StatSVN - Directory src/dr/app/beauti/

[root]/src/dr/app/beauti

alignmentviewer (17 files, 1061 lines)

ancestralStatesPanel (2 files, 8 lines)

clockModelsPanel (3 files, 2 lines)

components (1 files, 13 lines)

ancestralstates (3 files, 79 lines)

continuous (4 files, 54 lines)

discrete (4 files, 38 lines)

dnds (0 files, 0 lines)

dollo (3 files, 68 lines)

hpm (4 files, 38 lines)

sequenceerror (3 files, 36 lines)

tipdatesampling (3 files, 63 lines)

datapanel (7 files, 110 lines)

enumTypes (0 files, 0 lines)

generator (17 files, 92 lines)

mcmcpanel (1 files, 0 lines)

modelsPanel (0 files, 0 lines)

operatorspanel (1 files, 0 lines)

options (25 files, 133 lines)

priorsPanel (8 files, 52 lines)

siteModelsPanel (3 files, -2 lines)

taxonsetspanel (2 files, 25 lines)

tipdatepanel (4 files, 125 lines)

traitspanel (5 files, 55 lines)

treespanel (7 files, 1 lines)

types (19 files, 409 lines)

util (11 files, 168 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	582 (100.0%)	38370 (100.0%)	65.9
rambaut	288 (49.5%)	29175 (76.0%)	101.3
alexei.drummond	88 (15.1%)	4876 (12.7%)	55.4
dong.w.xie	146 (25.1%)	2427 (6.3%)	16.6
Michael.DefoinPLatel	8 (1.4%)	971 (2.5%)	121.3
jheled	45 (7.7%)	902 (2.4%)	20.0
sidneym	2 (0.3%)	10 (0.0%)	5.0
msuchard	4 (0.7%)	8 (0.0%)	2.0
dong.w.xie@gmail.com	1 (0.2%)	1 (0.0%)	1.0

Most Recent Commits

rambaut 2013-01-31 04:42 Rev.: 5367

Porting some fixes from 1.7 branch

10 lines of code changed in 2 files:

src/dr/app/beauti: BeautiFrame.java (+10 -2)

rambaut 2012-08-08 21:31 Rev.: 5110

Porting changes from branch 1.7 r5109

10 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+10 -27)

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

Porting fixes from 1.7.3 back into the trunk

26 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+26 -16)

dong.w.xie@gmail.com 2012-02-02 17:10 Rev.: 4630

change confused method name and fix prefix bug inside mergePatterns

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1 -2)

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.

140 lines of code changed in 7 files:

src/dr/app/beauti: BeautiApp.java (+12 -12), BeautiDefaultFileMenuFactory.java (+14 -13), BeautiFrame.java (+93 -71), BeautiMacFileMenuFactory.java (new)

dong.w.xie 2011-12-15 15:13 Rev.: 4546

trunk:solve Issue 565: hasIdenticalTaxa(List<AbstractPartitionData> partitionDataList) gives wrong boolean

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1 -1)

dong.w.xie 2011-12-07 10:58 Rev.: 4519

trunk:solve Issue 559: BEAUti throws exception if adding any additional partition with different taxa when already having data partitions

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1)

dong.w.xie 2011-12-07 10:45 Rev.: 4517

trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1 -1)

rambaut 2011-12-04 10:43 Rev.: 4501

Added a dialog box to rename a partition if it has the same name as an existing partition.

15 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+15 -11)

rambaut 2011-11-24 21:41 Rev.: 4484

Merged my fix for error when ENABLE_ANCESTRAL_STATES = false.

14 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+14 -13)

dong.w.xie 2011-11-23 14:22 Rev.: 4479

trunk:solve Issue 547: out of boundary if ENABLE_ANCESTRAL_STATES = false;

3 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+3 -4)

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

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

2 lines of code changed in 1 file:

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

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

Removed a few redundant imports

0 lines of code changed in 1 file:

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

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

Starting to rebuild generation of robust counting.

