StatSVN - Directory src/dr/app/tools/

Author	Changes	Lines of Code	Lines per Change
Totals	384 (100.0%)	31017 (100.0%)	80.7
rambaut	172 (44.8%)	11744 (37.9%)	68.2
msuchard	44 (11.5%)	4807 (15.5%)	109.2
philippe.lemey@gmail.com	29 (7.6%)	3886 (12.5%)	134.0
alexei.drummond	25 (6.5%)	3771 (12.2%)	150.8
sibon.li	14 (3.6%)	2555 (8.2%)	182.5
dong.w.xie	44 (11.5%)	2458 (7.9%)	55.8
Sibon.Li@gmail.com	16 (4.2%)	1065 (3.4%)	66.5
jheled	29 (7.6%)	497 (1.6%)	17.1
jheled@gmail.com	2 (0.5%)	129 (0.4%)	64.5
baele.guy@gmail.com	4 (1.0%)	78 (0.3%)	19.5
Michael.DefoinPLatel	1 (0.3%)	12 (0.0%)	12.0
dong.w.xie@gmail.com	2 (0.5%)	9 (0.0%)	4.5
fbielejec	2 (0.5%)	6 (0.0%)	3.0

Most Recent Commits

baele.guy@gmail.com 2013-04-10 02:01 Rev.: 5574

Then LG model can also be used in the ancestral sequence annotator.

7 lines of code changed in 2 files:

src/dr/app/tools: AncestralSequenceAnnotator.java (new)

fbielejec 2013-03-22 00:10 Rev.: 5519

no need for site count, this information can be parsed from partitions

6 lines of code changed in 2 files:

src/dr/app/tools: LogCombiner.java (+6)

msuchard 2013-02-21 07:13 Rev.: 5443

Porting typo fix from 1.7

6 lines of code changed in 2 files:

src/dr/app/tools: TreeAnnotator.java (+6 -6)

jheled@gmail.com 2012-12-23 12:48 Rev.: 5299

Add '-heights ca' option to set heights which do not suffer from the "negative branches" problem. citation later ....

123 lines of code changed in 1 file:

src/dr/app/tools: TreeAnnotator.java (+123 -6)

rambaut 2012-11-15 14:41 Rev.: 5229

Branch specific substitution models now working. NewTreeLikelihood will replace BeagleTreeLikelihood in a future commit. AncestralStateTL and MarkovJumpsTL now descend from NewTreeLikelihood. EpochBranchModel uses a different XML format from EpochBranchSubstitutionModel (now depreciated). Also implemented a branch-specific substitution model.

2 lines of code changed in 1 file:

src/dr/app/tools: AncestralSequenceAnnotator.java (+2 -2)

sibon.li 2012-06-29 12:29 Rev.: 5058

Deleted a non-essential tool that I wrote.

0 lines of code changed in 1 file:

src/dr/app/tools: CompareBAliPhyToIndelible.java (del)

sibon.li 2012-05-04 10:46 Rev.: 4935

Fixed AncestralSequenceAnnotator to use KALIGN instead of CLUSTAL (much faster)

17 lines of code changed in 1 file:

src/dr/app/tools: AncestralSequenceAnnotator.java (+17 -3)

jheled@gmail.com 2012-04-26 18:26 Rev.: 4932

A terrible hack which disables 2d HPD for the dmv attribute (by name)

6 lines of code changed in 1 file:

src/dr/app/tools: TreeAnnotator.java (+6 -2)

baele.guy@gmail.com 2012-03-27 01:08 Rev.: 4893

Added an XML parser for MixtureModelLogAnalyser.

71 lines of code changed in 2 files:

src/dr/app/tools: MixtureModelLogAnalyser.java (+71 -3)

rambaut 2012-03-01 22:09 Rev.: 4744

Fixed some issues with LogCombiner that had been introduced in v1.7. Thanks to Matthew Hall for suggesting code fixes. Needs testing.

70 lines of code changed in 3 files:

src/dr/app/tools: LogCombiner.java (+67 -23), LogCombinerDialog.java (new)

sibon.li 2012-02-28 12:09 Rev.: 4743

Correction, parsers pending updates to other files. Currently commented out

331 lines of code changed in 2 files:

src/dr/app/tools: AncestralSequenceAnnotator.java (+19 -37), CompareBAliPhyToIndelible.java (new 312)

dong.w.xie@gmail.com 2012-02-21 15:23 Rev.: 4721

trunk: merge the change of BEAST parser doc

9 lines of code changed in 2 files:

src/dr/app/tools: BeastParserDoc.java (+9 -5)

rambaut 2011-12-21 19:33 Rev.: 4557

Fix for Issue 88: a check that the resampling frequency is a multiple of the original sampling frequency.

11 lines of code changed in 1 file:

src/dr/app/tools: LogCombiner.java (+11 -2)

sibon.li 2011-12-08 11:39 Rev.: 4525

Improved presentation for AncestralSequenceAnnotator and GetAncestralSequenceFromSplitTrait

14 lines of code changed in 3 files:

src/dr/app/tools: AncestralSequenceAnnotator.java (+7 -3), GetAncestralSequenceFromSplitTrait.java (+7 -2)

rambaut 2011-11-16 05:20 Rev.: 4435

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

1 lines of code changed in 1 file:

src/dr/app/tools: AncestralSequenceAnnotator.java (+1)

dong.w.xie 2011-09-15 17:18 Rev.: 4315

trunk: update my tool with rescale height in starting tree.

