February 2012 Commit Log

Number of Commits:
88
Number of Active Developers:
11
sibon.li 2012-02-28 12:09 Rev.: 4743

Correction, parsers pending updates to other files. Currently commented out

791 lines of code changed in 4 files:

sibon.li 2012-02-28 12:05 Rev.: 4742

Added two new parsers for BLUE integration

467 lines of code changed in 2 files:

rambaut 2012-02-28 04:54 Rev.: 4741

New cleaner AntigenicLikelihood

1 lines of code changed in 1 file:

rambaut 2012-02-28 04:30 Rev.: 4740

New cleaner AntigenicLikelihood

11 lines of code changed in 1 file:

rambaut 2012-02-28 04:09 Rev.: 4739

New cleaner AntigenicLikelihood

220 lines of code changed in 1 file:

rambaut 2012-02-28 04:09 Rev.: 4738

Removed unwanted import.

0 lines of code changed in 2 files:

rambaut 2012-02-28 03:08 Rev.: 4737

Tracer ant file fixes

3 lines of code changed in 1 file:

rambaut 2012-02-28 03:07 Rev.: 4736

Updated Tracer ant file libs

1 lines of code changed in 1 file:

rambaut 2012-02-27 23:38 Rev.: 4735

Fixed caching on DTBRM

62 lines of code changed in 1 file:

rambaut 2012-02-27 23:37 Rev.: 4734

Parser rules missing an expected element

2 lines of code changed in 1 file:

rambaut 2012-02-27 23:36 Rev.: 4733

Added button to allow the setting of dates for selected taxa

165 lines of code changed in 2 files:

rambaut 2012-02-27 23:36 Rev.: 4732

Back to work on antigenic analysis

200 lines of code changed in 2 files:

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:

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

trunk: merge

25 lines of code changed in 2 files:

graham853 2012-02-24 23:23 Rev.: 4728

Merged r4725 to trunk

20 lines of code changed in 2 files:

julia.pal.r@gmail.com 2012-02-24 13:11 Rev.: 4727

Not finished but descent version of GPOperator

569 lines of code changed in 4 files:

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

trunk: merge

16 lines of code changed in 7 files:

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:

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

trunk: update version history

9 lines of code changed in 1 file:

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:

rambaut 2012-02-21 09:07 Rev.: 4716

I think PriorDialog validation is now working as one might expect.

45 lines of code changed in 3 files:

fbielejec 2012-02-21 08:44 Rev.: 4715

parse epoch model correctly

38 lines of code changed in 1 file:

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:

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:

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

trunk: merge Issue 585

10 lines of code changed in 1 file:

rambaut 2012-02-18 06:23 Rev.: 4707

Debugging DTBRM

11 lines of code changed in 2 files:

fbielejec 2012-02-18 03:32 Rev.: 4706

one boolean

14 lines of code changed in 3 files:

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:

dong.w.xie@gmail.com 2012-02-17 11:18 Rev.: 4703

trunk: merge Issue 582: BEAUti Species Set cannot revert back to Taxon Set if uncheck *BEAST, and update version history

8 lines of code changed in 2 files:

rambaut 2012-02-16 20:40 Rev.: 4701

Fix for Issue 581 - NormalDistribution was hanging when asked for a CDF when stdev was 0. Now uses better CDF function (that was already implemented) that has bound checking.

4 lines of code changed in 1 file:

rambaut 2012-02-15 11:38 Rev.: 4699

Removed a couple of bug fixes to do with Tracer rather than BEAST.

0 lines of code changed in 1 file:

dong.w.xie 2012-02-15 11:30 Rev.: 4696

trunk: update version history

16 lines of code changed in 1 file:

rambaut 2012-02-15 09:59 Rev.: 4695

Very very minor thing - TreeLikelihoodParser was looking at the wrong system property to see whether to use the Java core. This means that the advertised '-java' option wasn't working.

