Lines of Code
[root]/src/dr/app/beauti/taxonsetspanel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 41 (100.0%) | 3156 (100.0%) | 76.9 |
| dong.w.xie | 24 (58.5%) | 3035 (96.2%) | 126.4 |
| rambaut | 8 (19.5%) | 68 (2.2%) | 8.5 |
| dong.w.xie@gmail.com | 7 (17.1%) | 38 (1.2%) | 5.4 |
| alexei.drummond | 1 (2.4%) | 11 (0.3%) | 11.0 |
| jheled | 1 (2.4%) | 4 (0.1%) | 4.0 |
BEAUti now generates a hierarchical coalescent simulator that generates monophyletic groups and required clade heights. Clade heights can be given in the Taxon Sets table in the column called 'age'. These should lie inside any hard prior bounds (this is not done automatically).
31 lines of code changed in 2 files:
Cleaned up the tipdate sampling options (the joint prior model wasn't generating code so hid this option). Removed requirement for taxon sets to be at least 2 taxa.
6 lines of code changed in 1 file:
trunk: merge
2 lines of code changed in 3 files:
trunk: merge Issue 579 and 580
1 lines of code changed in 1 file:
trunk: merge bug fixing of Species Set panel from branch 1.7
21 lines of code changed in 2 files:
trunk: merge Issue 573: BEAUti taxon set panel taxon set table incorrectly auto selection
14 lines of code changed in 1 file:
trunk:solve Issue 515: cast Exception after click taxon set combo box in BEAUti Taxon Set panel
21 lines of code changed in 1 file:
Starting to rebuild generation of robust counting.
1 lines of code changed in 1 file:
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:
trunk: solve Issue 545: BEAUti taxon set compatibility should be focused on each tree
2 lines of code changed in 1 file:
trunk: solve Issue 533: Taxon set validation fires twice
0 lines of code changed in 2 files:
trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.
1 lines of code changed in 1 file:
trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.
2 lines of code changed in 2 files:
trunk: update Species Set panel GUI part to take Taxa object instead, and ready to implement XML generator next time.
251 lines of code changed in 2 files:
trunk: finish Species Set panel GUI part, and wait for XML example to implement XML generator.
65 lines of code changed in 1 file:
trunk: initial dev for Species Set panel when *BEAST calibration that is only allowed on species tree
815 lines of code changed in 1 file:
Trunk: solve Issue 442: BEAUti: taxon set table does not refresh after changing tree model.
902 lines of code changed in 2 files:
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:
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).
7 lines of code changed in 1 file:
Trunk: merge Issue 413: BEAUti: duplicate class PartitionModelOptions causes
model link conflict.
1 lines of code changed in 1 file:
Trunk: solve Issue 396: make alias "forParent" of "includeStem" in TMRCAPasrer
5 lines of code changed in 1 file:
Trunk: Issue 363: Add tooltips for all UI elements
19 lines of code changed in 1 file:
Trunk: solve Issue 391: BEAUti: add forParent for taxon set
25 lines of code changed in 1 file:
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.
14 lines of code changed in 1 file:
Trunk: start merge BEAUti from branch 1.5 in
57 lines of code changed in 1 file:
BEAUTi: solve Issue 147: BEAUTi: if no leaf nodes selected in Taxon Set panel, the corresponding tmrca should not appear in Prior panel.
14 lines of code changed in 1 file:
automatic idea changes and generify
4 lines of code changed in 1 file:
BEAUTi: add some GUI event, and reset panel.
11 lines of code changed in 1 file:
BEAUTi: bug fixing for clock setting in calibrication.
0 lines of code changed in 1 file:
BEAUTi: cotinue Issue #100 and Issue #124.
1) add some events in GUI to fire Tip Calibration and Node Calibration;
2) tidy up 5 FixRateType;
3) TODO: the calculation of ini rate and root height for Node Calibration.
8 lines of code changed in 1 file:
intellij tidy
11 lines of code changed in 1 file:
Fixed an issue in BEAUti not finding a PNG because a class had been moved. Also added an attempt to load the Quaqua look-and-feel which provides a nicer file dialog box on the Mac. This happens at runtime and shouldn't affect compilation or running if the library isn't available.
8 lines of code changed in 1 file:
Refactory BEAUTI package structure, add few panel packages and util package.
832 lines of code changed in 1 file: