Directory src/dr/app/beauti/options/

Lines of Code

Developers

Most Recent Commits

rambaut 2013-05-10 03:29 Rev.: 5642

Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.

15 lines of code changed in 4 files:

• src/dr/app/beauti/options: BeautiOptions.java (+5 -4), DateGuesser.java (new)

rambaut 2013-04-23 21:44 Rev.: 5603

Adding date precision to the BEAUti/Pathogen date guessing panel

73 lines of code changed in 1 file:

• src/dr/app/beauti/options: DateGuesser.java (+73 -21)

rambaut 2013-03-11 01:12 Rev.: 5474

Some serious effort to build a post-analysis tool for antigenic mapping.

19 lines of code changed in 1 file:

• src/dr/app/beauti/options: DateGuesser.java (+19 -5)

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

trunk: merge Issue 677

94 lines of code changed in 10 files:

• 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)

rambaut 2013-01-31 04:42 Rev.: 5367

Porting some fixes from 1.7 branch

2 lines of code changed in 2 files:

• src/dr/app/beauti/options: ClockModelOptions.java (new)

rambaut 2012-10-11 02:35 Rev.: 5193

Created a new cleaner coalescent simulator parser to help generate nested subtrees from taxon sets. Updating BEAUti to generate simulated trees that conform to monophyly constrants and hard bounds on tmrcas.

1 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+1)

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.

12 lines of code changed in 2 files:

• src/dr/app/beauti/options: PartitionTreePrior.java (new)

rambaut 2012-08-08 21:31 Rev.: 5110

Porting changes from branch 1.7 r5109

2 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+2 -2)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

18 lines of code changed in 4 files:

• src/dr/app/beauti/options: BeautiOptions.java (+5), PartitionData.java (+5), PartitionOptions.java (+4 -4), PartitionTreePrior.java (+4 -4)

akaruiws 2012-07-16 17:56 Rev.: 5068

Provide more realistic default value for model parameter just like providing more realistic starting tree to the analysis to prevent numerical instability or whatever silly stuff that does not allow the analysis to start running.

1 lines of code changed in 2 files:

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

alexei.drummond 2012-07-16 15:55 Rev.: 5067

fixed microsatellite initial value errors in geomDist and propLinear parameters (if in doubt, shouldn't start on boundary values as a general rule).

2 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionSubstitutionModel.java (+2 -2)

msuchard 2012-04-20 09:52 Rev.: 4926

Fixed issue 621: BEAUti now provides unbounded logPopSizes and an initial value on the correct scale.

22 lines of code changed in 2 files:

• src/dr/app/beauti/options: PartitionOptions.java (+13 -8), PartitionTreePrior.java (+9 -7)

rambaut 2012-03-09 00:34 Rev.: 4797

Few more fixes to truncation of prior distributions

10 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreeModel.java (+10 -8)

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

trunk: merge

6 lines of code changed in 3 files:

• src/dr/app/beauti/options: BeautiOptions.java (+1 -1), Parameter.java (+5 -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 2012-02-13 15:40 Rev.: 4677

trunk: merge Issue 579 and 580

25 lines of code changed in 4 files:

• src/dr/app/beauti/options: STARBEASTOptions.java (new), TraitData.java (new)

dong.w.xie@gmail.com 2012-02-10 14:33 Rev.: 4668

trunk: merge changes from branch 1.7

7 lines of code changed in 2 files:

• src/dr/app/beauti/options: TreeModelOptions.java (new)

dong.w.xie@gmail.com 2012-02-09 16:51 Rev.: 4660

trunk: merge bug fixing of Species Set panel from branch 1.7

7 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+7)

dong.w.xie@gmail.com 2012-02-09 15:55 Rev.: 4658

trunk: merge Issue 573: BEAUti taxon set panel taxon set table incorrectly auto selection

7 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+7)

dong.w.xie@gmail.com 2012-02-09 10:58 Rev.: 4656

trunk: merge Issue 572 : BEAUti tmrca gives wrong prefix

8 lines of code changed in 2 files:

• src/dr/app/beauti/options: BeautiOptions.java (+3 -1), Parameter.java (+5 -2)

rambaut 2012-02-02 21:51 Rev.: 4631

Fix for issue 568
The a partition prefix is now given if there is > 1 partition (plus some issues with the pattern lists inside merge patterns fixed - these don't now have ids).

0 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionData.java (-11)

dong.w.xie@gmail.com 2012-02-02 17:10 Rev.: 4630

change confused method name and fix prefix bug inside mergePatterns

2 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+2 -2)

rambaut 2012-01-04 02:27 Rev.: 4569

Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.

