February 2011 Commit Log

Number of Commits:
52
Number of Active Developers:
6
dong.w.xie 2011-02-28 13:11 Rev.: 3836

Trunk: add more validation in BEAUti checkOptions().

31 lines of code changed in 6 files:

dong.w.xie 2011-02-28 10:20 Rev.: 3835

Trunk: fix a bug of the enablility of "Create partition from trait" button should relate to available traits not taxa.

7 lines of code changed in 2 files:

dong.w.xie 2011-02-28 10:02 Rev.: 3834

Trunk: Use OldClockModelPanel for BEAUti 1.7, because PartitionClockModelPanel has no function developed yet.

3 lines of code changed in 1 file:

rambaut 2011-02-26 05:31 Rev.: 3832

Cleaned up MDS

190 lines of code changed in 2 files:

dong.w.xie 2011-02-25 15:20 Rev.: 3831

Trunk new Trace: fix some bugs.

42 lines of code changed in 9 files:

dong.w.xie 2011-02-25 11:56 Rev.: 3830

Trunk new Trace: more corrections to use 2d ArrayList ArrayList<ArrayList> not List[].

87 lines of code changed in 12 files:

dong.w.xie 2011-02-25 10:44 Rev.: 3829

Trunk new Trace: fix BSP plot in analysis, which should use 2d ArrayList ArrayList<ArrayList> not List[].

12 lines of code changed in 2 files:

rambaut 2011-02-25 05:13 Rev.: 3828

Fixed threshold observations in MDS.

6 lines of code changed in 1 file:

dong.w.xie 2011-02-24 16:56 Rev.: 3827

Trunk new Trace: fix bug of returning double format for integer value, because Integer is stored as Double in Trace.

39 lines of code changed in 4 files:

dong.w.xie 2011-02-24 13:06 Rev.: 3826

Trunk new Trace: if combined traces exists, the change type function should apply to all log files including combined traces as well.

39 lines of code changed in 1 file:

rambaut 2011-02-24 11:37 Rev.: 3825

More work on MDS

26 lines of code changed in 2 files:

dong.w.xie 2011-02-24 11:07 Rev.: 3824

Trunk new Trace: if combined traces exists, the filter has to be applied to all log files including combined traces, as Alexei advised.

77 lines of code changed in 6 files:

msuchard 2011-02-24 10:11 Rev.: 3823

Changing scaling behavior under dynamic scheme in BeagleTreeLikelihood (again)

1 lines of code changed in 1 file:

rambaut 2011-02-24 05:15 Rev.: 3822

Working on MDS

254 lines of code changed in 3 files:

dong.w.xie 2011-02-23 16:30 Rev.: 3821

Trunk new Trace: finally fix the bug of FilterPanels not showing in FilterJDialog.

104 lines of code changed in 5 files:

msuchard 2011-02-23 16:07 Rev.: 3820

Updated MaskParameter to specify mod x masking for specification of hierarchical priors in multidimensional scaling

29 lines of code changed in 2 files:

dong.w.xie 2011-02-23 11:49 Rev.: 3818

Trunk new Trace: fix filter not working bug.

47 lines of code changed in 6 files:

msuchard 2011-02-23 11:13 Rev.: 3817

Adding min thresholded (truncated) observations to MDS

42 lines of code changed in 1 file:

dong.w.xie 2011-02-22 20:54 Rev.: 3816

Trunk new Tracer: fix the bug of missing possible values displayed in FilterDiscretePanel after filter applied.

64 lines of code changed in 4 files:

dong.w.xie 2011-02-22 13:52 Rev.: 3815

Trunk new Trace: make trace type change function working.

138 lines of code changed in 6 files:

dong.w.xie 2011-02-21 15:14 Rev.: 3814

Trunk new Trace: struggling with filter applied situation.

91 lines of code changed in 5 files:

dong.w.xie 2011-02-21 12:20 Rev.: 3813

Trunk new Trace: update Find Conditional Posterior Distributions... jdialog and jpanel and jtable, but panelParent cannot be repainted.

270 lines of code changed in 7 files:

philippe.lemey@gmail.com 2011-02-20 05:06

tiny DnDsLog tweak

14 lines of code changed in 2 files:

dong.w.xie 2011-02-18 16:08 Rev.: 3810

Trunk new Trace: remove filter comb, add Find Conditional Posterior Distributions... in Analysis menu, create regarding jdialog and jpanel and jtable.

483 lines of code changed in 11 files:

akaruiws 2011-02-18 15:10 Rev.: 3809

Deleting the accidently committed file.

0 lines of code changed in 1 file:

dong.w.xie 2011-02-18 10:34 Rev.: 3808

Trunk new Trace: finally get rid of array copying functions getValues(?, [], ?) from Trace, which is memory consuming. Please use List<T> for your futher programming in Tracer.