8 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+8 -6)

rambaut 2011-11-20 22:00 Rev.: 4458

Added tool tips for all the tabs in BEAUti. The tabs are also now disabled until data is loaded to focus the user on what to do first.

54 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+54 -5)

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.

17 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+17 -2)

rambaut 2011-11-17 09:49 Rev.: 4441

BeastGenerator's check function now throws GeneratorExceptions (rather than IllegalArgumentException). As a bonus this exception can specify the name of a Tab to switch to as an aid to the user to fix the issue.

32 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+32 -12)

dong.w.xie 2011-11-01 14:03 Rev.: 4381

trunk: correct the bug created by previous fixes.

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1)

dong.w.xie 2011-11-01 13:00 Rev.: 4379

trunk: solve Issue 526: recover the function to allow different taxa in BEAUti

5 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+5)

dong.w.xie 2011-11-01 12:32 Rev.: 4378

trunk: solve Issue 525: BEAUti should link the trees for multi-partitions by default

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1 -5)

rambaut 2011-10-15 09:13 Rev.: 4359

Can still edit a trait called 'species' if it is not currently being used for *BEAST

0 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (-4)

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?

10 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+10)

dong.w.xie 2011-10-11 18:20 Rev.: 4349

trunk: initial dev for Species Set panel when *BEAST calibration that is only allowed on species tree

20 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+20 -2)

rambaut 2011-10-10 21:36 Rev.: 4347

Refined the interface for turning on and off *BEAST. 'species' is not a special trait until *BEAST is turned on.

25 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+25 -6)

dong.w.xie 2011-10-10 14:24 Rev.: 4346

trunk: solve Issue 510: BEAUti uncheck *BEAST but cannot reverse to normal BEAST properly

11 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+11 -7)

msuchard 2011-09-22 10:36 Rev.: 4330

Fixed integer overflow (when prior sampling) and mixed-math in RandomWalkOperator

2 lines of code changed in 1 file:

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

rambaut 2011-09-16 21:42 Rev.: 4320

Line wrapping of message

4 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+4 -3)

rambaut 2011-09-16 21:29 Rev.: 4319

Improvements to the StarBEAST interface and how it asks for a species designation.

5 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+5 -1)

rambaut 2011-09-16 04:23 Rev.: 4317

Fixing up discrete/continuous trait generation..

3 lines of code changed in 1 file:

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

rambaut 2011-09-16 03:04 Rev.: 4316

Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.

7 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+7 -2)

rambaut 2011-09-09 21:51 Rev.: 4300

Adding continuous traits in BEAUti

1 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+1 -1)

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

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

2 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+2)

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

0 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (-2)

rambaut 2011-07-28 02:40 Rev.: 4125

Fix for issue 464: http://code.google.com/p/beast-mcmc/issues/detail?id=464

Set the default locale to US at the beginning of the main() of each of the applications. We don't currently do any localization and the use of a comma as a decimal in some places but not other for those languages that use this was causing major incompatibilities.

4 lines of code changed in 1 file:

src/dr/app/beauti: BeautiApp.java (+4)

msuchard 2011-07-01 15:37 Rev.: 4089

Connecting DnDsComponent into BEAUti GUI button

2 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+2)

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: BeautiFrame.java (+1 -1)

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

Intermediate work on implementing Hierarchical Phylogenetics Models in BEAUti

2 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+2)

dong.w.xie 2011-03-16 09:53 Rev.: 3876

Trunk: solve Issue 442: BEAUti: taxon set table does not refresh after changing tree model.

6 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (+6 -6)

dong.w.xie 2011-03-14 16:27 Rev.: 3872

Trunk: more work on micro-sat data in BEAUti.

0 lines of code changed in 1 file:

src/dr/app/beauti: BeautiFrame.java (-5)

dong.w.xie 2011-03-10 12:11 Rev.: 3863

Trunk: make micro-satellite file successfully loaded in BEAUti data panel.
Start to use jdk1.6 code.

3 lines of code changed in 1 file:

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

(270 more)

Directory src/dr/app/beauti/

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