October 2010 Commit Log

Number of Commits:
73
Number of Active Developers:
7
rambaut 2010-10-28 22:44 Rev.: 3686

Cleaning up BEAUti a bit.

191 lines of code changed in 16 files:

msuchard 2010-10-28 03:38 Rev.: 3685

Enabling tipBranchSubstitutionModel for ancestral state reconstruction

399 lines of code changed in 7 files:

msuchard 2010-10-27 12:09 Rev.: 3684

Refactored BranchSiteModel to BranchSubstitutionModel to better reflect that this class specifies a substitution model for each branch, while SiteRateModel gives the site-specitic rate multiplier information.

288 lines of code changed in 18 files:

msuchard 2010-10-27 12:02 Rev.: 3683

Added example files

91 lines of code changed in 2 files:

msuchard 2010-10-27 12:01 Rev.: 3682

Almost certainly broke BeagleTreeLikelihood. Added support for BranchSiteModel (different substitution models across various sets of branches) and implemented an external vs internal branch-specific substitution process.

255 lines of code changed in 8 files:

msuchard 2010-10-27 09:36 Rev.: 3681

Fixed bugs I introduced allowing resource scaling and preferences to vary across data partitions

38 lines of code changed in 1 file:

rambaut 2010-10-27 01:30 Rev.: 3680

Many fixes for discrete trait generation.

92 lines of code changed in 10 files:

rambaut 2010-10-26 23:00 Rev.: 3679

Traits states now get logged with the proper partition prefix

3 lines of code changed in 1 file:

rambaut 2010-10-26 22:53 Rev.: 3678

updating version number in build.xml

2 lines of code changed in 1 file:

dong.w.xie 2010-10-26 11:45 Rev.: 3677

Trunk: correct spelling.

22 lines of code changed in 7 files:

rambaut 2010-10-26 04:14 Rev.: 3676

Only write one general substitution data type per discrete substitution model.

40 lines of code changed in 6 files:

rambaut 2010-10-26 03:57 Rev.: 3675

Spelling

3 lines of code changed in 1 file:

rambaut 2010-10-26 03:56 Rev.: 3674

Fixing up discrete model generation

44 lines of code changed in 5 files:

rambaut 2010-10-26 02:48 Rev.: 3673

Discrete traits models now take the union of states for all partitions that share the same discrete CTMC model.

56 lines of code changed in 7 files:

philippe.lemey@gmail.com 2010-10-26 00:12 Rev.: 3672

TimeSlicer update for compatibility with Google Earth 5.2 / cartographica

37 lines of code changed in 1 file:

rambaut 2010-10-25 19:56 Rev.: 3671

If you explicitly specify a file then it is analysed irrespective of what its extension is.

5 lines of code changed in 1 file:

rambaut 2010-10-25 19:50 Rev.: 3670

Please no exclaimation marks in UI messages!

1 lines of code changed in 1 file:

jheled 2010-10-25 19:15 Rev.: 3669

Give a more intuitive error message

5 lines of code changed in 1 file:

jheled 2010-10-25 19:13 Rev.: 3668

Give a sane message when no files are given (since files with a non-approved extension, even if explicitly given on the command line, are silently filtered out)

5 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-10-23 23:35 Rev.: 3667

TimeSlicer update for compatibility with Google Earth 5.2

43 lines of code changed in 2 files:

philippe.lemey@gmail.com 2010-10-23 22:14 Rev.: 3666

TimeSlicer update for compatibility with Google Earth 5.2

370 lines of code changed in 1 file:

msuchard 2010-10-23 09:31 Rev.: 3665

Added ability to provide BEAGLE flags and scaling scheme on a partition-by-partition basis

52 lines of code changed in 1 file:

rambaut 2010-10-23 03:56 Rev.: 3664

This is a very large commit. It addresses some architectural issues in BEAUti that were going to hinder implementation of continuous traits.

The main thing it does is to isolate creating and importing traits from creating partitions on those traits. A button on the data panel explicitly specifies that a trait should be used as a data partition (i.e., have a TreeLikelihood). This allows traits to be used for other purposes (such as defining Species in *BEAST). This has also allowed considerable simplification of code and tidying up.

There are a number of bug fixes as well over v1.6.0 that I will add to the issue list to keep track of them. Given the complex nature of these changes, I do not think these should be ported to the 1.6.0 branch but perhaps the bugs can be fixed.

These changes will have introduced bugs and possibly cause issues with XML generation that now need to be fixed (I will attempt to catch as many as possible).

3241 lines of code changed in 107 files:

rambaut 2010-10-23 03:49 Rev.: 3663

Removed automatic use of 'guess trait values' during an add trait. We may not have traits embedded in taxon labels and the user may wish to load them manually or import them.

Removed the disabled name text field and type combo box from the guess traits dialog as it was unclear why these were disabled. Replaced with a label describing what is being edited.

Made the GuessTraitsDialog box persistent so the settings remain in subsequent calls (it was tedious to have to reconstruct a complex regex).

