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dong.w.xie@gmail.com 2013-03-28 11:48 Rev.: 5551

more improvement of SeqGen

26 lines of code changed in 2 files:

• src/dr/app/seqgen: SeqGen.java (+26 -15)

dong.w.xie@gmail.com 2013-03-01 15:19 Rev.: 5460

tracer: big correction of tracer code for my previous development on "Conditional Posterior Distributions", which fixed bugs in GUI especially in Filter, and use EDT thread.

260 lines of code changed in 22 files:

• src/dr/app/tracer/application: TracerApp.java (+1 -1), TracerFrame.java (+1 -1)
• src/dr/app/tracer/traces: FilterAbstractPanel.java (new), FilterContinuousPanel.java (+5 -4), FilterDiscretePanel.java (new), FilterListPanel.java (+109 -51)
• src/dr/inference/trace: AbstractTraceList.java (+1 -1), Filter.java (new), FilteredTraceList.java (+37 -37), LogFileTraces.java (new), Trace.java (+40 -39)

dong.w.xie@gmail.com 2013-02-28 14:58 Rev.: 5459

tracer: doWork in EBSP needs to be reviewed, it seems a copy of BSP.

14 lines of code changed in 5 files:

• src/dr/app/tracer/analysis: ExtendedBayesianSkylineDialog.java (+1 -1)
• src/dr/app/tracer/application: AnalysisMenuFactory.java (new), TracerFrame.java (+3 -2)

dong.w.xie@gmail.com 2013-02-25 10:31 Rev.: 5458

trunk: merge Issue 677

124 lines of code changed in 14 files:

• src/dr/app/beauti/generator: BeastGenerator.java (+1 -1), TreeLikelihoodGenerator.java (+5 -5), TreeModelGenerator.java (+21 -17)
• src/dr/app/beauti/options: BeautiOptions.java (+28 -5), MicrosatelliteOptions.java (new 55), PartitionData.java (new), PartitionOptions.java (new), PartitionPattern.java (+5), PartitionTreeModel.java (-15)
• src/dr/app/beauti/util: BEAUTiImporter.java (+3)

dong.w.xie@gmail.com 2013-02-22 11:25 Rev.: 5454

trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.

126 lines of code changed in 13 files:

• src/dr/app/beauti/datapanel: DataPanel.java (new)
• src/dr/app/beauti/generator: BeastGenerator.java (+46 -2), InitialTreeGenerator.java (+10 -11), PatternListGenerator.java (new)
• src/dr/evolution/alignment: Patterns.java (+39)
• src/dr/evolution/datatype: Microsatellite.java (new)
• src/dr/evolution/io: MicroSatImporter.java (new)

dong.w.xie@gmail.com 2012-08-13 14:17 Rev.: 5129

trunk: merge Issue 656 : fix p=0 in Birth Death Serial Sampling Model, and update Unit tests.

51 lines of code changed in 8 files:

• src/dr/app/beauti/generator: TreePriorGenerator.java (+5 -4)
• src/dr/app/beauti/options: PartitionTreePrior.java (new)
• src/dr/evomodelxml/speciation: BirthDeathSerialSamplingModelParser.java (+7 -4)
• src/test/dr/evomodel/speciation: BirthDeathSSLikelihoodTest.java (new)

dong.w.xie@gmail.com 2012-08-10 13:05 Rev.: 5121

trunk: merge Issue 637: birth-death sampling model seems to not work smoothly

2 lines of code changed in 2 files:

• src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+2 -2)

dong.w.xie@gmail.com 2012-04-13 17:06 Rev.: 4923

update *BEAST tutorial

1014 lines of code changed in 27 files:

• doc/tutorial/StarBEAST: STARBEAST.pdf (new), STARBEAST.tex (+66 -66), gopher.xml (new 948)
• doc/tutorial/StarBEAST/figures: BEAST.png (new), BEAUti_DataPartitions2.png (new), BEAUti_GuessTrait.png (new), BEAUti_MCMC.png (changed), BEAUti_Trait2.png (new), BEAUti_Tree.png (new), FigTree.png (new), ImportNexus.png (new), Tracer1.png (new), Tracer2.png (changed), TreeAnnotator.png (new)

dong.w.xie@gmail.com 2012-03-12 11:11 Rev.: 4817

trunk: fix Junit test

1 lines of code changed in 2 files:

