August 2010 Commit Log

Number of Commits:
109
Number of Active Developers:
9
dong.w.xie 2010-08-31 15:29 Rev.: 3476

Trunk: correction of Issue 377: BEAUti: Random local clock model Bug, but no siteModel.mu

45 lines of code changed in 3 files:

beth.shapiro 2010-08-31 10:48 Rev.: 3475

Solved load issue for BEAUTi, which previously would not load without also including beast.jar

1 lines of code changed in 1 file:

rambaut 2010-08-31 10:42 Rev.: 3474

Added a check for AttributePatternsParser that the attribute actually exists in at least one taxon.

8 lines of code changed in 2 files:

mandevsgill 2010-08-31 08:06 Rev.: 3473

GMRFMultilocusSkyrideLikelihood has been cleaned up and appears to work properly.

1 lines of code changed in 2 files:

dong.w.xie 2010-08-30 11:04 Rev.: 3472

Trunk: update README and Version History

154 lines of code changed in 8 files:

rambaut 2010-08-29 12:06 Rev.: 3471

Added ability to drag and drop files to the DataPane to import them.

60 lines of code changed in 1 file:

rambaut 2010-08-29 09:17 Rev.: 3470

CompoundLikelihood was failing to record timings for non-threaded instances resulting in no times for priors.

2 lines of code changed in 1 file:

rambaut 2010-08-29 04:29 Rev.: 3469

Slight update to benchmark1.xml

2 lines of code changed in 1 file:

rambaut 2010-08-29 01:47 Rev.: 3468

Added a third benchmark file. old_benchmark.xml is the old (trivially small) one. benchmark1.xml is 1400-odd HA1 flu genomes (about 500 patterns) to test big trees with modest amounts of data. benchmark2.xml is 60-odd mitochondrial genomes resulting in >5000 site patterns to test modest trees with lots of data.

11535 lines of code changed in 6 files:

dong.w.xie 2010-08-27 16:15 Rev.: 3467

Trunk: refactory xml examples

0 lines of code changed in 2 files:

dong.w.xie 2010-08-27 16:07 Rev.: 3466

Trunk: delete DiscreteTraitBranchRateModelParser from dev, since it had been moved into release

0 lines of code changed in 1 file:

dong.w.xie 2010-08-27 16:03 Rev.: 3465

Trunk: refactory xml examples

5966 lines of code changed in 51 files:

dong.w.xie 2010-08-27 15:49 Rev.: 3464

Trunk: solve Issue 341: Random local clock model Bug

9 lines of code changed in 2 files:

dong.w.xie 2010-08-27 13:28 Rev.: 3463

Trunk: refactory xml examples

3370 lines of code changed in 56 files:

dong.w.xie 2010-08-27 11:20 Rev.: 3462

Trunk: refactory xml examples

0 lines of code changed in 2 files:

dong.w.xie 2010-08-27 11:12

Trunk: refactory xml examples

422 lines of code changed in 6 files:

dong.w.xie 2010-08-26 16:40

Trunk: refactory xml examples

3 lines of code changed in 2 files:

dong.w.xie 2010-08-26 16:31

Trunk: refactory xml examples

0 lines of code changed in 164 files:

dong.w.xie 2010-08-26 16:18

Trunk: refactory xml examples

0 lines of code changed in 11 files:

dong.w.xie 2010-08-26 16:11

Trunk: refactory xml examples

17429 lines of code changed in 220 files:

mandevsgill 2010-08-26 11:29 Rev.: 3449

Cleaned-up version of GMRFMultilocusSkyrideLikelihood. It appears to be working with the block update sampler.

58 lines of code changed in 3 files:

dong.w.xie 2010-08-26 10:49 Rev.: 3448

Trunk: solve Issue 235: Unlinked DiscretizedBranchRates for multiple loci have the wrong number of dimensions

2 lines of code changed in 1 file:

rambaut 2010-08-25 23:32 Rev.: 3447

Implemented some microtiming in CompoundLikelihood. This is turned on by a static constant in this class so won't be compiled unless switched on. The results can be obtained by dumping the CompoundLikelihood into a <report> element:

<report>
<posterior idref="posterior"/>
</report>

This will break down the total number of evalations, the total amount of time and the time per eval for every prior and likelihood. This will be useful for considering parallelization and threading options.

