Directory src/dr/app/beauti/datapanel/

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dong.w.xie@gmail.com 2013-02-22 11:25 Rev.: 5454

trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.

4 lines of code changed in 2 files:

• src/dr/app/beauti/datapanel: DataPanel.java (new)

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

Porting fixes from 1.7.3 back into the trunk

10 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+10 -2)

dong.w.xie@gmail.com 2012-02-17 11:18 Rev.: 4703

trunk: merge Issue 582: BEAUti Species Set cannot revert back to Taxon Set if uncheck *BEAST, and update version history

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1)

dong.w.xie 2011-12-07 10:45 Rev.: 4517

trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -5)

rambaut 2011-12-04 10:43 Rev.: 4501

Added a dialog box to rename a partition if it has the same name as an existing partition.

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

dong.w.xie 2011-11-25 13:46 Rev.: 4491

trunk:solve Issue 549: BeautiOptions.updateAll() stop user to customize clock rates

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

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.

9 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+9 -7)

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

0 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (-3)

dong.w.xie 2011-11-01 14:03 Rev.: 4381

trunk: correct the bug created by previous fixes.

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

dong.w.xie 2011-11-01 13:00 Rev.: 4379

trunk: solve Issue 526: recover the function to allow different taxa in BEAUti

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

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.

4 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+4)

rambaut 2011-09-20 20:40 Rev.: 4324

More 1.7 work

6 lines of code changed in 3 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+4 -8), SelectTraitDialog.java (+2 -2)

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.

35 lines of code changed in 2 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+10 -8), SelectTraitDialog.java (+25 -9)

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

Adding continuous traits in BEAUti

43 lines of code changed in 2 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+32 -23), SelectTraitDialog.java (+11 -7)

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -3)

rambaut 2011-07-28 11:40 Rev.: 4129

Fixed issue with 0 taxa in data table for traits - now shows '-' to denote that it isn't an alignment.

2 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+2 -2)

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.

8 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+8 -8)

dong.w.xie 2011-04-27 16:07 Rev.: 3963

Trunk: solve Issue 454: BEAUti: all the taxon sets are deleted when link/unlink tree

7 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+7 -5)

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/datapanel: DataPanel.java (+2 -11)

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

Trunk: big update in BEAUti micro-sat.

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5)

dong.w.xie 2011-03-23 11:24 Rev.: 3894

Trunk: solve Issue 445: BEAUti: clock rate configuration is not consistent between clock model panel and prior panel

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

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.

3 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+3 -3)

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.

8 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+8 -6)

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.

26 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+26 -24)

dong.w.xie 2011-03-01 15:17 Rev.: 3840

Trunk: solve Issue 420: Add error message : Partitions cannot have the same name

7 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+7)

dong.w.xie 2011-03-01 14:21 Rev.: 3839

Trunk: solve Issue 425: BEAUti can't re-link subst models anymore

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -6)

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

Trunk: add more validation in BEAUti checkOptions().

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

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.

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -3)

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/datapanel: DataPanel.java (+2 -2)

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

Many fixes for discrete trait generation.

4 lines of code changed in 2 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1), SelectTraitDialog.java (+3 -1)

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

Please no exclaimation marks in UI messages!

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

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

Give a more intuitive error message

5 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -3)

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).

172 lines of code changed in 2 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+56 -35), SelectTraitDialog.java (+116)

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

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

1 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+1 -1)

dong.w.xie 2010-09-17 12:23 Rev.: 3555

Trunk: merge *BEAST bug fix from branch 1.6

6 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+6 -4)

dong.w.xie 2010-09-14 11:03 Rev.: 3538

Trunk: solve Issue 395: BEAUti: *BEAST check box should be unchecked after all data partition is deteled

3 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+3 -2)

dong.w.xie 2010-09-10 16:55 Rev.: 3522

Trunk: solve Issue 337: Creating a 'CONTINUOUS' or 'INTEGER' trait gives Discrete model of substitution in SiteModelPanel

8 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+8 -5)

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.

8 lines of code changed in 7 files:

• src/dr/app/beauti/datapanel: DataPanel.java (+5 -5), SelectClockDialog.java (new), SelectModelDialog.java (+1 -1), SelectTreeDialog.java (new)

dong.w.xie 2010-09-03 14:02 Rev.: 3484

Trunk: solve Issue 381: Discrete trait model can select an inappropriate substitution model in the data partition table

50 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+50 -12)

dong.w.xie 2010-09-02 11:57 Rev.: 3483

Trunk: solve Issue 383: BEAUti: "species" trait should not appear in Data Panel

3 lines of code changed in 1 file:

• src/dr/app/beauti/datapanel: DataPanel.java (+3 -3)

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