October 2009 Commit Log

Number of Commits:
154
Number of Active Developers:
13
dong.w.xie 2009-10-29 16:16 Rev.: 2484

Solve Issue 227: Fix BeastDoc to generate tag doc for BEAST users, but need enhancement.

182 lines of code changed in 6 files:

dong.w.xie 2009-10-29 11:47 Rev.: 2483

Solve Issue 225: TreePartitionCoalescent is not existing, which had been renamed into MultiSpeciesCoalescent

2 lines of code changed in 1 file:

rambaut 2009-10-29 05:18 Rev.: 2482

Added some simple timing round the evaluation just after each operator which is stored by the operator and reported in the operator analysis table. On this note, I have added an attribute to <mcmc operatorAnalaysis="analysis.file"> which gives the name of the file to write the analysis to. If this isn't there then the file isn't written. We need to add this to BEAUti to use the same file name stem as the log and trees file (with an extension '.ops'?).

114 lines of code changed in 11 files:

sidneym 2009-10-28 15:47 Rev.: 2481

Issue 220: Fix shell scripts for Mac and Linux to cope with installation directory name containing space characters

20 lines of code changed in 19 files:

jheled 2009-10-28 11:26 Rev.: 2480

Have name of likelihood or tree in info message when there are several of those.

13 lines of code changed in 1 file:

rambaut 2009-10-28 01:38 Rev.: 2479

Updated the Mac/Linux build scripts: the command line shell scripts now provide linking for BEAGLE if required. Added spaces _back_ into Mac and Windows application/package names. There was no need to remove them and users expect spaces in the names of applications. Issue 220: http://code.google.com/p/beast-mcmc/issues/detail?id=220 still needs to be dealt with but the solution is _NOT_ just to remove spaces - see the issue for details.

16 lines of code changed in 5 files:

dong.w.xie 2009-10-27 14:58 Rev.: 2478

sovle Issue 217: Problems with the Mac OS X packaging. And remove the space from file names.

15 lines of code changed in 1 file:

dong.w.xie 2009-10-27 13:55 Rev.: 2477

The part of solution of Issue 217: Problems with the Mac OS X packaging, .app bundles should just have symbolic links to the jars and jnilibs in /lib/.

5 lines of code changed in 1 file:

dong.w.xie 2009-10-27 13:47 Rev.: 2476

The part of solution of Issue 217: Problems with the Mac OS X packaging, The libNative*.jnilib need to be put in the /lib/ folder.

3 lines of code changed in 1 file:

dong.w.xie 2009-10-27 13:36 Rev.: 2475

Issue 219: Our default ANT build script should be called build.xml.
And rename build_tracer.xml as well.

1437 lines of code changed in 6 files:

rambaut 2009-10-27 02:44 Rev.: 2474

Added a current tree statistic for logging.

18 lines of code changed in 2 files:

rambaut 2009-10-27 02:01 Rev.: 2473

Implemented an empirical tree distribution model and operator.

28 lines of code changed in 6 files:

rambaut 2009-10-27 00:37 Rev.: 2472

Implemented an empirical tree distribution model and operator.

233 lines of code changed in 6 files:

rambaut 2009-10-26 23:50 Rev.: 2471

Added a delay to the PerformanceReport in MCLogger. This is to skip the states when the JIT compiler is still optimizing. Currently this is set (in LoggerParser) to 5 x logEvery.

43 lines of code changed in 4 files:

jheled 2009-10-26 07:56 Rev.: 2470

pool swap operator

109 lines of code changed in 1 file:

jheled 2009-10-26 07:46 Rev.: 2469

parsers for stochastic values inference

7 lines of code changed in 1 file:

jheled 2009-10-26 07:46 Rev.: 2468

code police

35 lines of code changed in 6 files:

jheled 2009-10-26 07:46 Rev.: 2467

Make starting state compatible by modifying the gene trees. This is more natural as with *BEAST we typically place conditions on the species tree, not individual gene trees.