1 lines of code changed in 2 files:

dong.w.xie 2012-02-15 09:36 Rev.: 4694

trunk: add xml test batch file

5 lines of code changed in 1 file:

fbielejec 2012-02-15 08:08 Rev.: 4693

dont print

10 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-02-15 06:12 Rev.: 4692

Finished Likelihood

46 lines of code changed in 1 file:

fbielejec 2012-02-15 05:58

loop over the tree to determine the count

58 lines of code changed in 2 files:

fbielejec 2012-02-15 05:57

pass the tree as argument

53 lines of code changed in 3 files:

dong.w.xie@gmail.com 2012-02-14 17:11 Rev.: 4686

trunk: merge Issue 577: BEAUti generator for *BEAST + calibrated Yule is broken

48 lines of code changed in 3 files:

julia.pal.r@gmail.com 2012-02-14 10:22 Rev.: 4684

delete import

0 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-02-14 09:52 Rev.: 4683

Updating Likelihood, need to add the GMRF part

184 lines of code changed in 3 files:

fbielejec 2012-02-14 00:00 Rev.: 4681

memory efficiency

340 lines of code changed in 1 file:

rambaut 2012-02-13 22:06 Rev.: 4680

Merged version history from 1.7 branch (with text change)

6 lines of code changed in 1 file:

rambaut 2012-02-13 21:56 Rev.: 4679

Updated BeastMC3 to use the standard BEAST titles (from BeastVersion).

5 lines of code changed in 2 files:

dong.w.xie@gmail.com 2012-02-13 15:40 Rev.: 4677

trunk: merge Issue 579 and 580

32 lines of code changed in 6 files:

dong.w.xie@gmail.com 2012-02-13 14:13 Rev.: 4675

trunk: merge BEAST MC3 changes

453 lines of code changed in 7 files:

dong.w.xie@gmail.com 2012-02-13 08:39 Rev.: 4672

trunk: merge Issue 86: Missing validation in BayesianSkylineLikelihoodParser

5 lines of code changed in 2 files:

dong.w.xie@gmail.com 2012-02-10 16:33 Rev.: 4670

trunk: merge Issue 284:Tracer doing BSP will throw an exception if the log file/tree file are out of sync

46 lines of code changed in 3 files:

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

trunk: merge changes from branch 1.7

16 lines of code changed in 4 files:

alexei.drummond 2012-02-10 14:16 Rev.: 4666

wording change

3 lines of code changed in 4 files:

alexei.drummond 2012-02-10 14:07 Rev.: 4665

fixed random seed

6 lines of code changed in 2 files:

dong.w.xie@gmail.com 2012-02-10 10:35 Rev.: 4663

trunk: merge tutorial changes from branch 1.7

8012 lines of code changed in 18 files:

tbcbedford@gmail.com 2012-02-10 06:06 Rev.: 4661

IntelliJ somehow missed the delete of aicmAnalysisParser.

0 lines of code changed in 1 file:

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

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

28 lines of code changed in 3 files:

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

21 lines of code changed in 2 files:

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:

tbcbedford@gmail.com 2012-02-09 05:51 Rev.: 4654

I've reverted MarginalLikelihoodAnalysisParser to previous functionality. It is now deprecated. It's been replaced by harmonicMeanAnalysis and aicmAnalysis.

265 lines of code changed in 5 files:

tbcbedford@gmail.com 2012-02-09 03:29 Rev.: 4653

I added a new parser for AICM that calls a version of MarginalLikelihoodAnalysis behind the scenes. I thought this made more sense than specifying AICM with marginalLikelihoodAnalysis and analysisType. marginalLikelihoodAnalysis defaults to smoothed harmonic mean.

126 lines of code changed in 3 files:

tbcbedford@gmail.com 2012-02-09 03:19 Rev.: 4652

Ensuring backwards compatability of MarginalLikelihoodAnalysis with harmonicOnly setting.

