Directory src/dr/app/beauti/treespanel/

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dong.w.xie@gmail.com 2012-02-17 15:56 Rev.: 4705

trunk: merge Issue 583: BEAUti prior dialog text field validation should give sensible error message

1 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+1 -7)

rambaut 2012-01-04 01:03 Rev.: 4568

Cleaned up the interface for selecting starting trees.

1 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+1 -1)

rambaut 2012-01-03 23:14 Rev.: 4567

Cleaned up the interface for selecting starting trees.

123 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+123 -94)

dong.w.xie 2011-12-13 11:07 Rev.: 4540

trunk:solve Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on node ages, and add a nexus example with user specified starting tree

29 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+29 -19)

dong.w.xie 2011-11-23 12:45 Rev.: 4476

trunk:solve Issue 546: disable link tree prior function in BEAUti if using EBSP and GMRF

15 lines of code changed in 4 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (new), TreesPanel.java (new)

rambaut 2011-11-20 07:28 Rev.: 4456

Refactoring of the robust counting and sequence error model into a new tab ('States') which allows these options to be specified on a per partition basis. These options are still not finished yet but the panel can be hidden using the constant at the top of BeautiFrame.

2 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+2 -2)

dong.w.xie 2011-11-18 14:15 Rev.: 4451

trunk:solve Issue 493: Beauti does not show ploidy type for EBSP

1 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+1)

dong.w.xie 2011-11-18 10:22 Rev.: 4450

trunk: remove drop down list from TreePriorPanel, because the "none" functionality is provided
by the vanilla Yule. But still keep correctType in BEAUti options to make XML generate correctType = "exact".

13 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+13 -13)

dong.w.xie 2011-11-17 14:56 Rev.: 4445

trunk: show Calibrated Yule in tree prior drop list

1 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+1)

rambaut 2011-11-14 22:36 Rev.: 4417

Improvement on fix for Issue 539 - making the text area non-opaque lets the background come through. This improves the Mac look as it is in a recessed box (a darker shade that the window background). I guess this looks OK on other platforms too?

2 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+2 -1)

dong.w.xie 2011-11-14 16:34 Rev.: 4416

trunk: solve Issue 538: move tree prior panel to the left of table, and Issue 539: use the same background in citation text area in Tree panel, and some more code for calibrated Yule

16 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+6 -3), TreesPanel.java (+10 -10)

dong.w.xie 2011-11-09 11:59 Rev.: 4401

improve enum CorrectionType to suit for BEAUti, and finish Calibrated Yule GUI part, but need further work on xml generator.

16 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+16), TreesPanel.java (-1)

dong.w.xie 2011-11-09 11:32 Rev.: 4400

solve Issue 485: BEAUti trunk: tree prior is locked at Coalescent Constant, and Issue 536: Species tree prior is locked, and more dev on Calibrated Yule in BEAUti

9 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+5 -5), TreesPanel.java (+4 -2)

dong.w.xie 2011-11-09 10:46 Rev.: 4399

solve Issue 535: SpeciesTreesPanel are not necessary

149 lines of code changed in 4 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+132 -89), SpeciesTreesPanel.java (new), TreesPanel.java (+16 -30)

dong.w.xie 2011-11-08 16:55 Rev.: 4398

trunk: start BEAUti dev Calibrated Yule

7 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+7)

rambaut 2011-11-07 03:44 Rev.: 4392

Cleaning up bugs in XML generation...

4 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+4 -6)

dong.w.xie 2011-11-01 11:25 Rev.: 4377

trunk: solve Issue 524: link/unlink tree prior not working properly in BEAUti

10 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+3 -1), TreesPanel.java (+7 -27)

rambaut 2011-09-09 04:50 Rev.: 4298

Fixed an issue with parameter table not being updated after a change to TreePrior.

19 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+12 -2), TreesPanel.java (+7 -6)

dong.w.xie 2011-08-22 15:28 Rev.: 4228

trunk: merge Issue 494 from branch 1.6

2 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: TreesPanel.java (+2)

rambaut 2011-07-29 05:20 Rev.: 4133

Cleaned up selection of tree priors available for different situations.

23 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+22 -22), TreesPanel.java (+1 -9)

msuchard 2011-05-11 05:12 Rev.: 3976

Attempting to standardize citations in BEAUti for a more professional look; am unclear why we did not stick with the Citable interface.

