May 2009 Commit Log

Number of Commits:
101
Number of Active Developers:
8
rambaut 2009-05-31 07:32 Rev.: 1756

Updated tinyTest

2 lines of code changed in 1 file:

rambaut 2009-05-31 04:48 Rev.: 1755

Removed setStateFrequencies as calculateLogLikelihood gets passed these.

3 lines of code changed in 1 file:

dong.w.xie 2009-05-29 15:03 Rev.: 1754

BEAUTI work:
1) add SpeciesTreePanel choice for Tree panel, and switch to it when doing species analysis and switch back if not species analysis;
2) implement Birth Death for SpeciesTreePanel, but Yule is not available yet.

164 lines of code changed in 7 files:

dong.w.xie 2009-05-28 16:22 Rev.: 1753

Correct spelling error.

3 lines of code changed in 1 file:

dong.w.xie 2009-05-28 14:12 Rev.: 1752

BEAUTI:
Fix the bug to make species analysis available for single gene file.

69 lines of code changed in 4 files:

dong.w.xie 2009-05-28 11:14 Rev.: 1751

Improve Beauti by few little changes, including reset status label in Beauti frame, and initialization gene prefix of generator.

5 lines of code changed in 3 files:

dong.w.xie 2009-05-28 09:59 Rev.: 1750

Create dr.app.beauti.tipdatepanel package to make clear structure.

737 lines of code changed in 9 files:

rambaut 2009-05-27 23:13 Rev.: 1749

Added a default to GeneralDataType that '?' is treated as Unknown_State. Also when AncestralStateTreeLikelihood is logging states from GeneralDataType, it uses the full string codes rather than 1 letter chars.

32 lines of code changed in 3 files:

dong.w.xie 2009-05-27 14:29 Rev.: 1748

More BEAUTI work about guess trait value

12 lines of code changed in 2 files:

dong.w.xie 2009-05-27 12:58 Rev.: 1747

BEAUTI work:
1) Finish Guess Trait Value in Trait panel for speices analysis (Multispecies Coalescent), but regular expressions not working;
2) Add some validations for guess trait;
3) BUG: Need to correct tree prior and parameter for single gene file.

144 lines of code changed in 4 files:

dong.w.xie 2009-05-26 11:34 Rev.: 1746

More BEAUTI work:
1) Fix bug of isSpeciesAnalysis() in BeautiOptions;
2) Move BeautiOptions.TraitType into TraitGuesser.TraitType.

22 lines of code changed in 7 files:

dong.w.xie 2009-05-26 11:17 Rev.: 1745

BEAUTI work:
1) Move BeautiOptions.TRAIT_SPECIES = "species" into TraitGuesser.Traits.TRAIT_SPECIES (enum);
2) Refactory BeautiFrame and create setupSpeciesAnalysis();
3) Make Guess Trait Value in Trait panel available to speices analysis (Multispecies Coalescent), not finish yet, need further work.

541 lines of code changed in 10 files:

msuchard 2009-05-26 07:29 Rev.: 1744

Added option to SitePatternsParse that disables stripping out purely ambiguous patterns; these have some value when testing priors.

21 lines of code changed in 4 files:

rambaut 2009-05-26 02:21 Rev.: 1743

Seem to have a working UniformRootPrior.

231 lines of code changed in 2 files:

dong.w.xie 2009-05-25 10:28 Rev.: 1742

Fix bug of BEAUTi to validate species tree prior.

17 lines of code changed in 7 files:

jheled 2009-05-24 19:21 Rev.: 1741

Parse comments in Newick parser as well

28 lines of code changed in 2 files:

dong.w.xie 2009-05-22 15:53 Rev.: 1740

include new JUnit test done by Sibon into build.

1 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-05-22 12:02 Rev.: 1739

A functional Inverse Gaussian Model. Includes a unit test

218 lines of code changed in 3 files:

dong.w.xie 2009-05-22 11:20 Rev.: 1738

Add Multispecies Coalescent analysis message into status label panel in the bottom of BEAUTI frame, and refactory getSpeciesList() in beautiOption.

36 lines of code changed in 3 files:

msuchard 2009-05-22 11:14 Rev.: 1737

Cleaning up 2D KDE and HPD estimation. Almost ready to remove R dependency.

4 lines of code changed in 1 file:

nawi214 2009-05-22 09:41 Rev.: 1736

Needed to add dr/java16compat to include directories for building jars

6 lines of code changed in 1 file:

rambaut 2009-05-22 02:20 Rev.: 1735

Added a command line flag (-java) to BeastMain that sets a System property ("java_only"). This specifies that no JNI libraries should be used - only Java implementations. This is currently obeyed by TreeLikelihood's parser and BeagleFactory.

9 lines of code changed in 3 files:

dong.w.xie 2009-05-21 10:54 Rev.: 1734

Add validation for checking whether selecting Species tree prior in Tree panel.

