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

Author	Changes	Lines of Code	Lines per Change
Totals	273 (100.0%)	6870 (100.0%)	25.1
rambaut	136 (49.8%)	3540 (51.5%)	26.0
msuchard	99 (36.3%)	2938 (42.8%)	29.6
fbielejec	22 (8.1%)	313 (4.6%)	14.2
jheled	6 (2.2%)	44 (0.6%)	7.3
dong.w.xie	5 (1.8%)	16 (0.2%)	3.2
philippe.lemey@gmail.com	2 (0.7%)	9 (0.1%)	4.5
alexander.alekseyenko	1 (0.4%)	8 (0.1%)	8.0
baele.guy@gmail.com	2 (0.7%)	2 (0.0%)	1.0

Most Recent Commits

rambaut 2013-05-13 04:17 Rev.: 5648

Auto sets the size of the MarkovJump count register

27 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: MarkovJumpsTreeLikelihoodParser.java (new)

msuchard 2013-04-16 07:24 Rev.: 5592

Changing default behaviour to original.

3 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: ComplexSubstitutionModelParser.java (+3 -3)

msuchard 2013-04-16 07:21 Rev.: 5591

Passing eigendecomposition condition number checking up to XML level.

25 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: ComplexSubstitutionModelParser.java (+25 -7)

baele.guy@gmail.com 2013-04-10 01:48 Rev.: 5572

Allow the BEAGLE parser to use the LG amino acid model.

2 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: EmpiricalAminoAcidModelParser.java (+2)

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

working on XML import

13 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: EpochBranchModelParser.java (+13 -10)

msuchard 2013-01-15 12:01 Rev.: 5324

Can pass arbitrary root FrequencyModel to HomogeneousBranchModel.

1 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: BeagleTreeLikelihoodParser.java (new)

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.

13 lines of code changed in 4 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (new), BeagleTreeLikelihoodParser.java (+7 -3), MarkovJumpsTreeLikelihoodParser.java (+3 -1)

msuchard 2012-12-21 11:28 Rev.: 5293

Standardizing output for markov jumps

8 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: MarkovJumpsTreeLikelihoodParser.java (+8 -5)

msuchard 2012-11-28 10:34 Rev.: 5260

Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.

249 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: ALSTreeLikelihoodParser.java (new 140), MutationDeathModelParser.java (new 109)

rambaut 2012-11-27 09:43 Rev.: 5256

Forgot to change the parser name.

1 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: OldMarkovJumpsTreeLikelihoodParser.java (new)

rambaut 2012-11-27 09:33 Rev.: 5255

Inserting the old MJTL back in to the deep inheritance chain of OTL. For testing purposes only. If it has a line through it - it is going to go at some point.

231 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: OldMarkovJumpsTreeLikelihoodParser.java (+231)

rambaut 2012-11-27 09:23 Rev.: 5254

Inserting the old ASTL back in to the deep inheritance chain of OTL. MJTL next.

150 lines of code changed in 3 files:

src/dr/app/beagle/evomodel/parsers: OldAncestralStateTreeLikelihoodParser.java (new 148), OldTreeLikelihoodParser.java (new)

rambaut 2012-11-22 01:29 Rev.: 5251

Cleaned up the format of the complete history logging. Now has {SITE,{TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

1 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: CodonPartitionedRobustCountingParser.java (new)

rambaut 2012-11-16 00:57 Rev.: 5233

Final swapping of the parser names

240 lines of code changed in 3 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+1 -1), BeagleTreeLikelihoodParser.java (+239), NewTreeLikelihoodParser.java (del)

rambaut 2012-11-16 00:54 Rev.: 5232

Renamed NewTreeLikelihood to BeagleTreeLikelihood

254 lines of code changed in 9 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+4 -4), GammaSiteModelParser.java (+1 -1), MarkovJumpsTreeLikelihoodParser.java (+4 -4), NewTreeLikelihoodParser.java (new 5), OldTreeLikelihoodParser.java (+238), StarTreeLikelihoodParser.java (new), TreeLikelihoodParser.java (del)

rambaut 2012-11-16 00:50 Rev.: 5231

Renamed BeagleTreeLikelihood to OldBeagleTreeLikelihood

25 lines of code changed in 7 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+1 -5), MarkovJumpsTreeLikelihoodParser.java (-3), NewTreeLikelihoodParser.java (+1 -1), StarTreeLikelihoodParser.java (+2 -2), TipStateSwapOperatorParser.java (-1), TreeLikelihoodParser.java (new 21)

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

Updated copyright messages.