226 lines of code changed in 5 files:

rambaut 2010-10-23 03:49 Rev.: 3662

Fixed issue with TraitGuesser not extracting match within brackets (braces).

3 lines of code changed in 1 file:

alexei.drummond 2010-10-22 15:12 Rev.: 3661

q(x0) -> 1/q(x0) [whoops!]

2 lines of code changed in 1 file:

dong.w.xie 2010-10-20 10:20 Rev.: 3659

Trunk: merge change.

1 lines of code changed in 2 files:

msuchard 2010-10-20 00:30 Rev.: 3657

Updates to robust counting classes to provide branch-specific unconditioned counts

88 lines of code changed in 2 files:

msuchard 2010-10-19 10:27 Rev.: 3656

Do not partition data if site count is less than number of prospective partitions

1 lines of code changed in 1 file:

rambaut 2010-10-15 21:41 Rev.: 3655

Updated revision number of Pathogen

2 lines of code changed in 1 file:

rambaut 2010-10-15 21:40 Rev.: 3654

Added a constant boolean to BeastVersion to specify whether it is a prerelease version. If true then the Subversion revision number is appended to the version string. The SVN revision number should be updated automatically but this may require setting the subversion property "svn:keywords" with value "Rev" to do this.

7 lines of code changed in 1 file:

rambaut 2010-10-15 20:55 Rev.: 3653

Fixed a problem with pattern subsets where the last subset may have an extra pattern.

1 lines of code changed in 1 file:

rambaut 2010-10-15 20:51 Rev.: 3652

Updating the BeastVersion for the trunk to differentiate builds from the 1.6 branch.

4 lines of code changed in 1 file:

dong.w.xie 2010-10-14 16:21 Rev.: 3650

Trunk: merge change.

50 lines of code changed in 6 files:

dong.w.xie 2010-10-14 09:38 Rev.: 3646

Trunk: merge change.

7 lines of code changed in 1 file:

rambaut 2010-10-14 04:15 Rev.: 3644

Added common ancestor lines to pathogen. These help explore the outliers.

20 lines of code changed in 2 files:

dong.w.xie 2010-10-13 17:19 Rev.: 3643

Trunk: merge change.

5 lines of code changed in 2 files:

dong.w.xie 2010-10-13 15:48 Rev.: 3641

Trunk: merge issue 416, 417 and 418.

71 lines of code changed in 7 files:

dong.w.xie 2010-10-13 10:02 Rev.: 3638

Trunk: EBSP missing P.

1 lines of code changed in 2 files:

dong.w.xie 2010-10-12 18:19 Rev.: 3636

Trunk: merge issue 414.

125 lines of code changed in 5 files:

dong.w.xie 2010-10-12 10:47 Rev.: 3634

Trunk: merge issue 398.

1 lines of code changed in 1 file:

dong.w.xie 2010-10-12 10:24 Rev.: 3632

Trunk: merge issue 408.

17 lines of code changed in 1 file:

dong.w.xie 2010-10-12 09:51 Rev.: 3630

Trunk: merge issue 403.

3 lines of code changed in 1 file:

dong.w.xie 2010-10-12 09:36 Rev.: 3628

Trunk: fix build.

1 lines of code changed in 1 file:

dong.w.xie 2010-10-12 09:26 Rev.: 3627

Trunk: merge Issue 413: BEAUti: duplicate class PartitionModelOptions causes
model link conflict.

453 lines of code changed in 15 files:

dong.w.xie 2010-10-11 15:18 Rev.: 3626

Trunk: update EBSP tutorial

0 lines of code changed in 2 files:

rambaut 2010-10-10 20:55 Rev.: 3623

Experimenting with Path-O-Gen

215 lines of code changed in 4 files:

philippe.lemey@gmail.com 2010-10-09 17:20 Rev.: 3622

added a getCentroid method in Polygon2D

21 lines of code changed in 1 file:

rambaut 2010-10-09 01:38 Rev.: 3621

After some more extensive testing, I have now removed the node heights bound check as default. Certain moves still may make this check.

8 lines of code changed in 3 files:

rambaut 2010-10-08 21:16 Rev.: 3620

Decoupled the process of checking node heights are within bounds to confirm that an operator is correct from using it to reject a move. By default tree moves just call treeModel.endTreeEdit() to finish editing the tree. If they need to check whether the resulting tree is valid they can call checkTreeIsValid() which throws an exception if not. Most moves do not need this check if correctly implemented. Some I wasn't too sure about so I left the check in for those to give the same behaviour (but it is up to the operator whether this check is made and what to do about it).

TreeModel.endTreeEdit() can optionally make this test (switch on a flag at the top of TreeModel) but throws a runtimeException so stops the program if it fails.

365 lines of code changed in 39 files:

rambaut 2010-10-08 12:04 Rev.: 3618

Whilst I test the consequence of removing the height bound checking in TreeModel.endTreeEdit(), I have reinstated the test but it now throws a RuntimeException to see if any operators rely on this test failing to check for invalid moves.