150 lines of code changed in 17 files:

dong.w.xie 2011-02-17 16:46 Rev.: 3807

Trunk new Trace: remove static convert method from Trace.

22 lines of code changed in 6 files:

akaruiws 2011-02-17 15:37 Rev.: 3806

BMA for nucleotide substition models and gamma site model.

1092 lines of code changed in 12 files:

dong.w.xie 2011-02-17 15:31 Rev.: 3805

Trunk new Trace: 1) Try to replace Double[] as List<Double>, which save some memory, but it still crashes after loading a big log; 2) use traceType to detemine type, instead of prime type (T) of List<T> in Trace, and integer is stored as List<Double> currently for simlple solution of plotting.

404 lines of code changed in 38 files:

dong.w.xie 2011-02-16 16:32 Rev.: 3804

Trunk: starts using List instead array in Trace, and return List for getValues.

482 lines of code changed in 33 files:

msuchard 2011-02-16 10:34 Rev.: 3803

Hack to allow CompleteHistorySimulator to print out GeneralDataTypes. Several summary statistics in GeneralDataType still needs to be fixed when a sequence is a list of Strings and not chars.

5 lines of code changed in 2 files:

akaruiws 2011-02-15 17:04 Rev.: 3802

GTR examples added.

59 lines of code changed in 1 file:

akaruiws 2011-02-15 16:17 Rev.: 3801

TN93 example added.

11 lines of code changed in 1 file:

akaruiws 2011-02-15 15:29 Rev.: 3800

Some quick JUnit tests for NtdBMA model to check whether there are any major problems. More useful tests yet to come.

227 lines of code changed in 1 file:

akaruiws 2011-02-15 14:01 Rev.: 3799

Handle the variable change more efficiently.

27 lines of code changed in 1 file:

akaruiws 2011-02-15 13:00 Rev.: 3798

Model averaging for nucleotide models.

157 lines of code changed in 3 files:

msuchard 2011-02-15 09:54 Rev.: 3797

Modified CompleteHistorySimulator to report alignment of external and internal nodes

36 lines of code changed in 2 files:

dong.w.xie 2011-02-15 09:08 Rev.: 3796

Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.

478 lines of code changed in 50 files:

rambaut 2011-02-15 05:09 Rev.: 3795

Pathogen updates

173 lines of code changed in 3 files:

rambaut 2011-02-14 19:56 Rev.: 3794

Removed a bit of Java 1.6

10 lines of code changed in 1 file:

alexei.drummond 2011-02-12 17:51 Rev.: 3793

birth/death skyline

334 lines of code changed in 1 file:

rambaut 2011-02-09 05:18 Rev.: 3792

Pathogen updates

46 lines of code changed in 5 files:

rambaut 2011-02-09 05:17 Rev.: 3791

Fixed a few issues with TreeEvents being fired inappropriately. Also updates to AntigenicTreeLikelihood.

166 lines of code changed in 5 files:

rambaut 2011-02-07 23:33 Rev.: 3790

More work on AntigenicTraitLikelihood to allow for multiple measurements per antisera

211 lines of code changed in 2 files:

dong.w.xie 2011-02-04 16:36 Rev.: 3789

Trunk: new Tracer dev: comments for late dev

8 lines of code changed in 1 file:

dong.w.xie 2011-02-04 12:48 Rev.: 3788

Trunk: change Model Averaging indexVariable initial values from all 0 into i+1.

1 lines of code changed in 2 files:

dong.w.xie 2011-02-04 10:09 Rev.: 3787

Trunk: new Tracer dev: solve some generic type casting problems.

55 lines of code changed in 10 files:

rambaut 2011-02-04 04:23 Rev.: 3786

Fixed a parser that allows you to create patterns of constant sites which can then me merged with polymorphic sites to reconstruct a full pattern set.

3 lines of code changed in 4 files:

dong.w.xie 2011-02-03 16:30 Rev.: 3785

Trunk: new Tracer dev: make it complied, but there is still casting problem.

393 lines of code changed in 24 files:

rambaut 2011-02-02 08:07 Rev.: 3784

Added a parser that allows you to create patterns of constant sites which can then me merged with polymorphic sites to reconstruct a full pattern set.

94 lines of code changed in 2 files:

rambaut 2011-02-02 01:48 Rev.: 3783

Refactored out a simple class for doing BayesianMDS that AntigenicTraitLikelihood will build on. MdSL takes a simple case of pairwise distances (but allows missing data).

512 lines of code changed in 2 files:

msuchard 2011-02-01 02:27 Rev.: 3782

Bug found in branch-caching, so reverting default behavior to "false".

2 lines of code changed in 1 file:

January 2011 »

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