StatSVN - Directory src/dr/app/beauti/components/ancestralstates/

Lines of Code

src/dr/app/beauti/components/ancestralstates/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	29 (100.0%)	963 (100.0%)	33.2
rambaut	23 (79.3%)	871 (90.4%)	37.8
msuchard	1 (3.4%)	51 (5.3%)	51.0
fbielejec	3 (10.3%)	23 (2.4%)	7.6
dong.w.xie	2 (6.9%)	18 (1.9%)	9.0

Most Recent Commits

rambaut 2013-02-15 13:13 Rev.: 5409

Ported recent updates from 1.7 branch

7 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentOptions.java (new)

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

Porting fixes from 1.7.3 back into the trunk

125 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (new)

msuchard 2012-05-11 11:24 Rev.: 4950

Hopefully resolves issue 618. Codon-partitioned models do not throw XML errors with ancestral sequence reconstruction. There is still an issue with the "count" parameter name for non-dNdS robust counting. So, non-dNdS robust counting is temporarily disabled for CP models.

51 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+51 -30)

fbielejec 2012-04-16 23:27 Rev.: 4925

attempt at fixing RC xml gen

6 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+6 -7)

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

Merged changes from 1.7

3 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+3 -3)

rambaut 2012-03-07 04:17 Rev.: 4776

Merged changes in 1.7 - fixes generation of MarkovJumps.

47 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+47 -1)

rambaut 2012-01-04 02:27 Rev.: 4569

Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.

2 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentOptions.java (+2 -1)

rambaut 2011-12-12 10:56 Rev.: 4536

Restored (but renamed to improve clarity) the UI to enable state counting other than the dNdS Robust Counting.

14 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+6 -9), AncestralStatesComponentOptions.java (+8 -10)

dong.w.xie 2011-12-12 10:30 Rev.: 4535

trunk: revert r4509 but keep the changes in r4529

8 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+8 -8)

fbielejec 2011-12-12 09:51

fixing dnds robust counting

17 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+8 -5), AncestralStatesComponentOptions.java (+9 -9)

dong.w.xie 2011-12-06 15:04 Rev.: 4509

trunk: correct getPrefix in AncestralStatesComponentGenerator

10 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+10 -9)

rambaut 2011-11-24 19:18 Rev.: 4483

Started to implement ancestral state reconstruction at a node.

39 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+39 -6)

rambaut 2011-11-22 07:21 Rev.: 4469

Added explicit selection of dN/dS robust counting with additional citation text to keep Marc happy.

20 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+1 -1), AncestralStatesComponentOptions.java (+19 -6)

rambaut 2011-11-22 00:02 Rev.: 4465

dNdS Robust counting now working?

25 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+25 -24)

rambaut 2011-11-21 21:07 Rev.: 4464

Removed a few redundant imports

3 lines of code changed in 1 file:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+3 -4)

rambaut 2011-11-21 11:48 Rev.: 4461

More work on generating ancestral state reconstruction

75 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+70 -48), AncestralStatesComponentOptions.java (+5 -6)

rambaut 2011-11-21 00:03 Rev.: 4459

Starting to rebuild generation of robust counting.

217 lines of code changed in 4 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentFactory.java (new), AncestralStatesComponentGenerator.java (+179 -125), AncestralStatesComponentOptions.java (+34 -13)

rambaut 2011-11-20 21:32 Rev.: 4457

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.

294 lines of code changed in 3 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentFactory.java (+38), AncestralStatesComponentGenerator.java (+186), AncestralStatesComponentOptions.java (+70)