Directory src/dr/app/beauti/priorsPanel/

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rambaut 2012-03-13 00:23 Rev.: 4820

Merging a couple of changes from 1.7 branch

11 lines of code changed in 4 files:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (new), PriorsPanel.java (new)

dong.w.xie@gmail.com 2012-03-12 09:24 Rev.: 4816

trunk: merge prior dialog and distribution changes to trunk

140 lines of code changed in 6 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+23 -13), PriorDialog.java (new), PriorOptionsPanel.java (+92 -8), PriorsPanel.java (+1 -1)

rambaut 2012-03-09 05:09 Rev.: 4802

Merged changes from 1.7

5 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorsPanel.java (+5 -3)

rambaut 2012-03-09 00:34 Rev.: 4797

Few more fixes to truncation of prior distributions

4 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+4 -1)

rambaut 2012-03-08 21:51 Rev.: 4794

Don't use a truncated distribution unless this option is selected.

2 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+2 -2)

dong.w.xie@gmail.com 2012-02-27 14:35 Rev.: 4731

trunk: add a new constructor to exclude the lower bound or upper bound during validation, but this is not available in branch 1.7 at moment

10 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+10 -4)

dong.w.xie@gmail.com 2012-02-23 17:11 Rev.: 4724

trunk: merge

8 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+8)

dong.w.xie@gmail.com 2012-02-21 14:12 Rev.: 4717

trunk:solve Issue 589: BEAUti lost Uniform bound validation, and Issue 590: BEAUti prior dialog GUI logic bug

7 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+6 -9), PriorOptionsPanel.java (+1)

rambaut 2012-02-21 09:07 Rev.: 4716

I think PriorDialog validation is now working as one might expect.

31 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+22 -19), PriorsPanel.java (+9 -10)

dong.w.xie@gmail.com 2012-02-20 17:20 Rev.: 4714

trunk: merge Issue 587: BEAUti prior dialog ignores validation in the text field if pressing Enter key

1 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+1 -1)

dong.w.xie@gmail.com 2012-02-20 15:24 Rev.: 4712

trunk: merge Issue 584:BEAUti prior dialog validation bugs, and Issue 586: BEAUti prior dialog Cancel not working

30 lines of code changed in 3 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+16 -7), PriorOptionsPanel.java (+9), PriorsPanel.java (+5 -5)

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

34 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+34 -1)

rambaut 2012-02-03 04:37 Rev.: 4634

Hidden 'Create Hierarchical Prior' button in the 'Default Prior' dialog that appears when you try to generate - that is not the place to create hierarchical models.

1 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorsPanel.java (+1 -1)

rambaut 2012-02-03 03:51 Rev.: 4633

Altered how the prior dialog box that appears when you try to generate works. Now, if a prior is undefined the 'Continue' button is disabled. Selecting a valid prior enables it and allows you to generate the file.

64 lines of code changed in 3 files:

• src/dr/app/beauti/priorsPanel: DefaultPriorDialog.java (new), PriorsPanel.java (+13)

rambaut 2011-12-04 10:45 Rev.: 4502

Fixed Issue 519, http://code.google.com/p/beast-mcmc/issues/detail?id=519 where changing values in for uniform in prior dialog would cause a hang. The issue was that the dialog was wrapping the uniformDistribution in a TruncatedDistribution which then cause terrible problems with the numerical inverse PDF estimator. Now obeys the isTruncatable flag.

1 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+1 -1)

dong.w.xie 2011-12-01 11:08 Rev.: 4499

trunk:solve Issue 502: BEAUti prior panel: the lognormal prior chart cannot accept negative numbers for M=log(mean), but it should

4 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+4 -4)

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/priorsPanel: PriorsPanel.java (+1 -1)

dong.w.xie 2011-11-16 16:46 Rev.: 4437

trunk: more on BEAUti calibrated Yule.

1 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorsPanel.java (+1 -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

5 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+4 -2), PriorsPanel.java (+1)

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

Cleaning up bugs in XML generation...

22 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+4 -4), PriorOptionsPanel.java (+18 -18)

rambaut 2011-11-05 02:53 Rev.: 4390

More cleaning up and adjusting of uniform priors.