The switch (CompoundLikelihood.EVALUATION_TIMERS) is on at present as I don't believe it will have any performance implications but I will be checking this.

116 lines of code changed in 2 files:

jheled 2010-08-25 21:58 Rev.: 3446

Ignore nonesense ESS on constant values. integer ESS values in panel.

11 lines of code changed in 1 file:

rambaut 2010-08-25 19:06 Rev.: 3445

Reordered the PriorType Enum so that UNDEFINED is first. This is so it doesn't appear as an option in the RootHeightPriorCombo. The user shouldn't be able to select it as an option.

14 lines of code changed in 2 files:

dong.w.xie 2010-08-25 18:04 Rev.: 3444

Trunk: solve Issue 374: BEAUti: only one taxa set for 3 unlinked partitions

44 lines of code changed in 1 file:

msuchard 2010-08-25 12:15 Rev.: 3443

Fixed parsing of multidimensional continuous traits when trait parameter is first defined in likelihood (and not TreeModel), i.e. for Pagelesque type models

19 lines of code changed in 2 files:

dong.w.xie 2010-08-25 11:39 Rev.: 3442

Trunk: solve Issue 375: BEAUti: rootHeightPriorCombo disappear when switch between Undefined and others

29 lines of code changed in 1 file:

dong.w.xie 2010-08-25 10:57 Rev.: 3441

Trunk: remove build_all_BEAST Target and switch Hudson to use 'test'.

0 lines of code changed in 1 file:

rambaut 2010-08-25 07:05

Added back build_all_BEAST target for Hudson so we don't get rude emails. Hudson should be switched to use 'test' and then this target can be removed.

8 lines of code changed in 2 files:

msuchard 2010-08-25 06:52 Rev.: 3438

Porting TipStateSwapOperator over to BEAGLE against my better judgement. Random permutations of tip traits form very poor statistical tests.

224 lines of code changed in 7 files:

msuchard 2010-08-25 06:50 Rev.: 3437

Fixing (? I think) command-line bug that entered in r3435. Please code review. At a minimum, BEAST now runs for me.

2 lines of code changed in 1 file:

mandevsgill 2010-08-25 05:21 Rev.: 3436

GMRF multilocus likelihood appears to compute properly; operators still do not work and there is debugging material to remove.

742 lines of code changed in 4 files:

rambaut 2010-08-25 01:21 Rev.: 3435

Slight adjustment of how command line arguments work. Previously they could be partially specified (thus '-work' instead of '-working') but this means that you can't have an argument that is a substring of another (thus '-beagle' and '-beagle_cpu') without specifiying the shorter one first. Now you have to specify the full option.

2 lines of code changed in 1 file:

rambaut 2010-08-25 00:37 Rev.: 3434

Strange use of some private Sun API to obtain a line separator caused compile warnings. Changed to System.getProperty("line.separator"). If there was some reason for the previous technique it should have been commented.

10 lines of code changed in 4 files:

rambaut 2010-08-25 00:26 Rev.: 3433

Cleaned up the targets in build.xml. The default now is just 'build' which does a clean, compile and build of jar files. 'test' does the same but runs unit tests. 'windows', 'linux' and 'mac' will generate a release build for that system (if the appropriate packaging plugins are installed in ant).

8 lines of code changed in 1 file:

rambaut 2010-08-24 23:39 Rev.: 3432

Implemented a new option for default priors - an UNDEFINED prior. This comes up as red in the priors table and the XML will not generate until this is set (even to a uniform[0,+Inf] would be OK). At present, the only parameters to use this option are the rate parameters for discrete traits (i.e., 1 character partitions).

103 lines of code changed in 8 files:

rambaut 2010-08-24 21:07 Rev.: 3431

Removed other redundant stuff relating to DemographicLogger (a generic logging of demographic models can now be done using XML as described in issue 329: http://code.google.com/p/beast-mcmc/issues/detail?id=329).

