September 2009 Commit Log

Number of Commits:
144
Number of Active Developers:
8
dong.w.xie 2009-09-29 15:01 Rev.: 2322

BEAUTi: solve Issue 180: allMus is not dealing with multi-partition + codon, and allClockRate

122 lines of code changed in 9 files:

dong.w.xie 2009-09-29 09:41 Rev.: 2321

BEAUTi: solve Issue 179: species.popSize is a horrible choice of name, and reduce Warning

14 lines of code changed in 1 file:

rambaut 2009-09-29 00:47 Rev.: 2320

Final? adjustments to Mac build scripts - no includes native libraries in correct locations.

13 lines of code changed in 1 file:

rambaut 2009-09-29 00:29 Rev.: 2319

Added jarbundler blocks for LogCombiner and TreeAnnotator

31 lines of code changed in 1 file:

rambaut 2009-09-29 00:25 Rev.: 2318

More work on the Mac release script. The Linux release script also packages correctly. The Windows one is untested. Note that /release/common/examples needs to be populated with the example XML that we wish to distribute. Also /release/common/doc can have any documentation we wish to distribute.

157 lines of code changed in 6 files:

rambaut 2009-09-29 00:05 Rev.: 2317

Improved Mac executable generation and generalized the release scripts. Rather than taking /doc /example /native from the top level (which may have lots of crud in it) it now takes these folders from /release/common. Try to keep these clean with just the stuff we want released. Still a bit of work on the Mac executables to be done and I may have broken the Windows and Linux release targets.

5830 lines of code changed in 71 files:

rambaut 2009-09-28 23:40

Improved Mac executable generation and generalized the release scripts. Rather than taking /doc /example /native from the top level (which may have lots of crud in it) it now takes these folders from /release/common. Try to keep these clean with just the stuff we want released. Still a bit of work on the Mac executables to be done and I may have broken the Windows and Linux release targets.

116 lines of code changed in 5 files:

akaruiws 2009-09-28 20:07 Rev.: 2314

code broken as the signture of selectOperators were changed to selectOperators(). Now fixed by change it back to selectOperators(List<Operator> ops).

1 lines of code changed in 1 file:

akaruiws 2009-09-28 19:48 Rev.: 2313

delete comments as somehow it causes problems when compling by hudson.

1 lines of code changed in 1 file:

akaruiws 2009-09-28 19:45 Rev.: 2312

changed comments

1 lines of code changed in 1 file:

akaruiws 2009-09-28 19:41 Rev.: 2311

Add new ChangeType ALL_VALUES_CHANGED.

2 lines of code changed in 1 file:

akaruiws 2009-09-28 19:35

add setParameterValueNotifyChangedAll method.

26 lines of code changed in 2 files:

akaruiws 2009-09-28 19:20

add setParameterValueNotifyChangedAll method.

9 lines of code changed in 2 files:

dong.w.xie 2009-09-28 17:52 Rev.: 2306

BEAUTi: solve Issue 174: fixed rate in Clock panel not passing to XML

14 lines of code changed in 3 files:

msuchard 2009-09-28 09:10 Rev.: 2305

BEAST-side is ready for complex substitution models via BEAGLE; BEAGLE-CPU (complex) is working and runs much faster than BEAST-ComplexSubstitutionModel in Java

229 lines of code changed in 13 files:

akaruiws 2009-09-27 00:47 Rev.: 2304

MicrosatelliteSamplerTreeModel, which stores the microsatellite state of all nodes.

218 lines of code changed in 1 file:

dong.w.xie 2009-09-25 16:33 Rev.: 2303

BEAUTi: correct spell and remove Warning message.

36 lines of code changed in 8 files:

dong.w.xie 2009-09-25 12:25 Rev.: 2302

BEAUTi: more correction about range.

3 lines of code changed in 1 file:

dong.w.xie 2009-09-25 12:21 Rev.: 2301

BEAUTi: correct the misundering of r2300.

