StatSVN - Directory src/dr/app/beagle/tools/

Author	Changes	Lines of Code	Lines per Change
Totals	107 (100.0%)	5622 (100.0%)	52.5
fbielejec	91 (85.0%)	4981 (88.6%)	54.7
msuchard	6 (5.6%)	438 (7.8%)	73.0
rambaut	6 (5.6%)	113 (2.0%)	18.8
baele.guy@gmail.com	3 (2.8%)	86 (1.5%)	28.6
philippe.lemey@gmail.com	1 (0.9%)	4 (0.1%)	4.0

Most Recent Commits

fbielejec 2013-05-07 01:06 Rev.: 5632

adding demography models

4 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+4 -390)

fbielejec 2013-04-25 02:59 Rev.: 5607

take max TO value as site count to avoid exceptions being thrown

14 lines of code changed in 3 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+14 -6), Partition.java (-2)

fbielejec 2013-04-20 02:21 Rev.: 5601

updated buildfile

2 lines of code changed in 1 file:

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

fbielejec 2013-03-23 02:24 Rev.: 5526

working on new trees panel

0 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (-1)

fbielejec 2013-03-22 09:07 Rev.: 5522

removing siteCount from UI

163 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+163 -258)

fbielejec 2013-03-22 00:33 Rev.: 5521

removing siteCount from UI

2 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+1 -19), Partition.java (+1 -2)

fbielejec 2013-03-22 00:12 Rev.: 5520

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

12 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+12 -4)

fbielejec 2013-03-05 02:04 Rev.: 5468

working on XML import

1 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+1 -2)

fbielejec 2013-02-19 03:37 Rev.: 5430

cleaning up

2 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (-1), Partition.java (+2 -1)

fbielejec 2013-01-30 04:55 Rev.: 5357

simulator element generation

9 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+9 -9)

msuchard 2013-01-15 11:50 Rev.: 5323

Added getRootFrequencyModel to BranchModel interface. Consider deprecating getRootSubstitutionModel() as there are no substitutions occurring at the root. Also commented out @Override to interface functions since this is not Java 1.5 compatible.

9 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+9 -9)

fbielejec 2012-12-22 04:09 Rev.: 5297

working on XML generation

1 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+1 -1)

fbielejec 2012-11-21 06:50 Rev.: 5250

starting to work on XML generator

9 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+9 -9)

fbielejec 2012-11-16 21:15 Rev.: 5235

switching the simulator to new interfaces

334 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+330 -222), Partition.java (+4 -4)

fbielejec 2012-11-16 07:17 Rev.: 5234

preparing to switch to new interface

28 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+7 -7), Partition.java (+21 -18)

rambaut 2012-11-15 14:45 Rev.: 5230

Updated copyright messages.

75 lines of code changed in 4 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+25), CompleteHistorySimulator.java (new), Partition.java (+25)

fbielejec 2012-11-09 23:07 Rev.: 5220

commititng recent changes

2 lines of code changed in 1 file:

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

fbielejec 2012-10-09 02:46 Rev.: 5188

working on the UI

1 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+1 -1)

fbielejec 2012-10-07 02:44 Rev.: 5186

added padding with gaps for taxa unique for partitions

25 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+25 -8)

fbielejec 2012-09-28 21:06 Rev.: 5178

working on parallel implementation

133 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+133 -249)

fbielejec 2012-09-24 21:54 Rev.: 5175

changing to Callable

162 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+162 -45)

fbielejec 2012-09-19 00:53 Rev.: 5173

fixed setting ancestral sequence

53 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+52 -30), Partition.java (+1 -1)

fbielejec 2012-09-18 21:55 Rev.: 5172

partitions could be executed in parallel

140 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+138 -10), Partition.java (+2)

fbielejec 2012-09-18 19:31 Rev.: 5171

working on a parser for partitioned beagle sequence simulator

12 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+7 -5), Partition.java (+5 -12)

fbielejec 2012-09-18 02:30 Rev.: 5168

working on a parser for partitioned beagle sequence simulator

3 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+3 -2)

fbielejec 2012-09-18 02:13 Rev.: 5167

working on a parser for partitioned beagle sequence simulator

13 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+9 -9), Partition.java (+4)

fbielejec 2012-09-18 00:44 Rev.: 5166

changed the placement, starting to work on parser for partition element

65 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (-1), Partition.java (+65)

fbielejec 2012-09-18 00:14 Rev.: 5165

adding partitions to the Beagle simulator

110 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+110 -38)

fbielejec 2012-09-17 20:10 Rev.: 5163

adding partitions to the simulator

345 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+345 -339)

fbielejec 2012-09-07 02:06 Rev.: 5150

commiting parser changes

0 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (-23)

fbielejec 2012-07-18 12:25 Rev.: 5072

working on epoch tab

58 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+58 -9)

fbielejec 2012-06-25 05:40 Rev.: 5047

test method for codon model

20 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+20 -26)

fbielejec 2012-06-16 02:36 Rev.: 5037

cleaning code

0 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (-1)

fbielejec 2012-06-12 23:40 Rev.: 5033

simulate homogenous sequences

4 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+4)

fbielejec 2012-06-11 23:39 Rev.: 5032

cleaning code

29 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+29 -28)

fbielejec 2012-06-08 23:33 Rev.: 5029

branch rate issues

44 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+44 -40)

fbielejec 2012-06-08 00:53 Rev.: 5022

print warning from the parser

4 lines of code changed in 1 file:

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

fbielejec 2012-06-07 04:57 Rev.: 5021

code cleanup

36 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+36 -12)

fbielejec 2012-06-07 03:38 Rev.: 5020

make debugging easier

35 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+35 -51)

fbielejec 2012-06-07 02:35 Rev.: 5019

warn user he needs to supresses count statistics in case of codon models

6 lines of code changed in 1 file:

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

(48 more)

Directory src/dr/app/beagle/tools/

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