7 lines of code changed in 5 files:

rambaut 2010-08-24 21:01 Rev.: 3430

Removed DemographicLoggerParser from the release_parsers list as this class was a redundant stump that has now been deleted.

0 lines of code changed in 1 file:

dong.w.xie 2010-08-24 10:37 Rev.: 3429

Trunk: solve Issue 372: Failed to load parser in development parser

3 lines of code changed in 1 file:

dong.w.xie 2010-08-23 17:42 Rev.: 3428

Trunk: solve Issue 371 new change of PriorDialog broke two GUI functions

279 lines of code changed in 1 file:

dong.w.xie 2010-08-23 11:22 Rev.: 3427

Trunk: solve Issue 370: BEAST argument -overwrite not working

3 lines of code changed in 2 files:

rambaut 2010-08-23 08:01 Rev.: 3426

A reference to GeneralSubstitutionModel is put in the <prior> block if BSSVS is being used. This provides a check for ill-conditioned eigen decompositions.

2 lines of code changed in 1 file:

rambaut 2010-08-22 21:07 Rev.: 3425

Restored improper uniform priors on rate parameters but added a red colour to the prior table to warn about this.

56 lines of code changed in 7 files:

rambaut 2010-08-22 20:50 Rev.: 3424

Renamed an internal constant from JEFFREYS_PRIOR to ONE_OVER_X_PRIOR

25 lines of code changed in 7 files:

msuchard 2010-08-22 08:39 Rev.: 3423

In the middle of trying to get BEAGLE's dynamic scaling to work in BEAST

37 lines of code changed in 5 files:

rambaut 2010-08-21 04:14 Rev.: 3422

Restored a change made in r3291 and then overriden in r3332. This puts a proper (gamma[1,1]) prior on clock/relaxed clock rates if the partition has 1 site (i.e., is a discrete trait). An inproper uniform[0,+inf] prior remains otherwise - for user to set!.

85 lines of code changed in 1 file:

rambaut 2010-08-21 03:53 Rev.: 3421

Some final cosmetic tweaks for the Mac version of BEAUti.

39 lines of code changed in 7 files:

rambaut 2010-08-21 01:26 Rev.: 3420

Cleaned up the layout of PriorDialog. The Chart now expands in both dimensions as the dialog is resized.

73 lines of code changed in 1 file:

rambaut 2010-08-20 22:13 Rev.: 3419

Removed uses of '!' in dialog boxes and warnings as they are overly assertive. Took the opportunity to improve the clarity of some of the messages.

16 lines of code changed in 12 files:

rambaut 2010-08-20 21:58 Rev.: 3418

Trying to eliminate the use of annoying popup dialog boxes. The special value buttons are now simply disabled when the cursor is not in an appropriate text box.

60 lines of code changed in 2 files:

rambaut 2010-08-20 21:23 Rev.: 3417

Centred components in MCMCPanel for better visual effect.

5 lines of code changed in 1 file:

rambaut 2010-08-20 21:13 Rev.: 3416

Trying to make BEAUti look less Java-like. Have removed the white background for all the panels that are in scroll panes so that you can't see that they are (in a scrollpane) until the scroll bars activate. Have also turned off the horizontal scrollbars in these cases and checked that all the components are visible when the window is at its smallest size. However, I have not tested this on other platforms so would be interested in how it looks (both normally and when small) on Linux and Windows. If any changes to this are required, they should probably be put in platform specific conditionals (i.e., if (!MacOSX)).

58 lines of code changed in 9 files:

rambaut 2010-08-20 18:49 Rev.: 3415

Added a benchmark2.xml file with 62 complete mitochondrial genomes of carnivores. Gives >5000 unique site patterns.

580 lines of code changed in 1 file:

rambaut 2010-08-20 04:13 Rev.: 3414

Added command line option '-prefix <PREFIX>' to specify a string which will be prefixed to all output log files. This is an alternative to changing the log file names in the XML when running multiple replicate runs in the same location.

