StatSVN - Directory src/dr/app/beauti/ancestralStatesPanel/

Lines of Code

src/dr/app/beauti/ancestralStatesPanel/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	25 (100.0%)	924 (100.0%)	36.9
rambaut	16 (64.0%)	848 (91.8%)	53.0
msuchard	3 (12.0%)	53 (5.7%)	17.6
dong.w.xie	3 (12.0%)	12 (1.3%)	4.0
philippe.lemey@gmail.com	2 (8.0%)	8 (0.9%)	4.0
fbielejec	1 (4.0%)	3 (0.3%)	3.0

Most Recent Commits

philippe.lemey@gmail.com 2013-02-14 08:04 Rev.: 5395

text message changes for the renaissance counting method in AncestralStatesOptionsPanel

8 lines of code changed in 2 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+8 -8)

rambaut 2012-08-02 00:14 Rev.: 5081

Fix for Issue 643: Unable to specify a MRCA node to reconstruct ancestral states

5 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+5 -3)

rambaut 2012-05-15 20:53 Rev.: 4962

Very important bug fix - the check boxes in the States panel now line up.

9 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+9 -5)

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.

37 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+37 -9)

msuchard 2012-05-11 09:04 Rev.: 4949

Resolved XML problem with ancestral reconstruction for MRCA that were not the root.

2 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+2 -2)

rambaut 2012-03-02 05:02 Rev.: 4746

Fixed some issues with APOBEC error model generation.

2 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+2 -2)

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.

23 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+23 -23)

fbielejec 2011-12-12 09:52 Rev.: 4533

use dndsRobustCounting for consistency

3 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+3 -2)

dong.w.xie 2011-12-06 12:09 Rev.: 4508

trunk: solve Issue 555: Does sequence error model have to apply to every sequence data partition?

3 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+3 -1)

dong.w.xie 2011-12-05 13:52 Rev.: 4504

trunk:solve Issue 475: BEAUti hypervariable models do not fill in all necessary model attributes to run, and Issue 554: SequenceErrorModelComponentOptions did not create parameters properly

3 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+3)

dong.w.xie 2011-11-30 10:53 Rev.: 4497

trunk:solve Issue 552: BEAUTi keeps generating a dialog when load a binary datafile

6 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+6 -4)

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

Started to implement ancestral state reconstruction at a node.

42 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+42 -30)

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

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

75 lines of code changed in 3 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+67 -41), AncestralStatesPanel.java (new)

msuchard 2011-11-22 02:00 Rev.: 4467

Updated tool-text

14 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+14 -10)

rambaut 2011-11-21 11:58 Rev.: 4462

More work on generating ancestral state reconstruction

22 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+22 -62)

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

More work on generating ancestral state reconstruction

0 lines of code changed in 1 file:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (-1)

rambaut 2011-11-21 03:37 Rev.: 4460

Starting to rebuild generation of robust counting.

25 lines of code changed in 2 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+20 -12), AncestralStatesPanel.java (+5 -19)

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

Starting to rebuild generation of robust counting.

63 lines of code changed in 2 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+61 -30), AncestralStatesPanel.java (+2 -10)

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.

582 lines of code changed in 2 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+248), AncestralStatesPanel.java (+334)