31 lines of code changed in 2 files:

jheled 2009-10-26 07:45 Rev.: 2466

renamed class

322 lines of code changed in 5 files:

jheled 2009-10-26 07:45 Rev.: 2465

change name from copy-pased one to a more suitable name

39 lines of code changed in 3 files:

jheled 2009-10-26 07:45 Rev.: 2464

make attribute optional

2 lines of code changed in 1 file:

jheled 2009-10-26 07:44 Rev.: 2463

add conditional on root for yule

4 lines of code changed in 1 file:

jheled 2009-10-26 07:44 Rev.: 2462

add explicit degrees of freedom to up-down element

33 lines of code changed in 1 file:

jheled 2009-10-26 07:44 Rev.: 2461

add alternative computation for extream values

6 lines of code changed in 1 file:

rambaut 2009-10-24 12:48 Rev.: 2460

Implemented checks to see that all models, likelihood and parameters are being controlled by the MCMC. The checks are made in MCMCParser but the warnings are currently commented out.

468 lines of code changed in 30 files:

rambaut 2009-10-24 12:43 Rev.: 2459

Tweaks to how BEAGLE instances are selected

7 lines of code changed in 1 file:

jheled 2009-10-24 08:37 Rev.: 2458

Remove deprecated class Yule (superceeded by birth death)

Add option for conditioning on root height.

165 lines of code changed in 9 files:

jheled 2009-10-24 08:35 Rev.: 2457

correct spelling

6 lines of code changed in 1 file:

jheled 2009-10-24 08:35 Rev.: 2456

code police

8 lines of code changed in 3 files:

jheled 2009-10-24 06:45 Rev.: 2455

Seems like last jebl commit broke this file

15 lines of code changed in 1 file:

rambaut 2009-10-24 04:19 Rev.: 2454

Added a few more beagle options to BEAST main.

8 lines of code changed in 1 file:

rambaut 2009-10-24 02:38 Rev.: 2453

Fixed Issue 218 (http://code.google.com/p/beast-mcmc/issues/detail?id=218).

20 lines of code changed in 4 files:

rambaut 2009-10-24 00:49 Rev.: 2452

Updated the JEBL jar file and BeastDialog to use longs for the RNG seed text box.

5 lines of code changed in 2 files:

dong.w.xie 2009-10-23 15:53 Rev.: 2451

BEAUTi: solve Issue 128: BEAUTi: tree prior Logistic Growth is not available for calibration.

27 lines of code changed in 1 file:

msuchard 2009-10-23 11:29 Rev.: 2450

Implemented getTransitionMatrix in BEAGLE for use with microsat models and ancestral state reconstruction. Reconstruction no longer crashes; still need to confirm results

97 lines of code changed in 3 files:

alexander.alekseyenko 2009-10-23 02:57 Rev.: 2449

added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.

307 lines of code changed in 7 files:

rambaut 2009-10-23 01:20 Rev.: 2448

Added some more BEAGLE options to the main dialog box.

126 lines of code changed in 4 files:

rambaut 2009-10-22 21:38 Rev.: 2447

Added some BEAST command-line options to control the BEAGLE preference flags. For example -beagle_single to ask for single precision. These actually set a system preference beagle.preferred.flags so this can be set by the JVM. Cleaned up the presentation of information about what resource is being used - now the 'instance flags' are shown to show info about the implementation actually being used.

100 lines of code changed in 2 files:

dong.w.xie 2009-10-22 14:00 Rev.: 2446

Issue 212 BEAST Linux version: need chmod 755 *, which is caused by ANT Bug 550, have to tar manaully.

4 lines of code changed in 1 file:

dong.w.xie 2009-10-22 10:55 Rev.: 2445

BEAUTi: solve Issue 212 BEAST Linux version: need chmod 755 *, but ANT for Linux release in only working under Unix or NonStop Kernel (Tandem).