283 lines of code changed in 7 files:

rambaut 2010-08-19 22:46 Rev.: 3413

Accidentally deleted the last curly bracket from BeastMain just before checkin causing a broken build.

1 lines of code changed in 1 file:

rambaut 2010-08-19 21:34 Rev.: 3412

The use of any beagle command line option will turn on the use of BEAGLE (previously you needed to give '-beagle' and any other options required).

165 lines of code changed in 1 file:

rambaut 2010-08-19 21:31 Rev.: 3411

LoggerParser uses a special function to get the log file which may set different paths (for example to a working directory). Thus just checking that fileName exists may not work. So moved the check for existing file into XMLParser.getFilePrintWriter(). This has the added benefit that all loggers use this function and thus all have the overwriting behaviour.

Also added a check box to the BEAST options dialog box.

46 lines of code changed in 11 files:

rambaut 2010-08-19 20:56 Rev.: 3410

Reduced verbosity - 'allowOverwrite' attribute is now just 'overwrite'

1 lines of code changed in 1 file:

rambaut 2010-08-19 20:54 Rev.: 3409

Commented out newly added checkbox in MCMCPanel to set the allowOverwrite attribute (sorry Walter). I just don't think this is the place for the user to make this decision. I have left the generation of the attribute in and it will be set to false. If the user wants to override this they can use the BEAST commandline options '-overwrite'. The XML attribute is worth having for test scripts where you probably want to set it to true.

8 lines of code changed in 1 file:

rambaut 2010-08-19 20:50 Rev.: 3408

Added a command line option to BEAST '-overwrite' which will allow overwriting of log files (overriding any attribute in the XML). This works by setting a System property 'allow.overwrite=true'. This can also be set (true or false) using the JVM option -Dallow.overwrite=XXXX

17 lines of code changed in 2 files:

dong.w.xie 2010-08-19 17:15 Rev.: 3407

Trunk: delete redundant example XML for Issue 365: Folder called 'beauti1.5' in /examples

0 lines of code changed in 42 files:

dong.w.xie 2010-08-19 17:10 Rev.: 3406

Trunk: solve Issue 348: Windows BEAST exe <close> then <cancel>, window should NOT be closed

7 lines of code changed in 1 file:

dong.w.xie 2010-08-19 11:17 Rev.: 3405

Trunk: solve Issue 305: BEAST should warn/halt if log files already exist

30 lines of code changed in 4 files:

rambaut 2010-08-18 23:24 Rev.: 3404

Firstly, made writeComment take a VarArg number of strings to allow for multi-line comments. Comments now have a blank line before them to break up the XML visually.

Secondly, removed the 'booleanLikelihood' for LogisticModel as this was nasty. Instead, proper priors need to be put on the t50 parameter (a gamma is given as default). Also added gamma default prior to the doubling time parameter (and picked a larger initial value to help with numerical issues in logistic and expansion model).

Thirdly, normalized the generation of discrete trait models to always use generalSubstitutionModel.

Have generated all these model and tested that they run (but not that they produce reasonable results).

279 lines of code changed in 13 files:

rambaut 2010-08-18 13:00 Rev.: 3403

Moved message about default rate prior to the default prior warning dialog box as this is more likely to be noticed. Also added a warning about improper priors (currently only uniform where one or other bound is infinite). Would be nice for the table in this box to show these improper priors in red.

45 lines of code changed in 2 files:

dong.w.xie 2010-08-17 16:23 Rev.: 3402

Trunk: solve Issue 298: BEAUti should validate a user specified tree that is only bifurcating at the root

76 lines of code changed in 6 files:

dong.w.xie 2010-08-17 12:01 Rev.: 3401

Trunk: bring back incorrectly deleted solution by r3364, for Issue 274, 334, 314, 333, 342, 343, 320.

