December 2008 Commit Log

Number of Commits:
52
Number of Active Developers:
5
msuchard 2008-12-31 12:09 Rev.: 1399

More partials scaling issues

5 lines of code changed in 1 file:

msuchard 2008-12-31 09:50 Rev.: 1398

Messing around with dynamic rescaling of partials in newtreelikelihood. Trying for a rescaling mechanism that only runs after an under/over-flow

75 lines of code changed in 9 files:

msuchard 2008-12-25 08:54 Rev.: 1397

Tweaked BeastParser so that it only reports parser loadings under verbose-mode. Added dr.geo package to hold non-evolutionary geospatial stuff.

326 lines of code changed in 8 files:

msuchard 2008-12-25 05:22 Rev.: 1396

Minor tweak to get BranchingModels (BetaSplitting/Tetralogy) to work with new Paramater.ChangeType

2 lines of code changed in 1 file:

bloomquist 2008-12-20 12:53 Rev.: 1395

Added ancestral restriction to ARGCoalescentLikelihood.

116 lines of code changed in 2 files:

bloomquist 2008-12-20 07:02 Rev.: 1394

Modified so it works now.

8 lines of code changed in 2 files:

bloomquist 2008-12-19 20:14 Rev.: 1393

Added a hierarchical partition model for ARG model.

203 lines of code changed in 8 files:

bloomquist 2008-12-17 13:44 Rev.: 1392

Minor changes to the Distinct tree loggers.

63 lines of code changed in 2 files:

bloomquist 2008-12-17 10:57 Rev.: 1391

Added the ability to count distinct trees in argmodel.

116 lines of code changed in 4 files:

msuchard 2008-12-17 06:56 Rev.: 1390

Had to add a System.exit to BeastMain and changed numbering of GPU devices to 1,2,3 ...

63 lines of code changed in 7 files:

bloomquist 2008-12-13 13:13 Rev.: 1387

Modified some minor ARG Stuff. Added statistic to give total ARG length.

83 lines of code changed in 6 files:

bloomquist 2008-12-12 13:57 Rev.: 1386

Added the ability to flip multiple partitions at once in arg model.

31 lines of code changed in 1 file:

bloomquist 2008-12-12 12:17 Rev.: 1385

Small change on where it spits out the warning.

0 lines of code changed in 1 file:

bloomquist 2008-12-12 11:57 Rev.: 1384

Modifications to the ARG package.

85 lines of code changed in 6 files:

rambaut 2008-12-12 07:48 Rev.: 1383

Created a new parser called 'patternSubSet' which takes a SiteList (which includes Alignments and SitePatters) and creates a subset.

93 lines of code changed in 4 files:

msuchard 2008-12-12 04:23 Rev.: 1382

Sorry; did not mean to add this file; new version of Eclipse is messing around with me

16 lines of code changed in 2 files:

rambaut 2008-12-12 03:15 Rev.: 1381

Added the ability to turn tree normalization off - use 'scaleByTime="false"' by default.

3 lines of code changed in 1 file:

alexander.alekseyenko 2008-12-12 01:57 Rev.: 1380

added an example of binary stochastic Dollo model, +some minor related bug fixes.

268 lines of code changed in 3 files:

rambaut 2008-12-11 12:24 Rev.: 1379

Option added to patterns to divide the pattern list up into subsets for more efficient distribution amongst threads when not partitioned.

89 lines of code changed in 2 files:

msuchard 2008-12-11 11:35 Rev.: 1378

Tried using ReentrantLocks to speed-up blocking in ThreadedCompoundLikelihood.

0 lines of code changed in 1 file:

jheled 2008-12-10 21:39 Rev.: 1377

Bug fix: Range not implemented properly

17 lines of code changed in 1 file:

bloomquist 2008-12-07 05:09 Rev.: 1376

Fixed bug.

1 lines of code changed in 1 file:

rambaut 2008-12-06 05:19 Rev.: 1375

Finally got the LocalClockModel working. Can apply local clocks (relative rate or absolute) to a set of external branches or to any number of (possibly nested) clades. The clades should probably have monophyly enforced.

575 lines of code changed in 3 files:

rambaut 2008-12-05 22:00 Rev.: 1374

mtREV empirical frequencies didn't quite add up to 1.0 causing an exception. Have made the empirical AA models normalize their frequencies to handle this.

27 lines of code changed in 3 files:

msuchard 2008-12-05 17:47 Rev.: 1373

Parser option to specify GPU device number

17 lines of code changed in 3 files:

bloomquist 2008-12-05 07:27 Rev.: 1372

Added a partition likelihood for ARGModel

506 lines of code changed in 7 files:

rambaut 2008-12-05 03:22 Rev.: 1371

Cleaned this up a little and added an option to turn off scaling (just experimenting).

22 lines of code changed in 1 file:

rambaut 2008-12-04 23:35 Rev.: 1370

Updated the parser selection to allow a System property override (i.e., "-Dparsers=development" to the JVM). The parsers property is now just a single word, either 'release' or 'development' and the suffix "_parsers.properties" is added. I guess we could allow multiple parser lists to be specified so people can add their own for specific projects.

