Directory src/dr/app/beauti/siteModelsPanel/

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rambaut 2013-05-11 02:10 Rev.: 5644

Added tool tip for lambda tree signal parameter check box.

11 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (new)

rambaut 2013-05-10 22:32 Rev.: 5643

BEAUti: added Pagel's Lambda transform of tree shape to measure phylogenetic signal in continuous traits. Check box in sites panel for continuous trait partition. Lambda appears in priors table and operators table.

19 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+19)

rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

0 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (new)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

0 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (-1)

rambaut 2012-03-02 05:02 Rev.: 4746

Fixed some issues with APOBEC error model generation.

0 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (-20)

dong.w.xie 2011-12-06 12:09 Rev.: 4508

trunk: solve Issue 555: Does sequence error model have to apply to every sequence data partition?

3 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+3 -1)

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.

5 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+5 -96), SiteModelsPanel.java (-62)

rambaut 2011-11-15 05:14 Rev.: 4423

Added citations to amino acid models and a text box in BEAUti.

16 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+16 -2)

msuchard 2011-10-08 19:39 Rev.: 4342

Adding binary stochastic Dollo to BEAUti. Now can read Ringe dataset and generate an XML that runs.

61 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+61 -42)

rambaut 2011-09-16 04:23 Rev.: 4317

Fixing up discrete/continuous trait generation..

1 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+1)

rambaut 2011-09-16 03:04 Rev.: 4316

Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.

2 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+1), SiteModelsPanel.java (+1 -3)

rambaut 2011-09-09 22:55 Rev.: 4301

Adding continuous traits in BEAUti

564 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+561 -542), SiteModelsPanel.java (+3)

fbielejec 2011-09-09 01:33 Rev.: 4297

moved the getActiveFrame method to PanelUtils class

5 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+5 -18)

fbielejec 2011-09-09 01:09 Rev.: 4295

dNdS robust counting model is now set in the check box

51 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+51 -11)

fbielejec 2011-09-09 00:44 Rev.: 4294

working on dNdS robust counting UI

40 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+40 -52)

rambaut 2011-09-08 23:57 Rev.: 4293

UI alterations...

22 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+22 -116), SiteModelsPanel.java (-1)

fbielejec 2011-09-08 22:42 Rev.: 4290

dNdS robust counting model is now set in the combo-box

65 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+65 -19)

msuchard 2011-09-07 22:43 Rev.: 4288

Promoted stochastic Dollo to basic BEAUti-enabled

2 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+2 -2)

msuchard 2011-09-07 22:41 Rev.: 4287

Cleaning labels for robust counting

7 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+7 -5)

fbielejec 2011-08-05 20:09 Rev.: 4162

added option to SRD06 model settings

71 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+71 -36)

fbielejec 2011-08-03 13:12 Rev.: 4153

added option to remove dnds counting

51 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+51 -20)

msuchard 2011-07-01 15:37 Rev.: 4089

Connecting DnDsComponent into BEAUti GUI button

18 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+18 -1)

fbielejec 2011-07-01 01:29 Rev.: 4082

added DnDs counting button

526 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+526 -408)

msuchard 2011-06-29 15:07 Rev.: 4077

Added skeleton class for non-phylogenetic trait model for model comparison

4 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+4 -1)

rambaut 2011-04-20 22:28 Rev.: 3942

Another tweak to the previous fix for issue 436 - the sequence error model combo now shows "Off" when disabled.

6 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+6 -3)

rambaut 2011-04-20 21:13 Rev.: 3940

Second part of fix for issue 436 (http://code.google.com/p/beast-mcmc/issues/detail?id=436) - Sequence Error Model is disabled when multiple partitions are being used. Tool tip explains why it is disabled.

22 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+22 -3)

dong.w.xie 2011-03-28 17:06 Rev.: 3905

Trunk: big update in BEAUti micro-sat.

99 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+98 -38), SiteModelsPanel.java (+1)

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.

1 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: CreateModelDialog.java (new)

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.

7 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+7 -3)

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

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

27 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+27)

dong.w.xie 2011-03-11 14:03 Rev.: 3867

Trunk: correct a bug in BeautiImpoter that stops BEAUti framework to load micro-sat data, and make framework to recognize data type by searching partitions.

3 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+3)

dong.w.xie 2011-03-10 16:30 Rev.: 3864

Trunk: start to make micro-satellite available in BEAUti panels.

19 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+19 -1)

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.

4 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+4 -5)

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

Cleaning up BEAUti a bit.

2 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+2 -2)

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

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

4 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+4 -4)

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).

4 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+3 -5), SiteModelsPanel.java (+1 -1)

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.

9 lines of code changed in 3 files:

• src/dr/app/beauti/siteModelsPanel: CreateModelDialog.java (+1 -1), PartitionModelPanel.java (+2 -2), SiteModelsPanel.java (+6 -6)

rambaut 2010-08-20 21:13 Rev.: 3416

Trying to make BEAUti look less Java-like. Have removed the white background for all the panels that are in scroll panes so that you can't see that they are (in a scrollpane) until the scroll bars activate. Have also turned off the horizontal scrollbars in these cases and checked that all the components are visible when the window is at its smallest size. However, I have not tested this on other platforms so would be interested in how it looks (both normally and when small) on Linux and Windows. If any changes to this are required, they should probably be put in platform specific conditionals (i.e., if (!MacOSX)).

10 lines of code changed in 2 files:

• src/dr/app/beauti/siteModelsPanel: PartitionModelPanel.java (+6 -6), SiteModelsPanel.java (+4 -2)

rambaut 2010-08-16 20:35 Rev.: 3398

Addressing issue 358. Moved 'Sequence Error Model' to SiteModelPanel. Cleaned up ClockModelsPanel as a result - no longer need to put the Fixed Mean option in a scrollpane.

41 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+41 -10)

dong.w.xie 2010-08-11 17:32 Rev.: 3381

Trunk: solve Issue 339: GUI within scroll panes is just nasty

7 lines of code changed in 1 file:

• src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (+7 -4)

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