17 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+17 -18)

rambaut 2011-04-01 21:00 Rev.: 3923

Added Tanja's paper back to the Yule citation.

3 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+3 -2)

rambaut 2011-04-01 20:42 Rev.: 3922

Added reference for Yule model if we are going to be complete. Should we also cite Gernhard, T., 2008 or is this distribution the same when death rate=0?

5 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+5 -3)

dong.w.xie 2011-04-01 11:30 Rev.: 3917

Trunk: fix build.

2 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+2 -2)

dong.w.xie 2011-04-01 11:25 Rev.: 3916

Trunk: solve Issue 447: The Birth-Death models in the Trees Panel show a citation - other models do not.

72 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+67 -57), TreesPanel.java (+5 -5)

dong.w.xie 2011-04-01 09:52 Rev.: 3915

Trunk: solve Issue 449: BEAUti: Bayesian Skyline should be removed for multi-tree.

19 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+10 -5), TreesPanel.java (+9 -4)

dong.w.xie 2011-04-01 09:22 Rev.: 3913

Trunk: fix a small bug.

1 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+1)

rambaut 2011-04-01 03:06 Rev.: 3912

Added citations for other tree prior models (ESBP still needs to be added - sorry, I couldn't find it quick enough).

20 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+20 -14)

dong.w.xie 2011-03-31 13:07 Rev.: 3908

Trunk: more big update on BEAUti microsat.

2 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+2 -2)

dong.w.xie 2011-03-25 12:10 Rev.: 3900

Trunk: continue to implement Brith Death Serial Sampling in BEAUti.

35 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreePriorPanel.java (+35 -16)

dong.w.xie 2011-03-23 17:16 Rev.: 3896

Trunk: make auto scale function to fix BEAUti partition framework, which moves it from priorOptions into partitionOptions.getParameter(), and discard priorOptions.

5 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: OldTreesPanel.java (new)

dong.w.xie 2011-03-23 12:16 Rev.: 3895

Trunk: fix more bugs.

11 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+1 -1), TreesPanel.java (+10 -9)

dong.w.xie 2011-03-22 12:52 Rev.: 3892

Trunk: solve Issue 426: BEAUti does not preserve settings when re-linking, and Issue 444: BEAUti: model table select row not update.

40 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+34 -31), TreesPanel.java (+6)

dong.w.xie 2011-03-18 17:53 Rev.: 3881

Trunk: working on operators and generator.

7 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+7 -2)

dong.w.xie 2011-03-17 16:03 Rev.: 3880

Trunk: make clock model group working in GUI, but operators and generator not working yet.

16 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: TreesPanel.java (+16 -12)

dong.w.xie 2011-03-16 16:48 Rev.: 3877

Trunk: big change of implementing clock model group, including to correct some auto GUI event regarding "fix mean" and calibration. Not finished yet.

1 lines of code changed in 1 file:

• src/dr/app/beauti/treespanel: TreesPanel.java (+1 -1)

dong.w.xie 2011-03-14 16:27 Rev.: 3872

Trunk: more work on micro-sat data in BEAUti.

55 lines of code changed in 3 files:

• src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+9 -7), PartitionTreePriorPanel.java (+35 -25), TreesPanel.java (+11 -8)

dong.w.xie 2011-03-08 15:15 Rev.: 3860

Trunk: big check-in to add micro-satellite in BEAUti.
1) Because it uses patterns not alignment, PartitionPattern is added, and PartitionData is still used for all previous data type.
2) getDataType is corrected to get actual data type, where traits are generalDataType, and trait name is getting from getDataDescription.
3) add MICRO_SAT data type.

5 lines of code changed in 3 files:

• src/dr/app/beauti/treespanel: GenerateTreeDialog.java (new), TreesPanel.java (+3 -4)

rambaut 2010-10-28 22:44 Rev.: 3686

Cleaning up BEAUti a bit.

4 lines of code changed in 2 files:

• src/dr/app/beauti/treespanel: OldTreesPanel.java (+2 -2), TreesPanel.java (+2 -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).

9 lines of code changed in 5 files:

• src/dr/app/beauti/treespanel: OldTreesPanel.java (+2 -2), PartitionTreeModelPanel.java (+2 -2), PartitionTreePriorPanel.java (+2 -2), SpeciesTreesPanel.java (+2 -2), TreesPanel.java (+1 -1)

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