11 lines of code changed in 1 file:

dong.w.xie 2009-05-20 14:24 Rev.: 1733

Fix a text field bug in BEAUTI MCMC panel.

37 lines of code changed in 1 file:

dong.w.xie 2009-05-20 14:01 Rev.: 1732

Correct BEAUTI to generate correct xml for species tree, and allow the user to choose Birth Death model for species tree.

162 lines of code changed in 10 files:

rambaut 2009-05-20 10:42 Rev.: 1731

Fixed issue with Windowed version of TreeAnnotator not reporting progress to window.

9 lines of code changed in 2 files:

Sibon.Li@gmail.com 2009-05-19 16:45 Rev.: 1730

Added parser code for inverse gaussian model

3 lines of code changed in 3 files:

msuchard 2009-05-19 15:27 Rev.: 1729

Cleaning up 2D KDE and HPD estimation. Almost ready to remove R dependency.

18 lines of code changed in 1 file:

msuchard 2009-05-19 12:18 Rev.: 1728

Getting the traitGibbsOperator to work with tip and internal node flatGeoSpatialPriors

59 lines of code changed in 3 files:

dong.w.xie 2009-05-19 10:50 Rev.: 1727

Make BEAUTI MCMC panel to available for multi-tree log. Tree log name format is stem.partition.trees

89 lines of code changed in 4 files:

msuchard 2009-05-19 07:07 Rev.: 1726

Fixed small XML parsing bug.

3 lines of code changed in 1 file:

msuchard 2009-05-19 06:40 Rev.: 1725

Slowly moving 2D HPD estimation for trait locations from R into Java.

7 lines of code changed in 1 file:

msuchard 2009-05-18 13:52 Rev.: 1724

Slowly moving 2D HPD estimation for trait locations from R into Java.

105 lines of code changed in 2 files:

dong.w.xie 2009-05-18 11:34 Rev.: 1723

Simplify BEAUTI code to use writer.writeIDref replace writeTag(..., idref , ...).

113 lines of code changed in 8 files:

dong.w.xie 2009-05-18 11:10 Rev.: 1722

BEAUTI species work: take sppSplitPopulations value from partionModel(?).constant.popSize value, currently it is hard code to get(0).

5 lines of code changed in 1 file:

rambaut 2009-05-16 23:21 Rev.: 1721

Added a simple class and parser that takes a set of likelihoods and repeatedly calls makeDirty and getLogLikelihood on each, reporting the times.

91 lines of code changed in 2 files:

rambaut 2009-05-16 22:04 Rev.: 1720

Made the threshold at which the full evaluation test fail into a static constant at the top of the class.

4 lines of code changed in 1 file:

jheled 2009-05-16 13:05 Rev.: 1719

Control number of operator evaluation checks via minOpsFullEvaluations.

Add 'minOpsFullEvaluations="0" fullEvaluation="0"' to the <mcmc> attributes to disable checks altogether.

33 lines of code changed in 5 files:

jheled 2009-05-16 13:03 Rev.: 1718

code police

140 lines of code changed in 17 files:

msuchard 2009-05-16 08:49 Rev.: 1717

Wrote a Metropolized Gibbs operator to jointing update regression coefficients and their indicators in a GLM. Philippe was having some mixing issues.

250 lines of code changed in 3 files:

msuchard 2009-05-16 06:35 Rev.: 1716

Temporary solution before full code review: if fullEvaluationCount == 0, then switch off usingFullEvaluation

2 lines of code changed in 1 file:

dong.w.xie 2009-05-15 15:48 Rev.: 1715

More work in BEAUTI to generate multi-tree logs for species tree and gene tree.

79 lines of code changed in 3 files:

alexei.drummond 2009-05-14 15:51 Rev.: 1714

update coalescent test - was failing to run tree log analysis

8 lines of code changed in 1 file:

dong.w.xie 2009-05-14 11:06 Rev.: 1713

Allow multi-gene files in different log file and create species tree log in BEAUTI.
Refactoring BeastGenerator write logs methods.

269 lines of code changed in 2 files:

msuchard 2009-05-14 08:01 Rev.: 1712

Small runtime bug from ComplexSubstitutionModel call from getDiagnosis.

22 lines of code changed in 2 files:

msuchard 2009-05-13 17:13 Rev.: 1711

Can now Gibbs operate on root node traits as well (TraitGibbsOperator). InternalTraitGibbsOperator is now defunct. Will be removed soon.

118 lines of code changed in 2 files:

dong.w.xie 2009-05-13 16:48 Rev.: 1710

More work in BEAUTI generators to add species reference in <operators> and <mcmc>.

75 lines of code changed in 9 files:

dong.w.xie 2009-05-13 14:04 Rev.: 1709

Add few comments.