14 lines of code changed in 3 files:

dong.w.xie 2009-09-25 11:00 Rev.: 2300

BEAUTi: sovle Issue 176: LogNormal mean should > 0

65 lines of code changed in 3 files:

philippe.lemey@gmail.com 2009-09-24 22:51 Rev.: 2299

Tracer tweaks

34 lines of code changed in 1 file:

akaruiws 2009-09-24 22:34 Rev.: 2298

change handleParameterChangedEvent to handleVariableChangedEvent

3 lines of code changed in 1 file:

akaruiws 2009-09-24 22:01 Rev.: 2297

change handleParameterChangedEvent to handleVariableChangedEvent

4 lines of code changed in 1 file:

akaruiws 2009-09-24 17:57 Rev.: 2296

microsatellite data related parsers added

5 lines of code changed in 1 file:

alexei.drummond 2009-09-24 17:27 Rev.: 2295

55 lines of code changed in 1 file:

akaruiws 2009-09-24 17:11 Rev.: 2294

JUnit test for TwoPhaseModel of microsatellites

118 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-09-24 17:02 Rev.: 2293

Changed input format of ACLikelihood to allow incorporating other distributions (logSpace="true"/"false" replaced with distribution="logNormal"/"normal"/"inverseGaussian"

89 lines of code changed in 2 files:

akaruiws 2009-09-24 16:14 Rev.: 2292

Parser for TwoPhaseModel of microsatellites

75 lines of code changed in 1 file:

akaruiws 2009-09-24 15:42 Rev.: 2291

TwoPhaseModel of microsatellites

210 lines of code changed in 1 file:

akaruiws 2009-09-24 15:32 Rev.: 2290

change variable names.

24 lines of code changed in 1 file:

akaruiws 2009-09-24 15:20 Rev.: 2289

only allow one phase models be sub models.

1 lines of code changed in 1 file:

akaruiws 2009-09-24 14:59 Rev.: 2288

StoreIntoAmat changed.

7 lines of code changed in 1 file:

akaruiws 2009-09-24 14:52 Rev.: 2287

JUnit test for LinearBiasModel of microsatellites

206 lines of code changed in 1 file:

akaruiws 2009-09-24 14:47 Rev.: 2286

Parser for LinearBiasModel of microsatellites

102 lines of code changed in 1 file:

akaruiws 2009-09-24 14:38 Rev.: 2285

LinearBiasModel of microsatellites

186 lines of code changed in 1 file:

msuchard 2009-09-24 13:09 Rev.: 2284

Parsing for spline-interpolated empirical (prior) distributions appears to work.

99 lines of code changed in 3 files:

msuchard 2009-09-24 12:55 Rev.: 2283

Trying another build

0 lines of code changed in 1 file:

dong.w.xie 2009-09-24 12:33 Rev.: 2282

BEAUTi: remove Warning message

4 lines of code changed in 5 files:

alexei.drummond 2009-09-24 12:27 Rev.: 2281

implemented rate attributes in TreeModel.getNodeAttribute and getNodeRate in FlexibleTree (if stored as attribute named rate)

638 lines of code changed in 2 files:

msuchard 2009-09-24 11:52 Rev.: 2280

Preparing BEAST for complex computation in BEAGLE ... ready for fast microsat models?

0 lines of code changed in 1 file:

msuchard 2009-09-24 11:46 Rev.: 2279

Preparing BEAST for complex computation in BEAGLE ... ready for fast microsat models?

386 lines of code changed in 17 files:

dong.w.xie 2009-09-24 11:43 Rev.: 2278

The eclipse class path for jars.

20 lines of code changed in 1 file:

akaruiws 2009-09-24 00:44 Rev.: 2277

change to suit the new AymmetricQuadraticModel contructor.

4 lines of code changed in 1 file:

akaruiws 2009-09-24 00:36 Rev.: 2276

change to suit the new AymmetricQuadraticModel contructor.

25 lines of code changed in 1 file:

akaruiws 2009-09-24 00:27 Rev.: 2275

contructor changed, can indicate whether the object is a submodel of another. setupInfinitesimalRates changed.

66 lines of code changed in 1 file:

akaruiws 2009-09-24 00:17 Rev.: 2274

computeStationaryDistribution Method changed. Other new methods added.

35 lines of code changed in 1 file:

akaruiws 2009-09-24 00:03 Rev.: 2273

Add derived method of storeIntoAmat and change computeOneProbabilityEntry to handle complex eigen values.