14 lines of code changed in 2 files:

src/dr/app/tools: GenerateRelaxedClockXMLByData.java (new)

dong.w.xie 2011-09-14 17:26 Rev.: 4313

trunk: update my tool

84 lines of code changed in 1 file:

src/dr/app/tools: GenerateRelaxedClockXMLByData.java (+84 -44)

dong.w.xie 2011-09-14 11:14

trunk: rename a tool to generate relaxed clock xml by given data

343 lines of code changed in 3 files:

src/dr/app/tools: GenerateRelaxedClockXMLByData.java (+338), beatBattiEtAl.java (del)

dong.w.xie 2011-09-13 17:31 Rev.: 4308

trunk: create program to beat Battistuzzi et al who are slandering BEAST

0 lines of code changed in 1 file:

src/dr/app/tools: beatBattiEtAl.java (new)

rambaut 2011-08-19 00:53 Rev.: 4201

Work on discrete Antigenic MDS

45 lines of code changed in 2 files:

src/dr/app/tools: AntigenicPlotter.java (new)

sibon.li 2011-08-12 11:51 Rev.: 4183

Fixed a bug that made AncestralSequenceAnnotator not work properly for BAli-Phy files. Now provided it an option to take in BEAST input tree files

498 lines of code changed in 1 file:

src/dr/app/tools: AncestralSequenceAnnotator.java (+498 -239)

sibon.li 2011-08-12 11:17 Rev.: 4182

Work in progress on AncestralSequenceAnnotator, will be fixed by end of today

239 lines of code changed in 1 file:

src/dr/app/tools: AncestralSequenceAnnotator.java (+239 -498)

rambaut 2011-08-10 23:50 Rev.: 4179

Some refactoring of MatrixParameter (renamed getNumberOfParameters to getParameterCount). Also allowed MultivariateNormalPrior take a matrix parameter and assume the individual parameters within this represent independent draws from the MVN.

143 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+143 -2)

rambaut 2011-08-10 04:21 Rev.: 4172

Discrete AG model...

45 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+45 -1)

rambaut 2011-08-09 22:39 Rev.: 4171

First attempt at a discrete antigenic cluster classifier.

46 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+46 -4)

rambaut 2011-08-05 14:22 Rev.: 4159

Fix for AG plotter

1 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+1)

rambaut 2011-08-05 04:24 Rev.: 4156

6 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+6)

rambaut 2011-08-03 05:05 Rev.: 4152

Some additions to the tools for plotting antigenic maps.

85 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+85 -11)

rambaut 2011-08-02 19:00 Rev.: 4151

Improvements and tweaks to Antigenic MDS

26 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+26 -26)

rambaut 2011-08-01 21:27 Rev.: 4149

Improvements and tweaks to Antigenic MDS

86 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+86 -35)

rambaut 2011-07-31 19:44 Rev.: 4147

Seem to have got the Antigenic MDS working correctly with threshold assay values and replicate measurements.

78 lines of code changed in 1 file:

src/dr/app/tools: AntigenicPlotter.java (+78 -13)

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.

22 lines of code changed in 6 files:

src/dr/app/tools: LogAnalyser.java (new), LogCombiner.java (+8 -2), TreeAnnotator.java (+4), TreeLogAnalyser.java (new)

rambaut 2011-07-23 04:00 Rev.: 4116

uncommitting an erroneous revision

0 lines of code changed in 2 files:

src/dr/app/tools: SpliceBeastFiles.java (new)

dong.w.xie 2011-07-19 15:39 Rev.: 4113

update

148 lines of code changed in 2 files:

src/dr/app/tools: GetDateFromTree.java (new)

dong.w.xie 2011-07-15 17:17 Rev.: 4110

update my tool after bdss changed

43 lines of code changed in 1 file:

src/dr/app/tools: GetDateFromTree.java (+43 -32)

sibon.li 2011-07-15 12:41 Rev.: 4109

Created an app - GetAncestralSequenceFromSplitTrait, which does just that.

347 lines of code changed in 3 files:

src/dr/app/tools: GetAncestralSequenceFromSplitTrait.java (+339), MakeAncestralSequenceAnnotatedTree.java (new)

dong.w.xie 2011-07-14 16:44 Rev.: 4108

update my tool after bdss changed

4 lines of code changed in 1 file:

src/dr/app/tools: GetDateFromTree.java (+4 -4)

rambaut 2011-07-12 23:01 Rev.: 4107

Fixed an issue with JumpHistoryAnalyser not printing results.

15 lines of code changed in 2 files:

src/dr/app/tools: JumpHistoryAnalyser.java (new)

dong.w.xie 2011-07-12 18:19 Rev.: 4106

update my tool after bdss changed

15 lines of code changed in 1 file:

src/dr/app/tools: GetDateFromTree.java (+15 -15)

dong.w.xie 2011-07-08 14:53 Rev.: 4104

update my tool since BDSS changed

36 lines of code changed in 1 file:

src/dr/app/tools: GetDateFromTree.java (+36 -33)

(252 more)

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