27 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+15 -5), PriorOptionsPanel.java (+12 -9)

rambaut 2011-11-01 21:59 Rev.: 4384

Trying to fix up the confusion with uniform bounds. The parameter object in beauti now has 'uniformUpper' and 'uniformLower' rather than using the truncationUpper/Lower (uniform prior cannot be truncated now). Changed the logPDF function of UniformDistribution to take the log before the reciprocal to reduce chance of underflow (note however that taking the log of Double.MAX_VALUE (or twice that if the lower bound is -MAX_VALUE) may still fail). Testing now being undertaken...

5 lines of code changed in 3 files:

• src/dr/app/beauti/priorsPanel: DiscretePriorDialog.java (new), PriorOptionsPanel.java (+3 -3)

dong.w.xie 2011-10-17 16:43 Rev.: 4361

trunk: update Species Set panel GUI part to take Taxa object instead, and ready to implement XML generator next time.

22 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorsPanel.java (+22 -17)

dong.w.xie 2011-10-14 14:40 Rev.: 4358

trunk: Issue 514: NullPointerException when setting prior to tree model in BEAUti Prior panel

1 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+1 -1)

rambaut 2011-10-12 05:09 Rev.: 4354

Fixed an issue with repeatedly added listeners for Prior Dialog components.

7 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+4 -3), PriorOptionsPanel.java (+3)

msuchard 2011-09-12 21:57 Rev.: 4305

Fixes to HPM specification in BEAUti

59 lines of code changed in 3 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+25 -45), PriorDialog.java (+14 -1), PriorOptionsPanel.java (+20)

msuchard 2011-09-09 06:05 Rev.: 4299

Fixed prior graphs in BEAUti, inverse gamma cdf and started stochastic Dollo

16 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+15), PriorOptionsPanel.java (+1 -1)

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.

13 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+12), PriorOptionsPanel.java (+1 -1)

rambaut 2011-07-26 04:12 Rev.: 4120

Cleaned up the hierarchical prior button (disabled until a parameter is selected etc).

27 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorsPanel.java (+27 -2)

rambaut 2011-06-25 11:13 Rev.: 4071

Simplified the special buttons down to just -Inf and +Inf for the lower and upper bounds respectively.

40 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+40 -26)

rambaut 2011-06-25 11:00 Rev.: 4070

Continuing to fix things back up...

46 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: PriorDialog.java (+14 -1), PriorOptionsPanel.java (+32 -10)

rambaut 2011-06-25 07:44 Rev.: 4069

Continuing to fix things back up...

4 lines of code changed in 1 file:

• src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+4 -6)

rambaut 2011-06-25 04:09 Rev.: 4068

Some major refactoring of PriorDialog. Probably horribly broken but at least it compiles.

548 lines of code changed in 5 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+21 -27), PriorDialog.java (+53 -468), PriorOptionsPanel.java (+465 -24), SpecialNumberPanel.java (+9 -10)

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).

96 lines of code changed in 4 files:

• src/dr/app/beauti/priorsPanel: DiscretePriorDialog.java (+4 -3), HierarchicalPriorDialog.java (+16 -7), PriorDialog.java (+64 -35), PriorsPanel.java (+12 -12)

msuchard 2011-06-23 04:41 Rev.: 4060

Enabling basic hierarchical phylogenetics models by default

12 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+9 -14), PriorsPanel.java (+3 -2)

msuchard 2011-06-22 17:04 Rev.: 4059

Mostly working hierarchical phylogenetic models

222 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+191 -253), PriorsPanel.java (+31 -5)

msuchard 2011-06-22 06:54 Rev.: 4058

Merged with latest bug fixed. Also implemented Component insertion points inside of the operatior schedule for specially formated operations.

37 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+1 -1), PriorsPanel.java (+36 -1)

rambaut 2011-06-22 01:40 Rev.: 4057

Cleaned up PriorDialog to better render distributions if possible.

82 lines of code changed in 3 files:

• src/dr/app/beauti/priorsPanel: DiscretePriorDialog.java (+6 -4), PriorDialog.java (+33 -20), PriorsPanel.java (+43 -47)

msuchard 2011-06-20 16:21 Rev.: 4047

Intermediate work on implementing Hierarchical Phylogenetics Models in BEAUti

167 lines of code changed in 4 files:

• src/dr/app/beauti/priorsPanel: DiscretePriorDialog.java (+5 -4), HierarchicalPriorDialog.java (+85 -13), PriorDialog.java (+5 -4), PriorsPanel.java (+72 -13)

msuchard 2011-06-04 04:19 Rev.: 4003

Initial work on implementing hierarchical priors into BEAUti

513 lines of code changed in 2 files:

• src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (+453), PriorsPanel.java (+60 -2)

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