13 lines of code changed in 2 files:

dong.w.xie 2009-05-13 13:34 Rev.: 1708

Refactoring BEAUTI BeastGenerator and modify some String constant.

247 lines of code changed in 4 files:

msuchard 2009-05-13 11:41 Rev.: 1707

4 lines of code changed in 2 files:

msuchard 2009-05-13 11:38 Rev.: 1706

Commented out arbitrary precision polynomials; am still not happy with them.

141 lines of code changed in 1 file:

msuchard 2009-05-13 11:25 Rev.: 1705

Working on Welch's uniform prior; should now work for < 30 taxa

831 lines of code changed in 4 files:

dong.w.xie 2009-05-12 16:44 Rev.: 1704

Add species parameters and operator in Priors and Operators panel in Beauti.

109 lines of code changed in 7 files:

Sibon.Li@gmail.com 2009-05-12 15:54 Rev.: 1703

Updated and renamed the InverseGaussianDistributionModel (from ReciprocalRateDistributionModel)

268 lines of code changed in 2 files:

dong.w.xie 2009-05-12 15:12 Rev.: 1702

More work in Beauti to generate species tree properties and species tree model in XML.

161 lines of code changed in 7 files:

jheled 2009-05-12 11:33 Rev.: 1701

avoid string duplications

2 lines of code changed in 1 file:

dong.w.xie 2009-05-12 10:33 Rev.: 1700

Consistent to use String constant to generate tags & elements in xml.

30 lines of code changed in 3 files:

jheled 2009-05-12 10:17 Rev.: 1699

priors on species tree

315 lines of code changed in 2 files:

dong.w.xie 2009-05-11 17:04 Rev.: 1698

Enable the parameters and operators setting in Beauti to suit for multi-gene trees and species tree.

Creating parameters and operators in PartitionModel instead of BeautiOptions can add prefix into the name by executing override method getParameters(Name) and getOperators(Name).

738 lines of code changed in 8 files:

rambaut 2009-05-11 11:25 Rev.: 1697

UniformRootPrior updates the polynomial when the tree changes (and after a restore).

5 lines of code changed in 1 file:

msuchard 2009-05-10 10:22 Rev.: 1696

Implemented Welch's uniform construction based on a recursive polynomial construction

201 lines of code changed in 1 file:

jheled 2009-05-09 10:57 Rev.: 1695

assert incorrect with zero length branches

1 lines of code changed in 1 file:

jheled 2009-05-09 10:52 Rev.: 1694

ongoing battle with strings

74 lines of code changed in 6 files:

msuchard 2009-05-09 04:49 Rev.: 1693

Getting linear model sampling with BSSVS working.

595 lines of code changed in 11 files:

dong.w.xie 2009-05-08 16:50 Rev.: 1692

More for BEAUTI multi-gene trees

48 lines of code changed in 4 files:

dong.w.xie 2009-05-08 15:24 Rev.: 1691

To solve BEAUTI not handling multi-gene-tree for parameters problem.
1) move genePrefix and its setter and getter into parent class Generator;
2) refactoring BeastGenerator, and create OperatorsGenerator.

885 lines of code changed in 9 files:

dong.w.xie 2009-05-07 11:43 Rev.: 1690

More work to generate multi-gene-tree tags in Beauti for BEAST xml file. These changes focus on tree model.

152 lines of code changed in 6 files:

jheled 2009-05-07 08:01 Rev.: 1689

A trial tree operator

335 lines of code changed in 1 file:

jheled 2009-05-07 07:47 Rev.: 1688

more common strings fun.
create method for writing an idref

231 lines of code changed in 12 files:

jheled 2009-05-07 07:45 Rev.: 1687

code police

2 lines of code changed in 3 files:

rambaut 2009-05-07 00:33 Rev.: 1686

Fixed an issue with a null pointer in SequenceErrorModel.

44 lines of code changed in 3 files:

jheled 2009-05-06 22:58 Rev.: 1685

factor out common strings

33 lines of code changed in 2 files:

rambaut 2009-05-06 21:35 Rev.: 1684

Refactored the component stuff into into a factory pattern to make things neater. Compiles, runs and generate code that runs in BEAST (for both SequenceErrorModel and TipDateSampling - but haven't tested all combinations).

411 lines of code changed in 18 files:

Sibon.Li@gmail.com 2009-05-06 17:41 Rev.: 1683

Slightly editted comments on Inverse Gaussian distribution

1 lines of code changed in 1 file:

Sibon.Li@gmail.com 2009-05-06 17:37 Rev.: 1682

Implementation of the Inverse Gaussian distribution

240 lines of code changed in 1 file:

dong.w.xie 2009-05-06 16:50 Rev.: 1681

More work to generate multi-gene-tree tags in Beauti for BEAST xml file. Given multi-gene files corresponding to related data partitions, recommend to use the format gene.1st_property.2nd_property. (For example, given Primates.nex, there will be Primates.taxa, or Primates.clock.rate, etc.)

