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

Author	Changes	Lines of Code	Lines per Change
Totals	44 (100.0%)	759 (100.0%)	17.2
fbielejec	35 (79.5%)	541 (71.3%)	15.4
msuchard	4 (9.1%)	143 (18.8%)	35.7
rambaut	5 (11.4%)	75 (9.9%)	15.0

Most Recent Commits

fbielejec 2013-03-28 02:56 Rev.: 5549

starting to implement CLI

2 lines of code changed in 2 files:

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

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

removing siteCount from UI

2 lines of code changed in 3 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (new), PartitionParser.java (+1 -1)

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

removing siteCount from UI

0 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (-2)

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

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

18 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+18 -20)

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

simulator element generation

5 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+5 -5)

fbielejec 2013-01-29 03:57 Rev.: 5348

minor changes to Utils and partition element parser

1 lines of code changed in 1 file:

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

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

switching the simulator to new interfaces

7 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: PartitionParser.java (+7 -7)

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

Updated copyright messages.

75 lines of code changed in 4 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+25), CompleteHistorySimulatorParser.java (+25), PartitionParser.java (+25)

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

fixed setting ancestral sequence

5 lines of code changed in 2 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+3 -2), PartitionParser.java (+2 -2)

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

partitions could be executed in parallel

29 lines of code changed in 2 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+29 -2), PartitionParser.java (-4)

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

working on a parser for partitioned beagle sequence simulator

26 lines of code changed in 2 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+18 -6), PartitionParser.java (+8 -17)

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

working on a parser for partitioned beagle sequence simulator

17 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+17 -5)

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

working on a parser for partitioned beagle sequence simulator

150 lines of code changed in 2 files:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+8 -86), PartitionParser.java (+142 -2)

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

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

7 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: PartitionParser.java (+7)

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

adding partitions to the simulator

12 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+12 -9)

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

commiting parser changes

0 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (-4)

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

Porting fixes from 1.7.3 back into the trunk

0 lines of code changed in 1 file:

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

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

cleaning code

3 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+3 -3)

fbielejec 2012-06-16 02:32 Rev.: 5036

syntax rules in parser

24 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+24 -14)

fbielejec 2012-06-16 01:44 Rev.: 5035

print some logging messages

13 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+13 -1)

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

simulate homogenous sequences

31 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+31 -19)

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

print warning from the parser

9 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+9 -3)

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

make debugging easier

1 lines of code changed in 1 file:

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

fbielejec 2012-06-06 21:57 Rev.: 5016

set this method to return alignment only works well with all the conversion tools

7 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+7)

fbielejec 2012-06-02 22:35 Rev.: 5007

sanity check in parser

23 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+23 -3)

fbielejec 2012-05-21 23:45 Rev.: 4990

simplify the parser

3 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+3 -16)

fbielejec 2012-05-11 20:37 Rev.: 4953

working on parser

20 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+20 -7)

fbielejec 2012-05-08 04:16 Rev.: 4943

parser for beagle simulator

4 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+4 -2)

fbielejec 2012-05-06 23:25 Rev.: 4939

parser for beagle simulator

37 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+37 -38)

fbielejec 2012-05-06 23:14 Rev.: 4938

parser for beagle simulator

85 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: BeagleSequenceSimulatorParser.java (+85)

msuchard 2011-02-15 09:54 Rev.: 3797

Modified CompleteHistorySimulator to report alignment of external and internal nodes

7 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+7)

msuchard 2010-05-21 13:19 Rev.: 3178

Can now simulate sequences under a branch-specific substitution model; for example, different dN/dS per branch.

18 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+18 -1)

msuchard 2010-03-27 11:12 Rev.: 3078

Changing output options for CompleteHistorySimulator

6 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+6 -1)

msuchard 2010-03-25 13:02 Rev.: 3071

Can now simulate (and report) the complete history of any model in BEAST, most importantly codon models (with branch rate variation) and report the true number of synonymous and nonsynonymous mutations in a synthetic dataset.

112 lines of code changed in 1 file:

src/dr/app/beagle/tools/parsers: CompleteHistorySimulatorParser.java (+112)

Directory src/dr/app/beagle/tools/parsers/

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