Directory src/dr/app/beauti/clockModelsPanel/

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rambaut 2012-05-16 22:40 Rev.: 4973

Fix for http://code.google.com/p/beast-mcmc/issues/detail?id=627 - change in the clock group name now is propagated to the clock table popup.

1 lines of code changed in 2 files:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (new)

dong.w.xie 2011-12-15 13:38 Rev.: 4545

trunk:solve Issue 446: no indication that Checkboxes and rate text boxes are not editable in Clock Group table

18 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+18 -6)

rambaut 2011-11-07 03:43 Rev.: 4392

Cleaning up bugs in XML generation...

1 lines of code changed in 2 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (new)

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?

15 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+15 -4)

rambaut 2011-07-28 11:42 Rev.: 4130

Removed CTMC reference prior checkbox from clock model table (you select this in the improved prior dialog). Also moved note about this in tooltip for this checkbox to a text area that appears in the PriorDialog when this prior is selected.

2 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+2 -38)

rambaut 2011-06-24 20:49 Rev.: 4062

Some serious cleaning up of how priors are specified. This allows appropriate prior choices for different 'flavours' of parameters (non-negative, zero-one interval, discrete, HPM, CMTC rates). Truncation of the the prior is now a switch and bounds so can be applied to any prior (although the UI is not in place for this yet).

1 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+1 -1)

msuchard 2011-06-19 15:55 Rev.: 4044

Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti

31 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+31 -2)

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

Trunk: more big update on BEAUti microsat.

2 lines of code changed in 2 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+1 -1), OldClockModelsPanel.java (+1 -1)

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

Trunk: big update in BEAUti micro-sat.

7 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+7 -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.

7 lines of code changed in 3 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+2), PartitionClockModelPanel.java (+5 -2)

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

22 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+22 -20)

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/clockModelsPanel: ClockModelsPanel.java (+7 -2)

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

Trunk: working on operators and generator.

12 lines of code changed in 2 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+6 -7), OldClockModelsPanel.java (+6 -7)

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.

113 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+113 -45)

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.

63 lines of code changed in 2 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+7 -17), OldClockModelsPanel.java (+56 -41)

dong.w.xie 2011-03-15 17:14 Rev.: 3875

Trunk: implement clock model group table in BEAUti, to solve the problem that "fix mean rate" function cannot be applied to the different types of clock models, for example, molecular clock ~ trait clock ~ microsatellite clock model.

159 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+159 -10)

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.

0 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (-20)

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

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

14 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+14 -19)

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.

14 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+14 -7)

rambaut 2010-11-13 08:33 Rev.: 3714

AntigenicTraitLikelihood runs! Unlikely to work though. Changed MatrixParameter to set dimensions lazily. TreeTraitParserUtility now labels the individual rows of the compound parameter just as taxon labels so that ATL can pick them up.

142 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+142 -18)

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

Cleaning up BEAUti a bit.

167 lines of code changed in 3 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+146 -76), OldClockModelsPanel.java (+2 -1), PartitionClockModelPanel.java (+19 -8)

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).

760 lines of code changed in 3 files:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+235 -385), OldClockModelsPanel.java (+427), PartitionClockModelPanel.java (+98)

dong.w.xie 2010-09-09 11:45 Rev.: 3509

Trunk: Issue 363: Add tooltips for all UI elements

35 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+35 -4)

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.

7 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+7 -9)

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.

17 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+17 -37)

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

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

26 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+26 -16)

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.

12 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+12 -29)

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.

1 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+1 -2)

dong.w.xie 2010-08-03 11:29 Rev.: 3357

Trunk; BEAUti add Random Local Clock, but it seems BEAST model has bug

2 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+2 -1)

dong.w.xie 2010-04-15 13:23 Rev.: 3123

TRUNK: sovle Issue 296: The imported data has become global to all BEAUti windows

1 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+1 -1)

rambaut 2010-04-13 11:03 Rev.: 3113

Added a few models of sequence (tip) error to model the action of hypermutation by APOBEC editing in HIV.

37 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+37 -38)

dong.w.xie 2010-03-31 13:21 Rev.: 3090

TRUNK: BEAUti discrete traits prior and operator panels are working.

1 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+1 -1)

dong.w.xie 2010-03-30 17:23 Rev.: 3089

TRUNK: BEAUti discrete traits clock model panel is working.

73 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+73 -32)

dong.w.xie 2010-03-29 10:41 Rev.: 3081

TRUNK: BEAUti discrete traits site model panel is working.

111 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+111 -3)

dong.w.xie 2009-09-28 17:52 Rev.: 2306

BEAUTi: solve Issue 174: fixed rate in Clock panel not passing to XML

2 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+2 -1)

dong.w.xie 2009-09-24 12:33 Rev.: 2282

BEAUTi: remove Warning message

2 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+2 -14)

dong.w.xie 2009-09-07 15:50 Rev.: 2219

BEAUTi: solve Issue 144: In use in Operators panel cannot change for those operators belonging to PartitionClockModelTreeModelLink

10 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+10 -18)

dong.w.xie 2009-09-02 16:59 Rev.: 2176

BEAUTi: add and change the status message for clock rate, to avoid confusion.

4 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+4 -1)

dong.w.xie 2009-08-28 10:40 Rev.: 2156

BEAUTi: correct some wrong validation.

10 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+10 -10)

dong.w.xie 2009-08-28 10:11 Rev.: 2155

BEAUTi: add some GUI event, and reset panel.

10 lines of code changed in 1 file:

• src/dr/app/beauti/clockModelsPanel: ClockModelsPanel.java (+10 -10)

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