3 lines of code changed in 1 file:

dong.w.xie 2009-10-22 09:25 Rev.: 2444

BEAUTi: solve Issue 216 Default memory allocations for Linux packaging are too small

5 lines of code changed in 5 files:

dong.w.xie 2009-10-22 09:19 Rev.: 2443

BEAUTi: solve Issue 215 Default memory allocations for Mac packaging are too small

4 lines of code changed in 1 file:

msuchard 2009-10-22 05:32 Rev.: 2442

Added BiasedMultivariateDiffusionModel to development parsers list

1 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-10-22 03:11 Rev.: 2441

updated example file

1 lines of code changed in 1 file:

dong.w.xie 2009-10-21 14:04 Rev.: 2440

BEAUTi: solve Issue 211: BEAUTi: Amino Acid site model xml is wrong.
At moment, only Amino Acid data type is not adding Frequecies

31 lines of code changed in 1 file:

dong.w.xie 2009-10-21 10:40 Rev.: 2439

Correct ANT for Pathogen Hudson project, and remove warning

1 lines of code changed in 3 files:

dong.w.xie 2009-10-21 10:13 Rev.: 2438

Correct ANT for Pathogen Hudson project

6 lines of code changed in 1 file:

dong.w.xie 2009-10-21 09:38 Rev.: 2437

To create ANT for Pathogen Hudson project

2 lines of code changed in 1 file:

msuchard 2009-10-20 07:14 Rev.: 2436

Removed System.out error reporting; throwing an Exception should be sufficient (and catchable)

0 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-10-19 13:32 Rev.: 2435

Changed example file for Auto-correlated relaxed clock to incorporate new changes to input format in ACLikelihood

13 lines of code changed in 1 file:

dong.w.xie 2009-10-19 11:38 Rev.: 2434

BEAUTi: solve Issue 203: Launch4j bug affecting the link of NucleotideLikelihoodCore.dll

24 lines of code changed in 2 files:

dong.w.xie 2009-10-19 09:32 Rev.: 2433

BEAUTi: solve Issue 181: BEAUTi: need enhancement to default behaviour when adding additional alignment after unlinking all

26 lines of code changed in 3 files:

jheled 2009-10-19 09:05 Rev.: 2432

generics (code police)

52 lines of code changed in 7 files:

msuchard 2009-10-19 07:56 Rev.: 2431

File parsing tweaks to EmpiricalDistributionLikelihood

33 lines of code changed in 1 file:

benjamin.redelings 2009-10-17 04:50 Rev.: 2430

[NEW] Add a site model with free rate parameters.
It doesn't actually work yet, for some reason...

* dr/app/beast/development_parses.properties:
+ Add DirichletSiteModel
* src/dr/evomodel/sitemodel/DirichletSiteModel.java
+ New model class.

314 lines of code changed in 2 files:

rambaut 2009-10-17 03:46 Rev.: 2429

"-threads 0" turns multithreading off.

3 lines of code changed in 1 file:

msuchard 2009-10-17 03:23 Rev.: 2428

Fixed build file clean

1 lines of code changed in 1 file:

msuchard 2009-10-16 16:41 Rev.: 2427

Super-super-doper conditioning checks on transition matrices

35 lines of code changed in 4 files:

Sibon.Li@gmail.com 2009-10-16 13:16 Rev.: 2426

Added amino acid version of Dengue4.env.nex

0 lines of code changed in 1 file:

jheled 2009-10-16 10:10 Rev.: 2425

eigen values/vectors in comment

14 lines of code changed in 1 file:

jheled 2009-10-16 08:24 Rev.: 2424

auto intelliJ (OK, no brownie points)

38 lines of code changed in 4 files:

jheled 2009-10-16 08:23 Rev.: 2423

fix crash when no "main" taxa given

17 lines of code changed in 1 file:

rambaut 2009-10-16 08:16

Moved java16compat to dr.app as it is used by Tracer and BEAUti

229 lines of code changed in 8 files:

rambaut 2009-10-16 08:13 Rev.: 2420

figtreepanel.jar in 1.5 byte code.

3 lines of code changed in 2 files:

rambaut 2009-10-15 11:19 Rev.: 2418

Fix the pathogen build

219 lines of code changed in 6 files:

dong.w.xie 2009-10-15 11:05 Rev.: 2417

improve and correct error message for AminoAcidLikelihoodCore and NucleotideLikelihoodCore

3 lines of code changed in 3 files:

dong.w.xie 2009-10-15 10:42

update ANT build related to r2404-2405

2 lines of code changed in 2 files:

dong.w.xie 2009-10-15 10:27 Rev.: 2414

update Eclipse build related to r2404-2405

1 lines of code changed in 1 file:

jheled 2009-10-15 10:21 Rev.: 2413

code police

12 lines of code changed in 2 files:

jheled 2009-10-15 10:21 Rev.: 2412

math 2.0 package name

3 lines of code changed in 2 files:

jheled 2009-10-15 10:20 Rev.: 2411

change gamma to handle values near 0 and 1.

14 lines of code changed in 1 file:

rambaut 2009-10-15 09:53 Rev.: 2410

Updated figtreepanel

0 lines of code changed in 1 file:

jheled 2009-10-15 09:36 Rev.: 2409

another missed name change

9 lines of code changed in 1 file:

jheled 2009-10-15 09:14 Rev.: 2408

Change class name after file move

8 lines of code changed in 1 file:

rambaut 2009-10-15 09:06

Updated figtreepanel

3 lines of code changed in 2 files:

jheled 2009-10-15 09:04

version 2.0

0 lines of code changed in 2 files:

jheled 2009-10-15 08:59 Rev.: 2403

maybe an improvment, maybe not

77 lines of code changed in 1 file:

rambaut 2009-10-15 08:42 Rev.: 2402

TreeModel that draws a random tree from a set loaded from NEXUS file.

32 lines of code changed in 3 files:

rambaut 2009-10-15 08:05 Rev.: 2401

TreeModel that draws a random tree from a set loaded from NEXUS file.

350 lines of code changed in 6 files:

rambaut 2009-10-15 06:31 Rev.: 2400

Tracer ESS shows in SummaryStats

1 lines of code changed in 1 file:

rambaut 2009-10-15 06:21 Rev.: 2399

Class naming police...

217 lines of code changed in 2 files:

benjamin.redelings 2009-10-15 04:33 Rev.: 2398

[NEW] Really compute effective sample size of combined Traces

* app/tracer/traces/CombinedTraces.java
+ class CombinedTraces
- TraceDistribution[] traceStatistics: change type to TraceCorrelation
- getDistributionStatistics( )
+ Just call getCorrelationStatistics( )
- getCorrelationStatistics( )
+ return our cached TraceCorrelation object
- analyseTrace( )
+ Just compute a TraceCorrelation object from the concatenated values.

15 lines of code changed in 1 file:

jheled 2009-10-15 03:21 Rev.: 2397

code police

17 lines of code changed in 1 file:

mtholder 2009-10-15 02:13 Rev.: 2396

The plugins directory can now be specified as a system property beast.plugins.dir this property should not be necessary when running beast through an IDEs, but is needed when invoking from a terminal from a different directory. Perhaps the need for the property can be removed -- from inside the IDE the plugins directory is found because it is a subdir of the top of the beast tree

22 lines of code changed in 1 file:

jheled 2009-10-15 01:10 Rev.: 2395

code police

15 lines of code changed in 1 file:

mtholder 2009-10-15 01:07 Rev.: 2394

removing path to a local file on my machine that was inadvertently committed the previous commit

1 lines of code changed in 1 file:

mtholder 2009-10-15 01:02 Rev.: 2393

Beginnings of the Plugin system implemented

148 lines of code changed in 4 files:

dong.w.xie 2009-10-14 13:32 Rev.: 2392

BEAUTi: solve Issue 205: Tittle information disappeared in the console using windows paramter to run BEAST

14 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-10-14 13:31 Rev.: 2391

Fixed up an error message in InverseGaussianDistributionModel

1 lines of code changed in 1 file:

bloomquist 2009-10-14 09:46 Rev.: 2390

Lowered the number of stochastic tests for the gamma distribution.

