Directory src/dr/app/oldbeauti/

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rambaut 2012-11-16 00:54 Rev.: 5232

Renamed NewTreeLikelihood to BeagleTreeLikelihood

4 lines of code changed in 2 files:

• src/dr/app/oldbeauti: BeastGenerator.java (new)

msuchard 2011-09-22 10:36 Rev.: 4330

Fixed integer overflow (when prior sampling) and mixed-math in RandomWalkOperator

10 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+10 -9)

dong.w.xie 2011-03-16 09:53 Rev.: 3876

Trunk: solve Issue 442: BEAUti: taxon set table does not refresh after changing tree model.

7 lines of code changed in 2 files:

• src/dr/app/oldbeauti: TaxaPanel.java (+7 -4)

dong.w.xie 2011-03-01 10:49 Rev.: 3838

Trunk: solve Issue 433: Typo in BEAUTi and example files

1 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+1 -2)

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).

45 lines of code changed in 3 files:

• src/dr/app/oldbeauti: BeastGenerator.java (+13 -14), BeautiOptions.java (new)

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).

2 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+2 -2)

rambaut 2010-09-07 10:37 Rev.: 3497

Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.

49 lines of code changed in 25 files:

• src/dr/app/oldbeauti: BeautiApp.java (new), BeautiDefaultFileMenuFactory.java (new), BeautiFrame.java (new), BeautiMacFileMenuFactory.java (+4 -4), BeautiMenuBarFactory.java (new), DataPanel.java (new), DiscretePriorDialog.java (+2 -2), MCMCPanel.java (+4 -4), ModelPanel.java (new), OperatorsPanel.java (new), PriorDialog.java (+3 -3), PriorsPanel.java (+7 -7), TaxaPanel.java (+4 -4)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

1 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+1 -1)

dong.w.xie 2010-03-02 10:24 Rev.: 3002

Trunk refactoring: finish Logger (split parsers).

62 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+62 -61)

dong.w.xie 2010-03-02 09:47 Rev.: 3000

Trunk refactoring: 3rd part of operators (split parsers).

5 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+5 -7)

dong.w.xie 2010-03-01 13:11 Rev.: 2993

Trunk refactoring: 2nd part of operators (split parsers).

36 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+36 -35)

dong.w.xie 2010-02-26 14:25 Rev.: 2987

Trunk refactoring: 1st part of operators (split parsers).

3 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+3 -2)

dong.w.xie 2010-02-25 16:35 Rev.: 2984

Trunk refactoring: finish statistic model (split parsers).

9 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+9 -14)

dong.w.xie 2010-02-25 15:52 Rev.: 2982

Trunk refactoring: organize distribution parsers again.

0 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (-1)

dong.w.xie 2010-02-25 15:36 Rev.: 2981

Trunk refactoring: finish distribution (split parsers).

20 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+20 -20)

dong.w.xie 2010-02-25 13:51 Rev.: 2979

Trunk refactoring: organize distribution parsers.

2 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+2 -2)

dong.w.xie 2010-02-24 16:25 Rev.: 2974

Trunk refactoring: 1st part of Likelihoods (split parsers)..

30 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+30 -24)

dong.w.xie 2010-02-24 14:50 Rev.: 2972

Trunk refactoring: finish tree operators (split parsers)..

3 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+3 -3)

dong.w.xie 2010-02-24 11:53 Rev.: 2970

Trunk refactoring: correct ExchangeOperatorParser in operators (split parsers)..

5 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+5 -6)

dong.w.xie 2010-02-24 11:18 Rev.: 2969

Trunk refactoring: 1st part of operators (split parsers)..

12 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+12 -11)

dong.w.xie 2010-02-23 09:35 Rev.: 2959

Trunk refactoring: finish tree likihood model (split parsers)..

16 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+16 -16)

dong.w.xie 2010-02-22 14:29 Rev.: 2957

Trunk refactoring: finish tree model (split parsers)..

31 lines of code changed in 2 files:

• src/dr/app/oldbeauti: BeastGenerator.java (+28 -33), BeautiOptions.java (+3 -3)

dong.w.xie 2010-02-22 13:49 Rev.: 2956

Trunk refactoring: 1st part of tree model (split parsers)..

9 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+9 -5)

dong.w.xie 2010-02-22 10:42 Rev.: 2954

Trunk refactoring: organize tree and treelikelihood parsers.

2 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+2 -2)

dong.w.xie 2010-02-19 15:20 Rev.: 2946

Trunk refactoring: 1st part of speciation (split parsers)..

10 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+10 -10)

dong.w.xie 2010-02-19 14:54 Rev.: 2944

Trunk refactoring: finish Random Local Yule Model (split parsers).

6 lines of code changed in 2 files:

• src/dr/app/oldbeauti: BeastGenerator.java (+5 -1), BeautiOptions.java (+1 -1)

dong.w.xie 2010-02-19 14:41 Rev.: 2943

Trunk refactoring: finish coalescent (split parsers).

79 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+79 -80)

dong.w.xie 2010-02-19 10:08 Rev.: 2942

Trunk refactoring: 2nd part of coalescent (split parsers).

9 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+9 -9)

dong.w.xie 2010-02-18 16:36 Rev.: 2941

Trunk refactoring: finish branch rate and clock rate model (split parsers).

11 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+11 -11)

dong.w.xie 2010-02-18 16:25 Rev.: 2940

Trunk refactoring: 1st part of coalescent (split parsers).

38 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+38 -36)

dong.w.xie 2010-02-18 10:12 Rev.: 2939

Trunk refactoring: branch rate and clock rate model (split parsers).

1 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+1)

dong.w.xie 2010-02-17 16:04 Rev.: 2935

Trunk refactoring: make subst parsers more organized.

1 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+1)

dong.w.xie 2010-02-17 15:45 Rev.: 2934

Trunk refactoring: site model (split parsers).

21 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+21 -20)

dong.w.xie 2010-02-17 12:29 Rev.: 2930

Trunk refactoring: finish substitution model (split parsers).

18 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+18 -19)

dong.w.xie 2010-02-17 12:00 Rev.: 2929

Trunk refactoring: big part of substitution model (split parsers).

18 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+18 -19)

dong.w.xie 2010-02-17 10:32 Rev.: 2928

Trunk refactoring: fix BEAUti generator.

11 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+11 -11)

dong.w.xie 2010-02-09 10:14 Rev.: 2901

Trunk: fight to constant String.

2 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+2 -2)

dong.w.xie 2009-12-10 13:44 Rev.: 2678

Trunk: start merge BEAUti from branch 1.5 in

6 lines of code changed in 2 files:

• src/dr/app/oldbeauti: BeastGenerator.java (+2 -2), BeautiOptions.java (+4 -4)

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

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

8 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+8 -5)

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

Remove deprecated class Yule (superceeded by birth death)

Add option for conditioning on root height.

3 lines of code changed in 1 file:

• src/dr/app/oldbeauti: BeastGenerator.java (+3 -4)

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