66 lines of code changed in 3 files:

dong.w.xie 2009-05-06 15:16 Rev.: 1680

Fix bug that cannot start Beauti because of null point exception in setOption.

6 lines of code changed in 2 files:

dong.w.xie 2009-05-06 11:10 Rev.: 1679

Remove TipSpeciesPanel.java from Beauti

0 lines of code changed in 2 files:

jheled 2009-05-06 10:32 Rev.: 1678

oops, should have been in previous to last commit

1 lines of code changed in 1 file:

jheled 2009-05-06 10:31 Rev.: 1677

code police

29 lines of code changed in 2 files:

jheled 2009-05-06 10:31 Rev.: 1676

More of the same - string constants

684 lines of code changed in 28 files:

jheled 2009-05-06 09:58 Rev.: 1675

comment out non commited operators

3 lines of code changed in 1 file:

jheled 2009-05-06 09:55 Rev.: 1674

more string constants

155 lines of code changed in 16 files:

msuchard 2009-05-06 09:06 Rev.: 1673

New conditionally uniform tree prior seems OK

39 lines of code changed in 1 file:

jheled 2009-05-06 09:06 Rev.: 1672

A small improvment in reducing usage of litteral string constants.
Each constant should be defined in one place and referenced elsewhere.
The best place I found is in the various parsers. This may be wrong but now moving it elsewhere is a simple matter.

114 lines of code changed in 22 files:

msuchard 2009-05-06 06:56 Rev.: 1671

Small tweaks, but still not properly working

53 lines of code changed in 1 file:

rambaut 2009-05-06 03:05 Rev.: 1670

This may seem like a rather large load of edits but it is just to get the 'plugin' model generator working better. All the Generators are now created in BeastGenerator's constructor. I am going to implement a factory system for the plug in modules but thought I would submit my changes now before things move on too much. I updated before committing so hopefully no painful merges for anyone.

216 lines of code changed in 17 files:

dong.w.xie 2009-05-05 17:34 Rev.: 1669

Use java bean to improve code did previously in Beauti to generate multi-gene-tree tags in xml.

95 lines of code changed in 4 files:

dong.w.xie 2009-05-05 14:53 Rev.: 1668

More work to generate multi-gene-tree tags in Beauti for BEAST xml file. If options.traits.contains(options.TRAIT_SPECIES) is true, then go to Joseph's function, otherwise it will keep the same as previous.

41 lines of code changed in 2 files:

dong.w.xie 2009-05-05 14:50 Rev.: 1667

Automatically make all imported data partition change to unlinked model, when detect "species" in the trait file imported.

10 lines of code changed in 2 files:

dong.w.xie 2009-05-04 16:45 Rev.: 1666

Some initial code to generate multi-gene-trees in xml. The code is executed by checking condition options.traits.contains(options.TRAIT_SPECIES), which is sepcified to Species functions from Joseph.

92 lines of code changed in 3 files:

msuchard 2009-05-02 05:02 Rev.: 1665

Previously committed wrong version!

5 lines of code changed in 1 file:

msuchard 2009-05-02 04:02 Rev.: 1664

A mixture of cartogram models needs rescaling to control for average cartogram density

230 lines of code changed in 4 files:

dong.w.xie 2009-05-01 14:55 Rev.: 1663

More work to generate <species> in xml

51 lines of code changed in 2 files:

msuchard 2009-05-01 13:14 Rev.: 1662

Starting a mixture of Cartograms

190 lines of code changed in 4 files:

jheled 2009-05-01 09:56 Rev.: 1661

automatic intelliJ code cleanup

66 lines of code changed in 6 files:

jheled 2009-05-01 09:55 Rev.: 1660

don't go belly up when passed negative values. masking some situation which should be handled better - in this case the UPGMA trees having zero length branches leading to a bug in the coalecent code.

5 lines of code changed in 2 files:

jheled 2009-05-01 09:27 Rev.: 1659

More validity checks for traits file loading

42 lines of code changed in 2 files:

msuchard 2009-05-01 08:54 Rev.: 1658

Refactored all SpatialTemporalPolygon into Polygon2D and fixed store/restore bug in GeoSpatialCollectionModel. Also finally remembered to commit my SplineBasis class

292 lines of code changed in 5 files:

bloomquist 2009-05-01 07:30 Rev.: 1657

Someone changed <prec> to <precision>. Adjusted the examples accordingly.

18 lines of code changed in 3 files:

bloomquist 2009-05-01 07:15 Rev.: 1656

Made the AddRemoveOperator backwards compatible for the rate variation stuff.

33 lines of code changed in 1 file:

April 2009 »

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