• src/test/dr/distibutions: LogNormalDistributionTest.java (+1)

dong.w.xie@gmail.com 2012-03-12 09:24 Rev.: 4816

trunk: merge prior dialog and distribution changes to trunk

212 lines of code changed in 17 files:

• release/common: VERSION HISTORY.txt (+34 -2)
• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (new), PriorDialog.java (+24 -15), PriorOptionsPanel.java (+92 -8), PriorsPanel.java (+1 -1)
• src/dr/app/gui/components: RealNumberField.java (+9 -5)
• src/dr/math/distributions: GammaDistribution.java (+5 -2), InverseGammaDistribution.java (+2 -3), LaplaceDistribution.java (new), LogNormalDistribution.java (+6), TruncatedDistribution.java (new)

dong.w.xie@gmail.com 2012-02-27 14:35 Rev.: 4731

trunk: add a new constructor to exclude the lower bound or upper bound during validation, but this is not available in branch 1.7 at moment

37 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+10 -4)
• src/dr/app/gui/components: RealNumberField.java (+27 -3)

dong.w.xie@gmail.com 2012-02-27 10:40 Rev.: 4730

trunk: merge

25 lines of code changed in 2 files:

• release/common: VERSION HISTORY.txt (+13 -3)
• src/dr/math/distributions: TruncatedDistribution.java (+12 -4)

dong.w.xie@gmail.com 2012-02-23 17:11 Rev.: 4724

trunk: merge

16 lines of code changed in 7 files:

• src/dr/app/beauti/options: BeautiOptions.java (+1 -1), Parameter.java (+5 -2)
• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+8)
• src/dr/app/beauti/taxonsetspanel: SpeciesSetPanel.java (+1 -1), TaxonSetPanel.java (+1 -1)

dong.w.xie@gmail.com 2012-02-21 15:23 Rev.: 4721

trunk: merge the change of BEAST parser doc

13 lines of code changed in 4 files:

• src/dr/app/tools: BeastParserDoc.java (+9 -5)
• src/dr/xml: XMLDocumentationHandler.java (new)

dong.w.xie@gmail.com 2012-02-21 14:40 Rev.: 4719

trunk: update version history

9 lines of code changed in 1 file:

• release/common: VERSION HISTORY.txt (+9 -1)

dong.w.xie@gmail.com 2012-02-21 14:12 Rev.: 4717

trunk:solve Issue 589: BEAUti lost Uniform bound validation, and Issue 590: BEAUti prior dialog GUI logic bug

12 lines of code changed in 3 files:

• src/dr/app/beauti/generator: BeastGenerator.java (+5 -4)
• src/dr/app/beauti/priorsPanel: PriorDialog.java (+6 -9), PriorOptionsPanel.java (+1)

dong.w.xie@gmail.com 2012-02-20 17:20 Rev.: 4714

trunk: merge Issue 587: BEAUti prior dialog ignores validation in the text field if pressing Enter key

14 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+1 -1)
• src/dr/app/gui/components: RealNumberField.java (+13 -3)

dong.w.xie@gmail.com 2012-02-20 15:24 Rev.: 4712

trunk: merge Issue 584:BEAUti prior dialog validation bugs, and Issue 586: BEAUti prior dialog Cancel not working

33 lines of code changed in 4 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+16 -7), PriorOptionsPanel.java (+9), PriorsPanel.java (+5 -5)
• src/dr/app/gui/components: RealNumberField.java (+3 -2)

dong.w.xie@gmail.com 2012-02-20 10:45 Rev.: 4710

trunk: merge Issue 585

10 lines of code changed in 1 file:

• src/dr/app/beauti/options: ClockModelOptions.java (+10 -1)

dong.w.xie@gmail.com 2012-02-17 15:56 Rev.: 4705

trunk: merge Issue 583: BEAUti prior dialog text field validation should give sensible error message

55 lines of code changed in 4 files:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+34 -1)
• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+1 -7)
• src/dr/app/gui/components: RealNumberField.java (+20 -6)

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