Directory src/dr/app/beauti/traitspanel/

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rambaut 2013-05-11 17:33 Rev.: 5646

Fixed that BEAUti was putting stateTagName attribute into TreeLikelihood elements (even though they should only be there for ancestralStateTreeLikelihoods). Was giving a parser warning when run (no other consequences).

1 lines of code changed in 2 files:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (new)

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

Porting fixes from 1.7.3 back into the trunk

8 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+8 -2)

dong.w.xie@gmail.com 2012-02-02 17:10 Rev.: 4630

change confused method name and fix prefix bug inside mergePatterns

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+2 -2)

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.

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -2)

rambaut 2011-11-15 03:23 Rev.: 4422

When creating partitions from traits, doesn't allow mixed trait types and creates individual partitions for discrete traits but a single multivariate partition for continuous traits.

26 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+26 -1)

dong.w.xie 2011-10-31 15:19 Rev.: 4375

trunk: solve Issue 523: BEAUti Traits panel buttons enable/disable should adapt to data and traits

20 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+20 -2)

rambaut 2011-10-15 09:13 Rev.: 4359

Can still edit a trait called 'species' if it is not currently being used for *BEAST

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -2)

dong.w.xie 2011-10-13 12:00 Rev.: 4356

trunk: Issue 513: *BEAST constraint of the 'species' trait

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+2 -4)

rambaut 2011-10-12 03:12 Rev.: 4352

Fixed an issue with creating a 'species' trait when *BEAST was already on. Now checks that the user actually loads a species trait when asked to when switching on *BEAST.

Also, reinstated UCLN and UCED as clock options. UCGD and UCCD (Chauchy) are not currently implemented but could be. Also autocorrelated?

17 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+17 -1)

rambaut 2011-10-12 00:20 Rev.: 4351

Fixed warning messages

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+2 -2)

rambaut 2011-10-10 21:36 Rev.: 4347

Refined the interface for turning on and off *BEAST. 'species' is not a special trait until *BEAST is turned on.

12 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+12 -3)

dong.w.xie 2011-10-10 14:24 Rev.: 4346

trunk: solve Issue 510: BEAUti uncheck *BEAST but cannot reverse to normal BEAST properly

13 lines of code changed in 3 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (new), TraitsPanel.java (+11 -17)

rambaut 2011-09-16 21:42 Rev.: 4320

Line wrapping of message

4 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+4 -4)

rambaut 2011-09-16 21:29 Rev.: 4319

Improvements to the StarBEAST interface and how it asks for a species designation.

67 lines of code changed in 2 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+42 -9), TraitsPanel.java (+25 -13)

rambaut 2011-09-09 21:51 Rev.: 4300

Adding continuous traits in BEAUti

33 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+33 -4)

rambaut 2011-07-28 03:39 Rev.: 4127

Added check box when creating a new trait to automatically create the corresponding trait partition. This is on by default.

11 lines of code changed in 2 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+7), TraitsPanel.java (+4)

dong.w.xie 2011-04-28 14:57 Rev.: 3965

Trunk: solve Issue 455: BEAUti: If a trait has its name changed, the values are deleted

7 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+7)

dong.w.xie 2011-02-28 13:11 Rev.: 3836

Trunk: add more validation in BEAUti checkOptions().

0 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (-6)

dong.w.xie 2011-02-28 10:20 Rev.: 3835

Trunk: fix a bug of the enablility of "Create partition from trait" button should relate to available traits not taxa.

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+2 -10)

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

Cleaning up BEAUti a bit.

4 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+4 -4)

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:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+1 -1), GuessTraitDialog.java (+7 -36), TraitValueDialog.java (new 92), TraitsPanel.java (+126 -56)

dong.w.xie 2010-09-14 18:11 Rev.: 3539

Trunk: solve Issue 394: Beuati fails to guess species names

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: GuessTraitDialog.java (+2 -3)

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.