65 lines of code changed in 1 file:

akaruiws 2009-09-23 23:50 Rev.: 2272

Comments changed, new rules added. Printing details of microsatellite at the start becomes optional.

19 lines of code changed in 2 files:

akaruiws 2009-09-23 23:27 Rev.: 2271

Changed comments.

1 lines of code changed in 1 file:

akaruiws 2009-09-23 23:09 Rev.: 2270

Changed getState method. When the raw length is not a multiple of the repeat unit length, the state is always rounded up.

13 lines of code changed in 1 file:

dong.w.xie 2009-09-23 15:01 Rev.: 2269

BEAUTi:
1) solve Issue 172: BEAUTi: shareSameTreePrior should disable when only 1 tree model;
2) use html in label in Tree panel.

4 lines of code changed in 2 files:

dong.w.xie 2009-09-23 14:20 Rev.: 2268

BEAUTi: solve Issue 155: Warning message " ... does not match stored object with same id and tag name ..." confused user.

5 lines of code changed in 1 file:

dong.w.xie 2009-09-22 15:34 Rev.: 2267

BEAUTi:
1) part of code for Issue 171: Version update reminder in BEAUTi;
2) remove all "/" in the end of URL, which cause error for Wiki.

20 lines of code changed in 5 files:

dong.w.xie 2009-09-22 14:48 Rev.: 2266

BEAUTi: solve Issue 147: BEAUTi: if no leaf nodes selected in Taxon Set panel, the corresponding tmrca should not appear in Prior panel.

14 lines of code changed in 1 file:

dong.w.xie 2009-09-21 15:49 Rev.: 2265

BEAUTi: solve Issue 136: BEAUTi log screen should show actual name instead of Rate 1, 2, ....

45 lines of code changed in 2 files:

dong.w.xie 2009-09-21 15:08 Rev.: 2264

BEAUTi: fix the bug and add validation for Issue 168: GMRF 'Skyride' complains about 'Share same tree prior' even if only one tree

15 lines of code changed in 2 files:

dong.w.xie 2009-09-21 12:43 Rev.: 2263

BEAUTi: fix a bug of r2261 2).

22 lines of code changed in 1 file:

dong.w.xie 2009-09-18 15:58 Rev.: 2262

BEAUTi: solve Issue 139: ImportnaceNarrowExchange should be ImportanceNarrowExchange.

348 lines of code changed in 3 files:

dong.w.xie 2009-09-18 15:53 Rev.: 2261

BEAUTi:
1) solve Issue 94: Improve the prefix of PartitionClockModelTreeModelLink;
2) OperatorGenerator should use writeOperatorRef instead of writeParameter1Ref.

106 lines of code changed in 8 files:

dong.w.xie 2009-09-18 12:45 Rev.: 2260

BEAUTi: solve Issue 123: Beauti poor choice of name for re-linking partitions

30 lines of code changed in 2 files:

dong.w.xie 2009-09-17 14:08 Rev.: 2259

Add compress command for Linux/Unix release in ANT build.

1 lines of code changed in 1 file:

dong.w.xie 2009-09-17 12:12 Rev.: 2258

BEAUTi: solve Issue 140: more options for *beast.

6 lines of code changed in 3 files:

dong.w.xie 2009-09-17 11:51 Rev.: 2257

BEAUTi: Issue 140: more options for *beast.
But Population Size Model – Constant does not work yet.

112 lines of code changed in 4 files:

jheled 2009-09-17 08:26 Rev.: 2256

Warnings, Generify, Comments

14 lines of code changed in 5 files:

dong.w.xie 2009-09-16 13:56 Rev.: 2255

BEAUTi: solve Issue 165: BEAUTi: some priors parameters keep changing.

39 lines of code changed in 1 file:

dong.w.xie 2009-09-16 12:14 Rev.: 2254

BEAUTi:
1) solve Issue 135: Laplace prior has not been implemented in PriorParsers, but appearing in BEAUTi;
2) solve Issue 158: We should have the Inverse Gamma distribution in Beauti.