58 lines of code changed in 2 files:

jheled 2008-12-04 18:34 Rev.: 1369

Allow optional internal population points. The reduced model has only population sizes on the species tree nodes (including root branch)

61 lines of code changed in 2 files:

jheled 2008-12-04 17:44 Rev.: 1368

Make loading development parsers *really* work

2 lines of code changed in 2 files:

rambaut 2008-12-04 13:14 Rev.: 1367

Removed unwanted import (which was causing a compile error)

0 lines of code changed in 1 file:

rambaut 2008-12-04 13:13 Rev.: 1366

Switched to the development parser list.

1 lines of code changed in 1 file:

rambaut 2008-12-04 05:14 Rev.: 1365

Had accidentally commented out CoalescentSimulator parser. Also fixed ANT file to package up properties files.

4 lines of code changed in 2 files:

rambaut 2008-12-04 04:35 Rev.: 1364

Dug out the last version of BEAUti prior to the rewrite for multiple partitions. Re-added it as 'oldbeauti' so we have a backup program and one that still loads 'beauti' files.

11080 lines of code changed in 26 files:

rambaut 2008-12-04 03:52 Rev.: 1363

0 lines of code changed in 1 file:

rambaut 2008-12-04 03:29 Rev.: 1362

Updated the version to '1.5beta2' in preperation for packaging a version for the Molecular Evolution Workshop in Czech Rep next year.

2 lines of code changed in 1 file:

rambaut 2008-12-04 03:25 Rev.: 1361

Pruned the 'release_parsers.properties' file down to the set that I think are to be included in the next release of BEAST

11 lines of code changed in 3 files:

rambaut 2008-12-04 03:05 Rev.: 1360

Refactored the parser loading into a new private method.

60 lines of code changed in 1 file:

rambaut 2008-12-04 02:49 Rev.: 1359

Slight reworking of the plug-in system. A "beast.properties" file defines the root package of a plugin. See dr.evomodel.arg for an example (I thought the ARG was a good example of a plugin because all the files are in a single package). This can have names, descriptions, authors and citation properties that will presumably be printed up when the plugin is loaded. It also contains the name of the parsers list.

dr.app.beast also has a 'beast.properties' file which allows us to switch the parser file between the release and the development version.

Next thing is to implement a recursive search through the packages for 'beast.properties'.

83 lines of code changed in 7 files:

rambaut 2008-12-04 02:00 Rev.: 1358

-verbose command line option now reports all built-in and dynamically loaded parsers.

2 lines of code changed in 1 file:

rambaut 2008-12-04 01:51 Rev.: 1357

Implemented a dynamic parser loading system. BeastParser loads the 'core' set of parsers and then looks in a properties file for additional classes to load. See 'release_parsers.properties' for the full list. If the class itself is an XMLObjectParser then an instance is created. If it isn't then the system looks for static fields which are instances of XMLObjectParser and adds these.

I have created two lists - 'development_parsers.properties' which contains all the extra parsers that anyone has created. When developing, add your parsers here. 'release_parsers.properties' contains parsers that will be included in the next release of BEAST. If you don't want your stuff in the release version, please remove them from here.

This is a first stage towards a 'plug-in' system. I suggest that we create a new top level package called 'plugins' that people can create packages in. These would contain all the classes for a particular system (possibly in subpackages that mirror the beast hierarchy) and a parsers.properties file that specifies all the parsers. BEAST would then iterate through these packages and pick up the parsers.

617 lines of code changed in 13 files:

rambaut 2008-12-04 01:18 Rev.: 1356

Moved EBSPAnalysis from dr.inference package to avoid dependencies on dr.evolution and dr.evomodel in the inference package

424 lines of code changed in 1 file:

jheled 2008-12-03 19:40 Rev.: 1355

Convert to a model.
Add code which does normalization properly.

173 lines of code changed in 1 file:

jheled 2008-12-03 19:39 Rev.: 1354

28 lines of code changed in 1 file:

jheled 2008-12-03 19:38 Rev.: 1353

supervised automatic code improvments (Intellij)

78 lines of code changed in 11 files:

jheled 2008-12-03 19:35 Rev.: 1352

Add getter for type

5 lines of code changed in 1 file:

jheled 2008-12-03 19:33 Rev.: 1351

Epsilonic improvment

3 lines of code changed in 1 file:

bloomquist 2008-12-03 13:26 Rev.: 1350

Fixed some bugs.

207 lines of code changed in 4 files:

rambaut 2008-12-02 20:47 Rev.: 1349

Minor GUI tweaks

112 lines of code changed in 6 files:

bloomquist 2008-12-02 09:49 Rev.: 1348

Added a warning to ScaleOperator that warns the user the value of the parameter is 0. ScaleOperators cannot move values of 0.

15 lines of code changed in 1 file:

rambaut 2008-12-02 05:35 Rev.: 1347

Small modification to allow TreeAnnotator to parse bivariate locations when given by 2 different attributes (rather than as a 2 dimensional array).

24 lines of code changed in 1 file:

jheled 2008-12-01 14:55 Rev.: 1346

automatic code improvments (intellij)

143 lines of code changed in 8 files:

November 2008 »

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