploidHistory.java (+720 -560),
        AlloppFootLinks.java (del),
        AlloppLegLink.java (del),
        AlloppLeggedTree.java (+449 -751),
        AlloppMSCoalescent.java (new),
        AlloppMulLabTree.java (+479 -487),
        AlloppNetworkPrior.java (+81 -161),
        AlloppNetworkPriorModel.java (new),
        AlloppNode.java (+32 -128),
        AlloppSpeciesBindings.java (+111 -167),
        AlloppSpeciesNetworkModel.java (+604 -987),
        AlloppTreeLeg.java (del),
        MulMSCoalescent.java (+1 -1),
        MulSpeciesBindings.java (new),
        MulSpeciesTreeModel.java (new),
        PopsIOMSCoalescent.java (new),
        PopsIOSpeciesBindings.java (+1 -1)
      
- 
        src/dr/evomodelxml/operators:
        AlloppChangeNumHybridizationsParser.java (+55),
        AlloppHybPopSizesScaleParser.java (new 55)
      
- 
        src/dr/evomodelxml/speciation:
        AlloppNetworkPriorModelParser.java (new),
        AlloppSpeciesNetworkModelParser.java (+50 -26)
      
- 
        src/dr/util:
        AlloppMisc.java (new)
      
- 
        src/test/dr/evomodel/speciation:
        AlloppSpeciesNetworkModelTEST.java (+100 -415)