134 lines of code changed in 5 files:

msuchard 2010-08-17 04:54 Rev.: 3400

Placeholders for a new transition kernel to hopefully solve the uniform internal node prior issues

118 lines of code changed in 2 files:

rambaut 2010-08-16 20:47 Rev.: 3399

Instituted a minimum window size for Mac OS X only (640x480). This is actually too small to usefully use the interface but if a window this small is really required then we can adjust the UI. Removed long text on OperatorsPanel's Auto Optimize checkbox and put it as a tooltip instead.

15 lines of code changed in 2 files:

rambaut 2010-08-16 20:35 Rev.: 3398

Addressing issue 358. Moved 'Sequence Error Model' to SiteModelPanel. Cleaned up ClockModelsPanel as a result - no longer need to put the Fixed Mean option in a scrollpane.

58 lines of code changed in 2 files:

dong.w.xie 2010-08-16 17:56 Rev.: 3397

Trunk: give error message for previous checkin.

6 lines of code changed in 1 file:

dong.w.xie 2010-08-16 17:53 Rev.: 3396

Trunk: add acidently deleted solution for Issue 343: NullPointerException after double-click discrete traits in Data Partition panel.

4 lines of code changed in 1 file:

dong.w.xie 2010-08-16 17:34 Rev.: 3395

Trunk: solve Issue 311: BEAUti: prior generator is not picking up the correct value from prior panel

9 lines of code changed in 2 files:

dong.w.xie 2010-08-16 17:07 Rev.: 3394

Trunk: solve Issue 350: BEAUti prior dialog cannot enable resizable because of using OptionsPanel

34 lines of code changed in 2 files:

dong.w.xie 2010-08-16 11:19 Rev.: 3393

Trunk: solve Issue 357: window's programmer has broken compatibility with unix-based operating systems

4 lines of code changed in 1 file:

alexei.drummond 2010-08-13 16:52

jessie :-)

4 lines of code changed in 2 files:

dong.w.xie 2010-08-13 15:50 Rev.: 3390

Trunk: solve Issue 356: Add instruction to show user how to load specified starting tree from BEAUti

46 lines of code changed in 5 files:

dong.w.xie 2010-08-13 14:41 Rev.: 3389

Trunk: solve Issue 354: BEAUti: make auto wrap for HTMLEditorKit inside JEditorPane, and Issue 355: get rid of ">" when wrapping text using BEAUti TextUtil

15 lines of code changed in 3 files:

dong.w.xie 2010-08-13 14:04 Rev.: 3388

Trunk: solve Issue 351: message label on the bottom of BEAUti frame is floating when no space enough

68 lines of code changed in 4 files:

mandevsgill 2010-08-13 11:53 Rev.: 3387

Testing SVN

0 lines of code changed in 1 file:

msuchard 2010-08-13 11:30 Rev.: 3386

Started work with Mandev on multilociGMRF

451 lines of code changed in 3 files:

dong.w.xie 2010-08-12 16:57 Rev.: 3385

Trunk: solve Issue 352: BEAUti: NullPointerException if leave any trait value empty after activate BSSVS

32 lines of code changed in 4 files:

dong.w.xie 2010-08-12 15:41 Rev.: 3384

Trunk: JDialog cannot resize because of OptionsPanel.

9 lines of code changed in 1 file:

dong.w.xie 2010-08-12 12:47 Rev.: 3383

Trunk: more BEAUti work.

20 lines of code changed in 7 files:

dong.w.xie 2010-08-12 10:55 Rev.: 3382

Trunk: correct Prior table and disable last column resize because low resolution display issue.

5 lines of code changed in 1 file:

dong.w.xie 2010-08-11 17:32 Rev.: 3381

Trunk: solve Issue 339: GUI within scroll panes is just nasty

97 lines of code changed in 8 files:

msuchard 2010-08-11 13:11 Rev.: 3380

Placeholders for an awesome new transition kernel to hopefully solve the uniform internal node prior issues

191 lines of code changed in 2 files:

msuchard 2010-08-11 08:12 Rev.: 3379

Added ability to set parameter-independent bounds on UniformOperator; should help prior sampling with a hard-boundary on rootHeight

27 lines of code changed in 3 files:

dong.w.xie 2010-08-10 12:09 Rev.: 3378

Trunk: solve Issue 347: change BEAUti default prior of ucld.stdv and kappa, and fix few little bugs.