1 lines of code changed in 1 file:

bloomquist 2009-10-14 09:25 Rev.: 2389

Commented my code.

11 lines of code changed in 1 file:

bloomquist 2009-10-14 08:57 Rev.: 2388

Changed the gamma distribution function test to use stochastic draws from the distribution.

5 lines of code changed in 1 file:

bloomquist 2009-10-14 08:41 Rev.: 2387

Lowered the margin of error for the JUNIT test.

1 lines of code changed in 1 file:

bloomquist 2009-10-14 08:24 Rev.: 2386

Wrote a JUNIT test for the pdf of the gamma distribution.

94 lines of code changed in 1 file:

dong.w.xie 2009-10-13 14:14 Rev.: 2385

BEAUTi: solve Issue 201: Editing file name stem in MCMC panel causes insertion point to jump to end

25 lines of code changed in 1 file:

akaruiws 2009-10-13 12:47 Rev.: 2384

Throws an error when can't compute stationary frequencies and rename the method that does the computation.

5 lines of code changed in 2 files:

msuchard 2009-10-11 15:51 Rev.: 2382

Super-doper conditioning checks on transition matrices

21 lines of code changed in 3 files:

msuchard 2009-10-11 13:07 Rev.: 2381

Biased multivariate diffusion for Oli; tweaks to tree attributes.

213 lines of code changed in 8 files:

sidneym 2009-10-11 10:38 Rev.: 2380

Issue 202: Add explicit target of JDK 1.5 to javac to allow building using JDK 1.6 but run on JDK 1.5 machines

2 lines of code changed in 1 file:

dong.w.xie 2009-10-09 15:54 Rev.: 2379

correct linux release directory in ANT

1 lines of code changed in 1 file:

dong.w.xie 2009-10-09 14:59 Rev.: 2378

fix launch4j configuratoin xml

1 lines of code changed in 1 file:

dong.w.xie 2009-10-09 14:51 Rev.: 2376

change build number for release 1.5.2

1 lines of code changed in 1 file:

dong.w.xie 2009-10-09 14:29 Rev.: 2374

organize examples

0 lines of code changed in 3 files:

dong.w.xie 2009-10-09 14:20 Rev.: 2373

organize examples

0 lines of code changed in 7 files:

dong.w.xie 2009-10-09 14:02 Rev.: 2372

remove examples noting working for current version

450 lines of code changed in 29 files:

alexei.drummond 2009-10-09 11:44 Rev.: 2371

Fixed some of the issues names to be a little bit more understandable

13 lines of code changed in 1 file:

dong.w.xie 2009-10-09 10:11 Rev.: 2370

Add doc and examples for release

63500 lines of code changed in 108 files:

jheled 2009-10-09 08:28 Rev.: 2369

code police and spelling

10 lines of code changed in 3 files:

rambaut 2009-10-09 04:17 Rev.: 2368

Added some info about BEAGLE to the dialog box

13 lines of code changed in 2 files:

rambaut 2009-10-09 02:42 Rev.: 2367

Added option to BeastDialog to show list of BEAGLE resources and stop. Added 'Automatic' thread pool option. With BEAGLE, this should be the best option if multiple resources are being used.

Mac ANT release builder now includes the standard BEAGLE library location in java.library.path (/usr/local/lib) so if it is installed there it should be found. Note that in order to use the current BEAGLE with NVidia Cuda, the application must be run in 32-bit mode (use Get Info in Finder).

261 lines of code changed in 4 files:

rambaut 2009-10-09 00:43 Rev.: 2366

Added the '-options' flag to the release scripts for Mac and Windows.

