July 2010 Commit Log

Number of Commits:
53
Number of Active Developers:
6
msuchard 2010-07-31 07:11 Rev.: 3355

Backwards compatibility so MarkovJumps XML blocks do not crash BEAST without BEAGLE.

2 lines of code changed in 1 file:

rambaut 2010-07-30 19:04 Rev.: 3354

A _very_ situation specific simulator for a project.

830 lines of code changed in 9 files:

akaruiws 2010-07-30 18:41 Rev.: 3353

Classes for modelling the relative rates of loci.

391 lines of code changed in 7 files:

dong.w.xie 2010-07-30 15:55 Rev.: 3352

TRUNK: *BEAST mapping file example

0 lines of code changed in 1 file:

dong.w.xie 2010-07-30 12:55 Rev.: 3351

TRUNK: change build

2 lines of code changed in 2 files:

msuchard 2010-07-30 06:25 Rev.: 3346

Updating geo-spatial regions for Gibbs sampling

107 lines of code changed in 4 files:

msuchard 2010-07-29 11:22 Rev.: 3345

Special tolerance test for super-high precision Colt eigendecomposition

1 lines of code changed in 1 file:

rambaut 2010-07-29 03:57 Rev.: 3344

Fixed Issue 331 <http://code.google.com/p/beast-mcmc/issues/detail?id=331>. I removed the help button until such time as it does something. I have added some tooltip text for the various buttons. This should be done for all UI in BEAUti. I also changed the two toolbars into a single one at the top of the panel so they didn't affect the rescaling of the splitpane.

51 lines of code changed in 2 files:

rambaut 2010-07-29 01:44 Rev.: 3343

Fixed Issue 336 <http://code.google.com/p/beast-mcmc/issues/detail?id=336>. The SubstModel table in Site Model Tab now has a minimum width.

8 lines of code changed in 2 files:

rambaut 2010-07-29 01:29 Rev.: 3342

Fixed Issue 339 <http://code.google.com/p/beast-mcmc/issues/detail?id=339>. This involves not installing the scroll pane as the rootPane of the frame if on the Mac OS X platform. For this platform it also sets a minumum window size of 800x600. At this size, some of the UI gets clipped in some panels but my goal now is to improve the UI to prevent this rather than forcing the user to scroll the panel. I will leave it up to developers on other platforms to decide whether to follow this pattern or to allow scrollable UIs.

20 lines of code changed in 2 files:

akaruiws 2010-07-28 22:07 Rev.: 3341

Prevent repetitive rate calculations.

16 lines of code changed in 1 file:

alexei.drummond 2010-07-28 20:38 Rev.: 3340


328 lines of code changed in 3 files:

akaruiws 2010-07-28 20:20 Rev.: 3339

Automatically create bounds for the category parameter and correction to adding parameter to model.

6 lines of code changed in 1 file:

akaruiws 2010-07-28 17:50 Rev.: 3338

Correction of typos.

1 lines of code changed in 2 files:

dong.w.xie 2010-07-28 16:35 Rev.: 3337

TRUNK: fix breaken code in test, but wait Alexei to verify the test.

5 lines of code changed in 1 file:

alexei.drummond 2010-07-28 16:16 Rev.: 3336

fixed tests (by removing! yikes!)

2 lines of code changed in 1 file:

alexei.drummond 2010-07-28 15:48 Rev.: 3335

removed unmappable character

35 lines of code changed in 1 file:

dong.w.xie 2010-07-28 15:45 Rev.: 3334

TRUNK: correct dev parser name

1 lines of code changed in 1 file:

alexei.drummond 2010-07-28 15:44 Rev.: 3333

updated Birth-death serial sampling model

67 lines of code changed in 4 files:

dong.w.xie 2010-07-28 14:36 Rev.: 3332

TRUNK: a simple solution for Issue 321: Default priors in BEAUTi still lead to IMPROPER posterior

51 lines of code changed in 2 files:

dong.w.xie 2010-07-28 11:11 Rev.: 3330

TRUNK: solve Issue 319: BEAUti: checkbox 'allow different taxa in partitions' should be a message instead

119 lines of code changed in 3 files:

msuchard 2010-07-28 11:00 Rev.: 3329

Special tolerance test for super-high precision Colt eigendecomposition

5 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-07-28 07:23 Rev.: 3328

10 lines of code changed in 1 file:

rambaut 2010-07-28 05:46 Rev.: 3327

Forgot a couple of other things...

48 lines of code changed in 2 files:

msuchard 2010-07-28 05:39 Rev.: 3326

Minor fix for debugging

7 lines of code changed in 1 file:

rambaut 2010-07-28 05:02 Rev.: 3325

Cleaned up the GeneralSubstitutionModel parser even more. This involved getting rid of SVSIrreversibleSubstModel (old code, Marc promises me). RootFreqs are gone - only worked with the old Irreversible model. Can be done other ways now. svsComplexSubstitutionModel and svsGeneralSubstitutionModel are synonyms of this parser and should allow backwards compatibility.