50 lines of code changed in 7 files:

dong.w.xie 2010-08-09 17:33 Rev.: 3377

Trunk: more work on new *BEAST GUI, and solve Issue 338: Clock model panel is confusingly laid out, and Issue 346: Show user a guide for an example of *BEAST or trait mapping file format.

63 lines of code changed in 4 files:

dong.w.xie 2010-08-09 12:02 Rev.: 3376

Trunk: more work on new *BEAST GUI, and solve Issue 345: BEAUti: user want to be able to edit trait value at any time

45 lines of code changed in 3 files:

akaruiws 2010-08-09 11:49 Rev.: 3375

Jeffrey's prior for parameters of Normal distribution.

130 lines of code changed in 2 files:

dong.w.xie 2010-08-06 12:38 Rev.: 3371

Trunk: make *BEAST work with check box only.

30 lines of code changed in 4 files:

dong.w.xie 2010-08-06 11:25 Rev.: 3370

Trunk: make buttons work for new change of traits.

61 lines of code changed in 4 files:

rambaut 2010-08-06 04:08 Rev.: 3369

1 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-08-05 18:35 Rev.: 3368

continuous xml example update

5 lines of code changed in 6 files:

dong.w.xie 2010-08-05 16:33 Rev.: 3367

Trunk: fix bugs of new change of traits.

9 lines of code changed in 2 files:

dong.w.xie 2010-08-05 11:48 Rev.: 3366

Trunk: correct birth death serial sampling model : logL += Math.log(psi() * q(y) * p0(y)).

1 lines of code changed in 1 file:

rambaut 2010-08-05 04:21 Rev.: 3365

These models now allow a null indicator parameter in the constructor in which case they create one full of ones.

24 lines of code changed in 3 files:

rambaut 2010-08-05 04:13 Rev.: 3364

This is rather a large update as I was making changes in a branch and have merged them back in. This allows any trait name to be created (not just 'Location' and 'Species'). The idea is that the discrete model is not phylogoegraphy specific - you can model any discrete change. Have added a check box to say use *BEAST - at this point you should create a Species trait. Have cleaned up a few othe UI issues. Almost certainly there will be XML generation issues as a result and we should concentrate on testing and fixing these.

673 lines of code changed in 32 files:

dong.w.xie 2010-08-04 18:36 Rev.: 3363

Trunk: solve Issue 333: Unlink buttons are enabled even when only one partition is loaded.

3 lines of code changed in 1 file:

dong.w.xie 2010-08-04 18:30 Rev.: 3362

Trunk: solve Issue 343: NullPointerException after double-click discrete traits in Data Partition panel

3 lines of code changed in 1 file:

dong.w.xie 2010-08-04 18:17 Rev.: 3361

Trunk: solve Issue 342: NullPointerException after cancelled 'Create New Trait' dialog

1 lines of code changed in 1 file:

dong.w.xie 2010-08-04 18:00 Rev.: 3360

Trunk: solve Issue 334: NullPointerException after cancelled 'Import Traits'.

15 lines of code changed in 1 file:

dong.w.xie 2010-08-03 15:35 Rev.: 3359

Trunk: solve Issue 314: Error message for alignments with different taxa to refer to one tree in BEAST & BEAUti, and Issue 320: BEAUti: need validation of changing tree in data panel after allowing different taxa

23 lines of code changed in 2 files:

dong.w.xie 2010-08-03 12:11 Rev.: 3358

Trunk: solve Issue 274: BEAUti: add error message in XML if XML is truncated

170 lines of code changed in 3 files:

dong.w.xie 2010-08-03 11:29 Rev.: 3357

Trunk; BEAUti add Random Local Clock, but it seems BEAST model has bug

57 lines of code changed in 6 files:

rambaut 2010-08-01 11:18 Rev.: 3356

A _very_ situation specific simulator for a project.

1 lines of code changed in 2 files:

July 2010 »

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