12 lines of code changed in 3 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+1 -1), GuessTraitDialog.java (+5 -5), TraitsPanel.java (+6 -6)

dong.w.xie 2010-09-06 18:07 Rev.: 3496

Trunk: add a comment

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -1)

dong.w.xie 2010-09-06 15:33 Rev.: 3491

Trunk: solve Issue 388: BEAUti: "species" should NOT be used as a trait name

13 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+13 -3)

rambaut 2010-09-01 10:45 Rev.: 3477

Fixed issue where pressing "Guess Traits" to create a new trait resulted in the Guess Traits Dialog appearing twice.

8 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+8 -3)

rambaut 2010-08-20 22:13 Rev.: 3419

Removed uses of '!' in dialog boxes and warnings as they are overly assertive. Took the opportunity to improve the clarity of some of the messages.

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -1)

dong.w.xie 2010-08-17 12:01 Rev.: 3401

Trunk: bring back incorrectly deleted solution by r3364, for Issue 274, 334, 314, 333, 342, 343, 320.

8 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+8 -7)

dong.w.xie 2010-08-13 15:50 Rev.: 3390

Trunk: solve Issue 356: Add instruction to show user how to load specified starting tree from BEAUti

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+1 -15)

dong.w.xie 2010-08-13 14:41 Rev.: 3389

Trunk: solve Issue 354: BEAUti: make auto wrap for HTMLEditorKit inside JEditorPane, and Issue 355: get rid of ">" when wrapping text using BEAUti TextUtil

3 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+3)

dong.w.xie 2010-08-12 16:57 Rev.: 3385

Trunk: solve Issue 352: BEAUti: NullPointerException if leave any trait value empty after activate BSSVS

4 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+4 -4)

dong.w.xie 2010-08-09 17:33 Rev.: 3377

Trunk: more work on new *BEAST GUI, and solve Issue 338: Clock model panel is confusingly laid out, and Issue 346: Show user a guide for an example of *BEAST or trait mapping file format.

32 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+32 -2)

dong.w.xie 2010-08-09 12:02 Rev.: 3376

Trunk: more work on new *BEAST GUI, and solve Issue 345: BEAUti: user want to be able to edit trait value at any time

41 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+41 -34)

dong.w.xie 2010-08-06 12:38 Rev.: 3371

Trunk: make *BEAST work with check box only.

2 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+2 -2)

dong.w.xie 2010-08-06 11:25 Rev.: 3370

Trunk: make buttons work for new change of traits.

45 lines of code changed in 2 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+29 -5), TraitsPanel.java (+16 -7)

rambaut 2010-08-05 04:13 Rev.: 3364

This is rather a large update as I was making changes in a branch and have merged them back in. This allows any trait name to be created (not just 'Location' and 'Species'). The idea is that the discrete model is not phylogoegraphy specific - you can model any discrete change. Have added a check box to say use *BEAST - at this point you should create a Species trait. Have cleaned up a few othe UI issues. Almost certainly there will be XML generation issues as a result and we should concentrate on testing and fixing these.

63 lines of code changed in 3 files:

• src/dr/app/beauti/traitspanel: CreateTraitDialog.java (+8 -8), GuessTraitDialog.java (+20 -31), TraitsPanel.java (+35 -19)

dong.w.xie 2010-08-04 18:17 Rev.: 3361

Trunk: solve Issue 342: NullPointerException after cancelled 'Create New Trait' dialog

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -1)

dong.w.xie 2010-08-04 18:00 Rev.: 3360

Trunk: solve Issue 334: NullPointerException after cancelled 'Import Traits'.

15 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+15 -15)

rambaut 2010-07-29 03:57 Rev.: 3344

Fixed Issue 331 <http://code.google.com/p/beast-mcmc/issues/detail?id=331>. I removed the help button until such time as it does something. I have added some tooltip text for the various buttons. This should be done for all UI in BEAUti. I also changed the two toolbars into a single one at the top of the panel so they didn't affect the rescaling of the splitpane.

39 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+39 -22)

dong.w.xie 2010-07-15 12:35 Rev.: 3316

TRUNK: fix *BEAST GUI bug to load mapping file

1 lines of code changed in 1 file:

• src/dr/app/beauti/traitspanel: TraitsPanel.java (+1 -1)

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