101 lines of code changed in 5 files:

jheled 2009-09-16 11:25 Rev.: 2253

maybe correct code

4 lines of code changed in 1 file:

dong.w.xie 2009-09-16 10:41 Rev.: 2252

BEAUTi: finish generator of r2250.

1 lines of code changed in 2 files:

msuchard 2009-09-16 03:22 Rev.: 2251

Doing a fresh build under 10.6.1 caused a Java heap space error

4 lines of code changed in 1 file:

dong.w.xie 2009-09-15 17:16 Rev.: 2250

BEAUTi: solve Issue 156: LogNormal in prior panel in Beauti.

57 lines of code changed in 3 files:

dong.w.xie 2009-09-15 16:38 Rev.: 2249

BEAUTi: fix the warning code.

12 lines of code changed in 2 files:

dong.w.xie 2009-09-15 16:37 Rev.: 2248

BEAUTi: fix a bug of r2247.

12 lines of code changed in 2 files:

dong.w.xie 2009-09-15 11:26 Rev.: 2247

BEAUTi: keep reducing BeastGenerator.

461 lines of code changed in 2 files:

dong.w.xie 2009-09-15 11:16 Rev.: 2246

BEAUTi: refactorying generator.

199 lines of code changed in 3 files:

dong.w.xie 2009-09-15 11:04 Rev.: 2245

BEAUTi: solve Issue 131: rewrite Parameter and Operator class by Builder pattern, and all referring methods.

163 lines of code changed in 7 files:

philippe.lemey@gmail.com 2009-09-15 07:47 Rev.: 2244

Tracer tweaks

24 lines of code changed in 1 file:

dong.w.xie 2009-09-14 17:09 Rev.: 2243

BEAUTi: continue to reduce ModelOptions

96 lines of code changed in 5 files:

dong.w.xie 2009-09-14 14:41 Rev.: 2242

BEAUTi: continue big refactorying of partition model

58 lines of code changed in 5 files:

dong.w.xie 2009-09-14 14:15 Rev.: 2241

BEAUTi: big refactory regarding partition model

65 lines of code changed in 10 files:

dong.w.xie 2009-09-14 13:06 Rev.: 2240

BEAUTi: more tidy up and improvement

18 lines of code changed in 6 files:

dong.w.xie 2009-09-14 12:38 Rev.: 2239

BEAUTi: continue the code using Builder parttern in Parameter, and tidy up createParameter... methods

143 lines of code changed in 8 files:

dong.w.xie 2009-09-11 14:27

BEAUTi:
1) solve Issue 163: unlink trees if allow different taxa;
2) fix a bug of incorrect list of data partitions in each partition model;

25 lines of code changed in 4 files:

dong.w.xie 2009-09-11 11:22 Rev.: 2236

Remove Eclipes configuration files

0 lines of code changed in 2 files:

msuchard 2009-09-11 09:16 Rev.: 2235

BeagleTreeLikelihood now takes advantage of BEAGLE's resource flexibility

17 lines of code changed in 2 files:

msuchard 2009-09-11 06:47 Rev.: 2234

Switched default BEAGLE CPU version from hybrid to pure C
; appears to offer performance gains

0 lines of code changed in 1 file:

dong.w.xie 2009-09-10 15:29 Rev.: 2233

BEAUTi: keep reducing ModelOptions by create enum DateUnitsType, and fix the bug of r2223.

88 lines of code changed in 8 files:

dong.w.xie 2009-09-10 14:46 Rev.: 2232

BEAUTi: reduce ModelOptions.

10 lines of code changed in 3 files:

dong.w.xie 2009-09-09 15:05 Rev.: 2231

BEAUTi: solve Issue 157: LogNormal in Beauti: Exception occurred during event dispatching.
There was a problem with Exponential as well.

5 lines of code changed in 1 file:

dong.w.xie 2009-09-09 14:53 Rev.: 2230

BEAUTi: continue Builder parttern in Parameter.

91 lines of code changed in 8 files:

dong.w.xie 2009-09-09 13:16 Rev.: 2229

BEAUTi: start to create Builder parttern in Parameter, and simplify prior's parameters.

