Directory src/test/dr/beauti/

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dong.w.xie 2010-09-27 13:49 Rev.: 3578

Trunk: tidy up JUnit test in app

0 lines of code changed in 2 files:

• src/test/dr/beauti: BeautiTester.java (del), BeautiTesterConfig.java (del)

dong.w.xie 2010-04-15 13:23 Rev.: 3123

TRUNK: sovle Issue 296: The imported data has become global to all BEAUti windows

45 lines of code changed in 2 files:

• src/test/dr/beauti: BeautiTesterConfig.java (+45 -45)

dong.w.xie 2010-03-26 16:15 Rev.: 3075

TRUNK: BEAUti Phylogeographic big update to treat traits as partition data, not complete yet.

3 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+3 -3)

dong.w.xie 2010-03-22 11:45 Rev.: 3065

TRUNK: BEAUti definitely this time.

1 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+1 -1)

dong.w.xie 2010-03-04 10:26 Rev.: 3018

Trunk: solve Issue 282: BEAUti: AlignmentGenerator cannot print sequence with long sites properly.

1 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+1 -3)

dong.w.xie 2010-02-17 16:12 Rev.: 2936

Trunk refactoring: make evoxml parsers more organized.

7 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+7 -5)

dong.w.xie 2009-12-10 13:44 Rev.: 2678

Trunk: start merge BEAUti from branch 1.5 in

2 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+2 -2)

dong.w.xie 2009-09-10 15:29 Rev.: 2233

BEAUTi: keep reducing ModelOptions by create enum DateUnitsType, and fix the bug of r2223.

3 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+3 -2)

dong.w.xie 2009-08-21 11:50 Rev.: 2124

Fix the problem of BEAST using BEAUTi code, finding from r2123.

2 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+2 -2)

dong.w.xie 2009-08-21 11:01 Rev.: 2123

BEAUTi big refactory: move all enum into dr.app.beauti.enumTypes to spearate logic from GUI.
Note: some BEAST classes are using BEAUTi enum.

2 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+2)

dong.w.xie 2009-08-14 17:55 Rev.: 2072

BEAUTi: Issue #100,
1) complete GUI, and a further improvement will be continued;
2) need to add allClockRate delta operator, and implement it in BeastGenerator.

1 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+1 -1)

dong.w.xie 2009-07-28 19:43 Rev.: 1936

Big Change of BEAUTI:
1) implement FixRateType containing estimate, fix mean, fix 1st partition to replace fixSubstitionRate;
2) comment out "mu" for no condon model;
3) correct *BEAST xml by adding updown operators;
4) fix bug to import NEXUS file when it contains subsititution model.

3 lines of code changed in 3 files:

• src/test/dr/beauti: BeautiTester.java (+2 -2), BeautiTesterConfig.java (+1 -1)

dong.w.xie 2009-07-21 13:08 Rev.: 1888

Update Big Change of BEAUTi:
1) use List to store treeFileName and subtreeFileName, and update MCMC panel;
2) correct EBSP xml, but still have a problem in VDAnalysis;
3) start to fix *BEAST.

3 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+3 -2)

dong.w.xie 2009-07-08 17:32 Rev.: 1828

Update Big Change of BEAUTi: modify generator, but BranchRate generator still has problem.

13 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+13 -13)

dong.w.xie 2009-07-03 15:34 Rev.: 1822

Update Big Change of BEAUTi: the part of generator.

16 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+16 -16)

dong.w.xie 2009-07-01 12:41 Rev.: 1817

Update Big Change of BEAUTi: store the links between PD, PSM, PCM, PTM, PTP in the class using their class references, List<> of them in BeautiOption is not used anymore. And use getPartition...() in BeautiOption to get the current list of PD or PSM or PCM or PTM.

2 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+2 -2)

dong.w.xie 2009-06-30 11:40 Rev.: 1816

BEAUTi: replace all dataType with getter.

1 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+1 -1)

dong.w.xie 2009-06-29 17:19 Rev.: 1815

Renew Big Change of BEAUTi: update the structure containing multi-substitution models, multi-clock models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionClockModel; and PartitionData <=> PartitionTreeModel <=> PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PCM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also
PD~(PSM,PCM,PTM) and PTM~(PTP).

But updown operator does not init properly.

1 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+1 -1)

dong.w.xie 2009-06-19 14:35 Rev.: 1790

BEAUTi: rename partition series classes, and final relation is PartitionData => PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior.

13 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+13 -13)

dong.w.xie 2009-06-19 10:36 Rev.: 1789

BEAUTi: Rename DataPartition into PartitionData, and add PartitionPopulation, to create the structure of PartitionData => PartitionModel => PartitionTree => PartitionPopulation.

4 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+4 -4)

dong.w.xie 2009-06-11 16:02 Rev.: 1770

Further work of GTR parameter estimation test

14 lines of code changed in 1 file:

• src/test/dr/beauti: BeautiTesterConfig.java (+14 -3)

dong.w.xie 2009-06-08 17:39 Rev.: 1767

Refactory BeautiTester

553 lines of code changed in 2 files:

• src/test/dr/beauti: BeautiTester.java (+70), BeautiTesterConfig.java (+483)