3 lines of code changed in 2 files:

rambaut 2009-10-09 00:10 Rev.: 2365

I have created an options dialog box that appears when the "-option" command line is used. I suggest we use this for the Mac OS X and Windows executables. It provides the ability to change the seed, number of threads, switch on BEAGLE and select the input file.

221 lines of code changed in 3 files:

dong.w.xie 2009-10-08 15:39 Rev.: 2364

BEAUTi: solve Issue 200: *BEAST using Import Trait cannot add species in Trait table

3 lines of code changed in 2 files:

dong.w.xie 2009-10-08 13:44 Rev.: 2363

BEAUTi: solve Issue 195: BEAUTi ignores and resets change of prior

6 lines of code changed in 1 file:

dong.w.xie 2009-10-08 13:25 Rev.: 2362

BEAUTi: solve Issue 197: meanRate, coefficientOfVariation and covariance should have gene name in name="" attribute

10 lines of code changed in 1 file:

dong.w.xie 2009-10-08 09:52 Rev.: 2361

Fix the compiling error of IntelliJ: not throw exception in try block, which is caused by r2359

4 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-10-07 17:25 Rev.: 2360

InverseGaussian distribution can now take in either a shape or stdev parameter

102 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-10-07 17:18 Rev.: 2359

Modified NormaliseMeanTreeRate to use tree rates properly

18 lines of code changed in 1 file:

jheled 2009-10-07 17:00 Rev.: 2358

Small optimization - don't compute mean twice

13 lines of code changed in 1 file:

dong.w.xie 2009-10-07 16:05 Rev.: 2357

sovle Issue 160: Ant build for Mac version release

17 lines of code changed in 2 files:

dong.w.xie 2009-10-07 13:47 Rev.: 2356

BEAUTi: make ANT build windows release working. And solve windows part of Issue 154: No Nucleotide Likelihood Core in java.library.path

12 lines of code changed in 6 files:

jheled 2009-10-07 13:23 Rev.: 2355

fix issue 196

5 lines of code changed in 2 files:

jheled 2009-10-07 13:22 Rev.: 2354

remove unused attribute

1 lines of code changed in 1 file:

jheled 2009-10-07 13:21 Rev.: 2353

code police

24 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-10-07 04:19 Rev.: 2352

DiscreteRatePriorGenerator tweaks

531 lines of code changed in 1 file:

rambaut 2009-10-06 22:37 Rev.: 2351

Now resets operators' acceptance counts after the coercion delay period.

5 lines of code changed in 1 file:

rambaut 2009-10-06 21:19 Rev.: 2350

Updated MCMC parser rules for 'autoOptimizeDelay'.

9 lines of code changed in 3 files:

msuchard 2009-10-06 06:04 Rev.: 2349

Fixes to CachedDistributionLikelihood to work with MultivariateDistributionLikelihood. Tweaks to eigendecomposition routines, in case of invalid diagonalization

73 lines of code changed in 10 files:

philippe.lemey@gmail.com 2009-10-06 00:52 Rev.: 2348

adding phylogeography example xml

1137 lines of code changed in 1 file:

dong.w.xie 2009-10-05 17:15 Rev.: 2347

BEAUTi: solve Issue 192: BEAUTi: GUI event issues and exceptions regarding to add new trait

79 lines of code changed in 7 files:

akaruiws 2009-10-05 11:17 Rev.: 2346

correction to hasSubmodel method.

1 lines of code changed in 1 file:

benjamin.redelings 2009-10-05 05:25 Rev.: 2345

* build.xml
+ update to include new jars in lib/

10 lines of code changed in 1 file:

akaruiws 2009-10-04 23:37 Rev.: 2344

Changes made so that stationary distribution can be computed before the computation of transition probabilities for TPM.

22 lines of code changed in 3 files:

akaruiws 2009-10-04 22:13 Rev.: 2343

Methods added so that when running BEAST, detail of microsatellite model and its paramters are printed to stardard out.

53 lines of code changed in 5 files:

akaruiws 2009-10-04 10:40 Rev.: 2342

Calculates overall mean pairwise differences across multiple loci.