741 lines of code changed in 17 files:

dong.w.xie 2009-09-09 11:03 Rev.: 2228

BEAUTi: use DateParser string constant

4 lines of code changed in 1 file:

jheled 2009-09-09 08:26 Rev.: 2227

generify and auto intelliJ

103 lines of code changed in 35 files:

dong.w.xie 2009-09-08 15:48 Rev.: 2226

BEAUTi: solve Issue 148: illegal entry error for Clock Model panel

2 lines of code changed in 1 file:

jheled 2009-09-08 13:28 Rev.: 2225

ongoing development, add a base variable with logging

153 lines of code changed in 6 files:

jheled 2009-09-08 11:29 Rev.: 2224

generify via auto intelliJ

61 lines of code changed in 22 files:

dong.w.xie 2009-09-08 10:44 Rev.: 2223

BEAUTi: continue r2220, transfer logic level from BeautiFrame into BEAUTiImporter.

47 lines of code changed in 5 files:

jheled 2009-09-08 06:42 Rev.: 2222

ongoing development

266 lines of code changed in 8 files:

jheled 2009-09-08 06:36 Rev.: 2221

automatic idea changes and generify

8 lines of code changed in 2 files:

dong.w.xie 2009-09-07 17:30 Rev.: 2220

BEAUTi: extract logic from BeautiFrame and create BEAUTiImporter.
TODO: allowDifferentTaxa GUI JOption needs to be extracted out from BEAUTiImporter.

906 lines of code changed in 3 files:

dong.w.xie 2009-09-07 15:50 Rev.: 2219

BEAUTi: solve Issue 144: In use in Operators panel cannot change for those operators belonging to PartitionClockModelTreeModelLink

10 lines of code changed in 2 files:

jheled 2009-09-07 14:23 Rev.: 2218

automatic idea changes and generify

82 lines of code changed in 16 files:

jheled 2009-09-07 14:23 Rev.: 2217

compiler warning about non UTF8 char in comment

3 lines of code changed in 2 files:

dong.w.xie 2009-09-07 13:48 Rev.: 2216

Fix broken code, comment out sun.awt.X11.XLayerProtocol

1 lines of code changed in 1 file:

dong.w.xie 2009-09-07 13:44 Rev.: 2215

BEAUTi: refactory BeautiOptions, and add getPartitionClassType for PartitionOptions.

57 lines of code changed in 11 files:

jheled 2009-09-07 13:30 Rev.: 2214

gross in-effciency fixed

14 lines of code changed in 2 files:

jheled 2009-09-07 13:29 Rev.: 2213

code police

62 lines of code changed in 12 files:

jheled 2009-09-07 13:29 Rev.: 2212

auto intelliJ

14 lines of code changed in 6 files:

jheled 2009-09-07 13:28 Rev.: 2211

comment out unused code

458 lines of code changed in 22 files:

dong.w.xie 2009-09-07 12:54 Rev.: 2210

BEAUTi: solve Issue 151: MCMC tab numerical fields resets after GUI events

36 lines of code changed in 1 file:

jheled 2009-09-07 08:21 Rev.: 2209

commit development files (serves as a backup and versioning) - may and will substantially change or go away.

419 lines of code changed in 5 files:

jheled 2009-09-07 08:19 Rev.: 2208

Change explicit parameters into new style variables

228 lines of code changed in 8 files:

jheled 2009-09-07 08:16 Rev.: 2207

comments changes

46 lines of code changed in 31 files:

jheled 2009-09-07 08:15 Rev.: 2206

automatic intelliJ transforms

5 lines of code changed in 3 files:

jheled 2009-09-07 08:15 Rev.: 2205

code police

26 lines of code changed in 13 files:

jheled 2009-09-07 08:12

comment out unused code

85 lines of code changed in 4 files:

jheled 2009-09-07 08:06 Rev.: 2202

Turn inlined expressions into variables for easier debugging.

6 lines of code changed in 3 files:

jheled 2009-09-05 16:35 Rev.: 2201

xml warnings - my previous attempt was incomplete as expected. hopfully this is better

78 lines of code changed in 12 files:

jheled 2009-09-05 16:34 Rev.: 2200

an exception needs to be thrown, not returned. I wonder what I was on when I wrote this code, and what the designers of Java took with their breakfast

1 lines of code changed in 1 file:

dong.w.xie 2009-09-04 15:44 Rev.: 2199

BEAUTi: solve Issue 145: implement frequency for binary model as same as DNA data.