539 lines of code changed in 57 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+1 -1), BeagleOperationParser.java (+1 -1), BeagleSubstitutionEpochModelParser.java (new), BinarySubstitutionModelParser.java (+1 -1), BranchSpecificBranchModelParser.java (+1 -1), CodonPartitionedRobustCountingParser.java (+1 -1), CompleteHistoryLoggerParser.java (+1 -1), ComplexSubstitutionModelParser.java (+25), CompoundLikelihoodParser.java (+25), DnDsLoggerParser.java (+25), EmpiricalAminoAcidModelParser.java (+1 -1), EmpiricalCodonModelParser.java (new), EpochBranchModelParser.java (+25), ExternalInternalBranchSubstitutionModelParser.java (new), FrequencyModelParser.java (new), GLMSubstitutionModelParser.java (+25), GTRParser.java (new), GY94CodonModelParser.java (new), GammaSiteModelParser.java (+1 -1), GeneralSubstitutionModelParser.java (+25), HKYParser.java (new), HistoryFilterParser.java (new), MarkovJumpsLikelihoodLoggerParser.java (+25), MarkovJumpsTreeLikelihoodParser.java (+25), MarkovModulatedGY94CodonModelParser.java (+25), MarkovModulatedHiddenClassRewardParser.java (+25), MarkovModulatedSubstitutionModelParser.java (+25), NewTreeLikelihoodParser.java (+2 -2), PCACodonModelParser.java (+25), StarTreeLikelihoodParser.java (+1 -1), StratifiedTraitLoggerParser.java (+25), TN93Parser.java (new), TipStateSwapOperatorParser.java (+25), TreeLikelihoodParser.java (+1 -1)

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.

199 lines of code changed in 8 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+8 -29), BeagleSubstitutionEpochModelParser.java (+2), BranchSpecificBranchModelParser.java (+163), ExternalInternalBranchSubstitutionModelParser.java (+3), GammaSiteModelParser.java (+1 -1), MarkovJumpsTreeLikelihoodParser.java (+8 -13), NewTreeLikelihoodParser.java (+11 -5), TreeLikelihoodParser.java (+3 -1)

rambaut 2012-11-10 05:19 Rev.: 5227

Debuggin'

16 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: EpochBranchModelParser.java (+16 -14)

rambaut 2012-11-10 03:30 Rev.: 5226

Parsers for the new epoch implementations.

362 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: EpochBranchModelParser.java (+128), NewTreeLikelihoodParser.java (+234)

msuchard 2012-10-07 05:18 Rev.: 5187

Improved parsing for CPRC.

10 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: CodonPartitionedRobustCountingParser.java (+10)

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

commiting parser changes

9 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (-2), GammaSiteModelParser.java (+9 -4)

rambaut 2012-08-15 22:34 Rev.: 5133

Porting changes 5131 and 5132 from 1.7 branch.

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: TreeLikelihoodParser.java (+1 -1)

rambaut 2012-08-09 01:27 Rev.: 5118

Port from 1.7

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: GammaSiteModelParser.java (+1 -1)

rambaut 2012-08-08 22:32 Rev.: 5113

Porting changes from branch 1.7 r5111 and r5112

37 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: GammaSiteModelParser.java (+37 -42)

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

Porting fixes from 1.7.3 back into the trunk

50 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+25), GammaSiteModelParser.java (+25)

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

cleaning code

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+1 -1)

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

simulate homogenous sequences

5 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+5)

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

cleaning code

0 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (-2)

fbielejec 2012-06-11 23:21 Rev.: 5031

safeguard from a null pointer exception if branch rate model is not specified

10 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+10 -5)

fbielejec 2012-06-11 23:04 Rev.: 5030

throw meaningful xml parse exceptions

14 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+14 -10)

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

branch rate issues

9 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+9 -1)

fbielejec 2012-05-23 22:18 Rev.: 4997

working on parser for epoch ancestral state reco

3 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+3 -3)

fbielejec 2012-05-23 22:13 Rev.: 4996

working on epoch ancestral state reco

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+1 -1)

fbielejec 2012-05-23 21:51 Rev.: 4995

working on epoch ancestral state reco

38 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: AncestralStateTreeLikelihoodParser.java (+38 -12)

fbielejec 2012-05-22 02:05

general parser

13 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: GammaSiteModelParser.java (+3 -6)

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

simplify the parser

19 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: GammaSiteModelParser.java (+19 -23)

msuchard 2012-05-15 20:51 Rev.: 4961

Starting work on a complete history filter

121 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/parsers: CompleteHistoryLoggerParser.java (+33 -3), HistoryFilterParser.java (+88)

msuchard 2012-05-15 20:50 Rev.: 4960

Expanding robust counting dNdS to consider complete histories

28 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: CodonPartitionedRobustCountingParser.java (+28)

msuchard 2012-03-08 07:09 Rev.: 4789

Implemented TN93 under BEAGLE.

84 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: TN93Parser.java (+84)

(94 more)

Directory src/dr/app/beagle/evomodel/parsers/

Lines of Code

Developers

Most Recent Commits