67 lines of code changed in 2 files:

rambaut 2009-10-03 00:23 Rev.: 2341

Replaced 'preBurnin' with an autoOptimizeDelay (coercionDelay). The rationale for this is that the preBurnin meant that the initial state was not in the log files, it was unecessary and it cause a small inefficiency as the JIT compiler re-optimized after the preburnin chain had finished. We also didn't see warning messages until after the pre-burnin period. There is a new attribute to the MCMC parser - autoOptimizeDelay (to which the old preBurnin attribute now maps so old XML will run).

58 lines of code changed in 14 files:

dong.w.xie 2009-10-02 19:15 Rev.: 2340

BEAUTi: solve Issue 185: Guess Trait dialog doesn't offer user defined traits

361 lines of code changed in 11 files:

jheled 2009-10-02 18:57 Rev.: 2339

Do not terminate run if distribution quantile is not up to scratch. Just let the operator fail.

7 lines of code changed in 1 file:

jheled 2009-10-02 14:53 Rev.: 2338

More detailed error message

2 lines of code changed in 1 file:

akaruiws 2009-10-02 11:57 Rev.: 2337

Added an instance of MicrosatelliteSimulatorParser.

3 lines of code changed in 1 file:

akaruiws 2009-10-02 11:32 Rev.: 2336

Changed DataType to Microsatellite.

3 lines of code changed in 1 file:

akaruiws 2009-10-02 11:23 Rev.: 2335

Parser for microsatellite simulator.

80 lines of code changed in 1 file:

akaruiws 2009-10-02 11:12 Rev.: 2334

Implementatin of MicrosatelliteSimulator.

60 lines of code changed in 1 file:

akaruiws 2009-10-02 11:05 Rev.: 2333

Changed the scope of some instance variables from provite to protected to allow them be accessed by a derived class.

35 lines of code changed in 1 file:

rambaut 2009-10-01 23:24 Rev.: 2332

NexusExport now emits all attributes as Node attributes. This reverts change 2188. This exporter is used by TreeAnnotator (BEAST and LogCombiner both have their own tree writing code). BEAST writes both node and branch attributes, this distinction is lost by running through either LogCombiner or TreeAnnotator.

17 lines of code changed in 2 files:

akaruiws 2009-10-01 21:50 Rev.: 2331

Added various instances of parsers.

3 lines of code changed in 1 file:

akaruiws 2009-10-01 21:41 Rev.: 2330

Implementation of MicrosatelliteSamplterTreeLikelihoodParser.

0 lines of code changed in 1 file:

akaruiws 2009-10-01 21:34 Rev.: 2329

Changed the scope of variable likelihoodKnown from private to protected.

1 lines of code changed in 1 file:

akaruiws 2009-10-01 21:31 Rev.: 2328

Implementation of MicrosatelliteSamplerTreeLikelihood.

244 lines of code changed in 1 file:

akaruiws 2009-10-01 21:23 Rev.: 2327

Implementation of MicrosatUpDownOperator.

206 lines of code changed in 1 file:

akaruiws 2009-10-01 21:15 Rev.: 2326

Added scaleAllAndNotify method which is suppose to prevent several repeated event firing for the change of the same parameter when it values in all dimensions are changed by scaling.

33 lines of code changed in 1 file:

akaruiws 2009-10-01 21:03 Rev.: 2325

Parser for MicrosatelliteSamplerTreeModel.

0 lines of code changed in 1 file:

akaruiws 2009-10-01 20:57 Rev.: 2324

Modified handleVariableChangedEvent so that it is able to indicate that values of all dimensions of a parameter have changed. Added method areAllInternalNodeHeightsChanged in the TreeChangedEvent.

13 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-10-01 16:27 Rev.: 2323

Added an app called TreeLengthFinder that calculates tree length in bulk (like LogAnalyzer). Will change this at some point to make it calculate more tree stats

262 lines of code changed in 1 file:

September 2009 »

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