49 lines of code changed in 4 files:

jheled 2009-09-04 10:35 Rev.: 2198

comments added

2 lines of code changed in 1 file:

dong.w.xie 2009-09-04 10:34 Rev.: 2197

BEAUTi: add enum BinaryModelType.

60 lines of code changed in 6 files:

dong.w.xie 2009-09-04 10:33 Rev.: 2196

Change ANT to name next version as BEAST_v1.5.2.???, to escape characters for Linux/Unix version.

6 lines of code changed in 1 file:

jheled 2009-09-04 10:29 Rev.: 2195

code police

48 lines of code changed in 12 files:

jheled 2009-09-04 10:29 Rev.: 2194

automatic idea changes

12 lines of code changed in 6 files:

jheled 2009-09-04 10:28 Rev.: 2193

Added more checking for spurios elements, e.g.
<strictClockBranchRates id="branchRates">
<rate>
<blu/>
<parameter id="clock.rate" value="1.0"/>
<bla/>
</rate>
</strictClockBranchRates>

Please report back if you encounter erroneous reports

47 lines of code changed in 1 file:

dong.w.xie 2009-09-03 17:14 Rev.: 2191

Virus Pratical tex file, and update build number.

22833 lines of code changed in 36 files:

dong.w.xie 2009-09-03 17:02 Rev.: 2190

Virus Pratical xml examples.

0 lines of code changed in 32 files:

Sibon.Li@gmail.com 2009-09-03 16:05 Rev.: 2189

Tidied up the code for NormaliseMeanTreeRate

16 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-09-03 15:51 Rev.: 2188

NexusExporter made more consistent with the *.trees format

8 lines of code changed in 1 file:

dong.w.xie 2009-09-03 12:12 Rev.: 2186

draft of Virus Pratical examples including Tex and Nex files.

983 lines of code changed in 30 files:

dong.w.xie 2009-09-03 12:10 Rev.: 2185

add Issue list into version history.

28 lines of code changed in 1 file:

alexei.drummond 2009-09-03 11:32 Rev.: 2184

README and VERSION HISTORY walter still needs to add the list of issue numbers that have been resolved between 4th August and 3rd September.

38 lines of code changed in 2 files:

dong.w.xie 2009-09-03 09:50 Rev.: 2182

Updated the build number to match the upcoming release.

1 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-09-02 17:36 Rev.: 2180

TreeLogger now allows normaliseMeanRateTo tag, which normalises the mean rate

10 lines of code changed in 1 file:

dong.w.xie 2009-09-02 17:36 Rev.: 2179

BEAUTi: add more status messages for clock rate to avoid confusion.

4 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-09-02 17:35 Rev.: 2178

Updated NormaliseMeanTreeRate (now works properly)

71 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-09-02 17:34 Rev.: 2177

NexusExporter now allows tree names to be specified

19 lines of code changed in 1 file:

dong.w.xie 2009-09-02 16:59 Rev.: 2176

BEAUTi: add and change the status message for clock rate, to avoid confusion.

32 lines of code changed in 3 files:

dong.w.xie 2009-09-02 09:54 Rev.: 2175

Updated the build number to match the upcoming release.

1 lines of code changed in 1 file:

rambaut 2009-09-01 21:06 Rev.: 2174

Updated the version number to match the upcoming release.

2 lines of code changed in 1 file:

dong.w.xie 2009-09-01 16:24 Rev.: 2172

BEAUTi: fix more bugs regarding calibration calculation, and prior options.

178 lines of code changed in 10 files:

jheled 2009-09-01 09:58 Rev.: 2171

casting problem

10 lines of code changed in 1 file:

dong.w.xie 2009-09-01 09:22 Rev.: 2170

Check in jarbundler for Mac release ANT, and remove previous BEAUTi 1.5 XML examples for codon models, some of which are incorrect.

64 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-09-01 00:21 Rev.: 2169

Changed NormaliseMeanTreeRate a bit more

6 lines of code changed in 1 file:

August 2009 »

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