17 lines of code changed in 2 files:

baele.guy@gmail.com 2012-02-09 01:51 Rev.: 4651

adjusted toString method for harmonic mean and AICM

19 lines of code changed in 1 file:

dong.w.xie@gmail.com 2012-02-08 14:49 Rev.: 4650

trunk: fix Junit test

1 lines of code changed in 1 file:

baele.guy@gmail.com 2012-02-08 11:37 Rev.: 4649

adjusted toString method for stepping stone sampling

3 lines of code changed in 1 file:

baele.guy@gmail.com 2012-02-08 11:36 Rev.: 4648

adjusted toString method for path sampling

1 lines of code changed in 1 file:

rambaut 2012-02-08 11:24 Rev.: 4647

An odd import in this file (unused).

0 lines of code changed in 1 file:

rambaut 2012-02-08 11:12 Rev.: 4646

A few final adjustments for 1.7 packaging.

21 lines of code changed in 3 files:

dong.w.xie@gmail.com 2012-02-08 09:42 Rev.: 4643

trunk: update version history for 1.7

22 lines of code changed in 2 files:

dong.w.xie@gmail.com 2012-02-07 14:53 Rev.: 4642

trunk: move confused native files to \deprecated folder

63 lines of code changed in 4 files:

dong.w.xie@gmail.com 2012-02-07 10:20 Rev.: 4641

trunk:solve Issue 569: BirthDeathEpidemiologyModel bug

7 lines of code changed in 1 file:

fbielejec 2012-02-05 10:46 Rev.: 4640

high speed low drag paralell convolution code that will strike fear into the hearts of our enemies - redux

3 lines of code changed in 1 file:

fbielejec 2012-02-05 07:43 Rev.: 4639

high speed low drag paralell convolution code that will strike fear into the hearts of our enemies

121 lines of code changed in 1 file:

msuchard 2012-02-04 04:38 Rev.: 4638

Bug fix in randomization for SVSComplexSubstitutionModel

38 lines of code changed in 4 files:

msuchard 2012-02-04 04:14 Rev.: 4637

Fixed long-standing bug in DuplicatedParameter; need to fire multiple change events.

4 lines of code changed in 2 files:

rambaut 2012-02-03 11:02 Rev.: 4636

Fix for issue 570.

6 lines of code changed in 2 files:

rambaut 2012-02-03 04:55 Rev.: 4635

Addition to the Mac section of the ANT build to associate new BEAUti documents with the application.

9 lines of code changed in 1 file:

rambaut 2012-02-03 04:37 Rev.: 4634

Hidden 'Create Hierarchical Prior' button in the 'Default Prior' dialog that appears when you try to generate - that is not the place to create hierarchical models.

13 lines of code changed in 4 files:

rambaut 2012-02-03 03:51 Rev.: 4633

Altered how the prior dialog box that appears when you try to generate works. Now, if a prior is undefined the 'Continue' button is disabled. Selecting a valid prior enables it and allows you to generate the file.

64 lines of code changed in 3 files:

rambaut 2012-02-03 03:10 Rev.: 4632

Cleaned up a the id labels for Discrete patterns.

13 lines of code changed in 2 files:

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).

3 lines of code changed in 2 files:

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

change confused method name and fix prefix bug inside mergePatterns

8 lines of code changed in 4 files:

dong.w.xie@gmail.com 2012-02-02 16:38 Rev.: 4629

fix a bug of taxa prefix

1 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-02-02 12:30 Rev.: 4628

updating small changes in operators and adding lambda_parameter

29 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-02-02 11:32 Rev.: 4627

updating small changes in operators and adding lambda_parameter

99 lines of code changed in 4 files:

fbielejec 2012-02-02 03:26

reverting

0 lines of code changed in 3 files:

fbielejec 2012-02-01 22:54 Rev.: 4624

CPU implementation

0 lines of code changed in 1 file:

fbielejec 2012-02-01 22:33 Rev.: 4623

added the completely sequential equivalent

13 lines of code changed in 1 file:

fbielejec 2012-02-01 21:55 Rev.: 4622

fixed a bug

1 lines of code changed in 1 file:

fbielejec 2012-02-01 20:41 Rev.: 4621

working on routine populating transition matrices for many eigen buffers

58 lines of code changed in 1 file:

fbielejec 2012-02-01 20:40 Rev.: 4620

recompiled beagle.jar

0 lines of code changed in 1 file:

January 2012 »

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