19 lines of code changed in 15 files:

• src/dr/app/beauti/options: AbstractPartitionData.java (+2 -6), ClockModelGroup.java (new), ComponentOptions.java (+2 -1), DateGuesser.java (+2 -1), ModelOptions.java (new), Operator.java (new), Parameter.java (+2 -1), TraitData.java (+2 -1), TraitGuesser.java (new)

rambaut 2012-01-03 23:14 Rev.: 4567

Cleaned up the interface for selecting starting trees.

0 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreeModel.java (-9)

dong.w.xie 2011-12-20 12:25 Rev.: 4554

trunk:solve Issue 548: Beauti does not generate functional xml for msat data analysis

49 lines of code changed in 4 files:

• src/dr/app/beauti/options: AbstractPartitionData.java (+2 -23), BeautiOptions.java (+16 -3), PartitionData.java (+23), PartitionPattern.java (+8)

dong.w.xie 2011-12-15 15:13 Rev.: 4546

trunk:solve Issue 565: hasIdenticalTaxa(List<AbstractPartitionData> partitionDataList) gives wrong boolean

5 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+5 -3)

dong.w.xie 2011-12-13 11:07 Rev.: 4540

trunk:solve Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on node ages, and add a nexus example with user specified starting tree

4 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreeModel.java (+4 -1)

dong.w.xie 2011-12-09 10:03 Rev.: 4526

trunk:solve Issue 562: BEAUTi : Birth Death Epidemiology Model update

51 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreePrior.java (+51 -34)

dong.w.xie 2011-12-07 10:45 Rev.: 4517

trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa

64 lines of code changed in 2 files:

• src/dr/app/beauti/options: AbstractPartitionData.java (+4), BeautiOptions.java (+60 -37)

dong.w.xie 2011-12-05 16:19 Rev.: 4506

trunk: more fixes of Issue 556: BEAUti "birth-death serially sampled model" correction required

20 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreePrior.java (+20 -14)

dong.w.xie 2011-12-05 13:52 Rev.: 4504

trunk:solve Issue 475: BEAUti hypervariable models do not fill in all necessary model attributes to run, and Issue 554: SequenceErrorModelComponentOptions did not create parameters properly

9 lines of code changed in 3 files:

• src/dr/app/beauti/options: AbstractPartitionData.java (+6), PartitionData.java (+2 -6), PartitionPattern.java (+1 -3)

rambaut 2011-12-04 10:43 Rev.: 4501

Added a dialog box to rename a partition if it has the same name as an existing partition.

1 lines of code changed in 1 file:

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

dong.w.xie 2011-11-25 16:08 Rev.: 4494

trunk:solve Issue 515: cast Exception after click taxon set combo box in BEAUti Taxon Set panel

7 lines of code changed in 1 file:

• src/dr/app/beauti/options: BeautiOptions.java (+7)

dong.w.xie 2011-11-25 13:46 Rev.: 4491

trunk:solve Issue 549: BeautiOptions.updateAll() stop user to customize clock rates

36 lines of code changed in 2 files:

• src/dr/app/beauti/options: BeautiOptions.java (+18 -19), ClockModelOptions.java (+18 -1)

rambaut 2011-11-24 19:18 Rev.: 4483

Started to implement ancestral state reconstruction at a node.

0 lines of code changed in 5 files:

• src/dr/app/beauti/options: BeautiOptions.java (-6), Operator_Backup.java (del), Parameter_Backup.java (del), PartitionTreePrior.java (-3), TraitData.java (-5)

dong.w.xie 2011-11-24 14:30 Rev.: 4482

trunk:solve Issue 469: BEAUTi Covarion generation fails to add hfrequencies to operators.

2 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionSubstitutionModel.java (+2 -2)

dong.w.xie 2011-11-23 10:49 Rev.: 4475

trunk:solve Issue 511: Multiple partitions not prefixing the names of 'patterns' correctly, but it may break AncestralStatesComponentGenerator and DolloComponentGenerator, and needs Andrew to review.

18 lines of code changed in 2 files:

• src/dr/app/beauti/options: AbstractPartitionData.java (+7 -5), BeautiOptions.java (+11 -3)

dong.w.xie 2011-11-22 16:33 Rev.: 4471

trunk:solve Issue 463: Correct BirthDeathSerialSampling xml generator in BEAUti because of parser changed

4 lines of code changed in 1 file:

• src/dr/app/beauti/options: PartitionTreePrior.java (+4 -4)

dong.w.xie 2011-11-22 14:05 Rev.: 4470

trunk:solve Issue 452: Fixed rate relaxed molecular clock still generating upDownOperator on rate/ heights

20 lines of code changed in 2 files:

• src/dr/app/beauti/options: PartitionClockModel.java (new)

rambaut 2011-11-21 00:03 Rev.: 4459

Starting to rebuild generation of robust counting.

1 lines of code changed in 1 file:

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

(371 more)