84 lines of code changed in 6 files:

msuchard 2010-07-27 09:46 Rev.: 3324

Add ability to select a random subset of taxa for analysis

86 lines of code changed in 2 files:

akaruiws 2010-07-25 16:25 Rev.: 3323

Parser and corrections for DiscretizedLociRates.

92 lines of code changed in 3 files:

akaruiws 2010-07-24 18:11 Rev.: 3322

Models the relative loci rates using the given discritized parametric distribution.

88 lines of code changed in 1 file:

rambaut 2010-07-23 03:01 Rev.: 3321

Cleaned up GeneralSubstitutionModelParser so it generally uses SVSGeneralSubstitutionModel or SVSIrreversibleSubstitutionModel (creating indicators = 1 if not specified). The only case now where it will use GeneralSubstitutionModel is if relativeTo attribute is specified.

66 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-07-19 17:50 Rev.: 3320

adding the ability to consider unions of polygons in GeoSpatialCollection

23 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-07-19 17:50 Rev.: 3319

adding the ability to consider unions of polygons in GeoSpatialDistribution

17 lines of code changed in 1 file:

dong.w.xie 2010-07-16 11:26 Rev.: 3318

TRUNK: remove beagle-beast.jar from release to include beagle in beast jar.

3 lines of code changed in 1 file:

dong.w.xie 2010-07-15 16:07 Rev.: 3317

TRUNK: *BEAST mapping file - Gopher data example

0 lines of code changed in 2 files:

dong.w.xie 2010-07-15 12:35 Rev.: 3316

TRUNK: fix *BEAST GUI bug to load mapping file

76 lines of code changed in 3 files:

msuchard 2010-07-15 03:02 Rev.: 3315

TreeAnnotator requires classes recently moved into dr/app/gui; fixed

2 lines of code changed in 1 file:

msuchard 2010-07-15 02:04 Rev.: 3314

Bifractional diffusion is a pain

139 lines of code changed in 13 files:

msuchard 2010-07-14 21:31 Rev.: 3313

JUnitTest for empirical Bayes smoother

40 lines of code changed in 1 file:

msuchard 2010-07-14 20:56 Rev.: 3312

Mighty cool positive selection tools through simple nucleotide models.

732 lines of code changed in 6 files:

dong.w.xie 2010-07-14 16:33 Rev.: 3311

TRUNK: another bug fix for *BEAST generator

7 lines of code changed in 1 file:

dong.w.xie 2010-07-14 15:41 Rev.: 3310

TRUNK: fix *BEAST GUI bug

13 lines of code changed in 3 files:

msuchard 2010-07-14 09:00 Rev.: 3309

Cleaning up dN/dS summary statistics and adding TreeTraits for flu backbone

593 lines of code changed in 11 files:

msuchard 2010-07-13 23:46 Rev.: 3308

BEAST-BEAGLE JUnits (require BEAGLE, can disable on Hudson if necessary).

296 lines of code changed in 2 files:

msuchard 2010-07-13 23:45 Rev.: 3307

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

86 lines of code changed in 1 file:

msuchard 2010-07-13 23:44 Rev.: 3306

Started work on multilocus GMRF Skyride

342 lines of code changed in 7 files:

msuchard 2010-07-13 23:31 Rev.: 3305

Keeping example file up-to-date

6 lines of code changed in 2 files:

msuchard 2010-07-13 15:21 Rev.: 3304

Pacifying Hudson.

5 lines of code changed in 2 files:

msuchard 2010-07-13 09:12 Rev.: 3303

Can independently specify root distribution from CTMC stationary distribution

496 lines of code changed in 7 files:

msuchard 2010-07-13 02:36 Rev.: 3302

Checking normalization of CTMC likelihood over all possible alignments

244 lines of code changed in 4 files:

msuchard 2010-07-12 20:07 Rev.: 3301

Branch rate models can now return a logDensity so that they may include the correct normalization constants.

23 lines of code changed in 3 files:

dong.w.xie 2010-07-08 11:08 Rev.: 3300

TRUNK: solve Issue 325: processValues[] in DiscreteTraitBranchRateModel should be the size of number of states NOT number of rates

43 lines of code changed in 4 files:

msuchard 2010-07-02 22:03 Rev.: 3299

Fix with traitName in SampledMultivariateTraitLikelihood

8 lines of code changed in 2 files:

akaruiws 2010-07-01 17:32 Rev.: 3298

Gibbs sampling for a single msat ancestral state.

224 lines of code changed in 9 files:

June 2010 »

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