11 lines of code changed in 3 files:

rambaut 2010-10-08 11:47 Rev.: 3617

Removed another use of IntersectionBounds in CompoundParameter unless it is actually required. About a 10% speed up on benchmark1.xml. Further work could probably get a bit more out of this but I am not sure it would be worth it. These inefficiencies only become apparent with very large trees that don't take too long to evaluate.

13 lines of code changed in 1 file:

dong.w.xie 2010-10-08 11:23 Rev.: 3615

Trunk: EBSP tutorial and script

14354 lines of code changed in 20 files:

rambaut 2010-10-08 11:17 Rev.: 3614

examples/benchmark1.xml used to take 160 seconds - it now takes 35. This is because it is a very large tree (1442 tips). The likelihood calculation was taking 22 seconds of the 160, most of the rest was spent checking the bounds of the node heights. It turned out that TreeModel.endTreeEdit() was checking the bounds of every node after every tree move. This check is simply to ensure that the tree move was behaving correctly (program stops with a RuntimeException if it doesn't). So, commented out this check and 3 fold speed up.

Actually it turned out all the nodes had their bounds added twice so this check was even more costly.

We could include this check in the initial phase of the run or as an assert.

28 lines of code changed in 2 files:

alexei.drummond 2010-10-08 10:52 Rev.: 3612

Small changes to StarBEAST tutorial

529 lines of code changed in 4 files:

alexei.drummond 2010-10-08 10:23 Rev.: 3611

Removed System.out.println's from DiscretizedBranchRates

10 lines of code changed in 1 file:

rambaut 2010-10-08 09:35 Rev.: 3610

Adjusted Parameter to not use IntesectionBounds unless multiple bounds are added.

14 lines of code changed in 1 file:

rambaut 2010-10-07 22:45 Rev.: 3608

Relaxed the test of RandomWalkOperator to allow for a loss of precision in the looping algorithm.

1 lines of code changed in 2 files:

rambaut 2010-10-07 21:42 Rev.: 3607

Implemented algorithm for a reflected random walk avoiding a loop. Refactored the old looping algorithm out into a method and created a unit test to compare the two. Currently for the test with a very large number of loop iterations, the results are different at the 4th decimal place, probably as a result of loss of precision in the repeated subtractions in the loop.

146 lines of code changed in 2 files:

rambaut 2010-10-06 23:41 Rev.: 3605

Fixed an issue where an IntegerRandomWalkOperator was actually just generating a RandomWalkOperator (the wrong string was being used).

7 lines of code changed in 4 files:

dong.w.xie 2010-10-06 14:13 Rev.: 3604

Trunk: merge issue 411

2 lines of code changed in 1 file:

dong.w.xie 2010-10-06 13:53 Rev.: 3602

Trunk: merge issue 411

15 lines of code changed in 2 files:

dong.w.xie 2010-10-06 09:16 Rev.: 3600

Trunk: *BEAST tutorial

1587 lines of code changed in 23 files:

dong.w.xie 2010-10-05 14:46 Rev.: 3599

Trunk: merge Issue 410: "Improper priors" on posterior statistics from branch 1.6.

42 lines of code changed in 9 files:

dong.w.xie 2010-10-04 10:56 Rev.: 3596

Trunk: @Override is JDK1.6 code.

45 lines of code changed in 18 files:

aaron.darling 2010-10-02 15:30 Rev.: 3595

Adding a very hackish and trivial example XML for using the metagenome HiddenLinkageModel.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

1880 lines of code changed in 1 file:

aaron.darling 2010-10-02 15:24 Rev.: 3594

Allow the use of a native general likelihood core. Change handling of TipPartialsModel change events so only affected nodes with TipPartialsModels get marked dirty -- saves lots of recompute.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

16 lines of code changed in 1 file:

aaron.darling 2010-10-02 15:18 Rev.: 3593

Several small changes to TreeLoggerParser that structure it in a way that allows subclasses to use much of its functionality without reimplementing or copying code.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

33 lines of code changed in 1 file:

aaron.darling 2010-10-02 15:16 Rev.: 3592

Warn the user when the native general likelihood core could not be loaded.

1 lines of code changed in 2 files:

aaron.darling 2010-10-02 15:16 Rev.: 3591

Making a tiny change to TreeLogger API so that the tree can be manipulated by other classes. This gets used by the HiddenLinkageTreeLogger to avoid duplicating all the code in TreeLogger.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

10 lines of code changed in 1 file:

aaron.darling 2010-10-02 15:14 Rev.: 3590

Adding some additional stray files that are part of the metagenome linkage model.

Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.

202 lines of code changed in 3 files:

aaron.darling 2010-10-02 15:12 Rev.: 3589

Adding parsers for metagenome models.
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.

13 lines of code changed in 1 file:

aaron.darling 2010-10-02 15:11 Rev.: 3588

Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.

1488 lines of code changed in 14 files:

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