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

Lines of Code

src/dr/evomodel/beagle/parsers/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	35 (100.0%)	796 (100.0%)	22.7
rambaut	19 (54.3%)	681 (85.6%)	35.8
msuchard	8 (22.9%)	95 (11.9%)	11.8
jheled	8 (22.9%)	20 (2.5%)	2.5

Most Recent Commits

rambaut 2009-08-04 03:47 Rev.: 2009

Moving BEAGLE/BEAST out of the main package into dr.app. This will allow us to deploy the jar file separately from BEAST.

0 lines of code changed in 8 files:

src/dr/evomodel/beagle/parsers: CompoundLikelihoodParser.java (del), FrequencyModelParser.java (del), GTRParser.java (del), GY94CodonModelParser.java (del), GammaSiteModelParser.java (del), HKYParser.java (del), MarkovModulatedGY94CodonModelParser.java (del), TreeLikelihoodParser.java (del)

rambaut 2009-07-31 07:14 Rev.: 1956

The JNIWrapper now seems to work - the 'TinyTest' in BeagleFactory now reports:

BEAGLE library loaded
BEAGLE bootstrap: CPU - Success
logL = -1574.6362268149937 (PAUP logL = -1574.63623)

6 lines of code changed in 2 files:

src/dr/evomodel/beagle/parsers: TreeLikelihoodParser.java (+6 -4)

jheled 2009-06-23 07:20 Rev.: 1794

automatic idea changes, change type return type of getChild

3 lines of code changed in 4 files:

src/dr/evomodel/beagle/parsers: GTRParser.java (+1 -1), GammaSiteModelParser.java (+2 -2)

jheled 2009-05-06 10:31 Rev.: 1676

More of the same - string constants

3 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: TreeLikelihoodParser.java (+3 -2)

jheled 2009-05-06 09:55 Rev.: 1674

more string constants

7 lines of code changed in 2 files:

src/dr/evomodel/beagle/parsers: GTRParser.java (+3 -5), GammaSiteModelParser.java (+4 -3)

msuchard 2009-04-14 12:06 Rev.: 1571

Debugging hidden codon models and need to test on larger computer system.

12 lines of code changed in 2 files:

src/dr/evomodel/beagle/parsers: MarkovModulatedGY94CodonModelParser.java (new)

msuchard 2009-04-07 21:19 Rev.: 1536

Added DuplicatedParameter for symmetric rates and assymetric indicators. Added ColtEigenSystem to compare numerical stability in beagle package.

3 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: MarkovModulatedGY94CodonModelParser.java (+3 -1)

msuchard 2009-04-06 10:56 Rev.: 1534

Working on path sampling final integration code; some fixes in CompoundSymmetricMatrix to enable MH proposals and retain positive definiteness.

3 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: MarkovModulatedGY94CodonModelParser.java (+3 -1)

msuchard 2009-03-31 12:18 Rev.: 1528

Removed NativeSubstitutionModel (old, defunct code for GPU) and started working on a covarion-like codon models. Here come the 128 and 196 state models!

64 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: MarkovModulatedGY94CodonModelParser.java (+64)

jheled 2009-03-27 09:51 Rev.: 1518

ongoing sp tree development

7 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: TreeLikelihoodParser.java (+7 -9)

msuchard 2009-03-25 07:34 Rev.: 1515

Changed BEAGLE tree parser so user can specify a precision preference instead of requirement. Removed some redundant code (static names)

8 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: TreeLikelihoodParser.java (+8 -4)

rambaut 2009-03-25 06:23 Rev.: 1514

Goldman Yang 94 model ported to beagle

109 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: GY94CodonModelParser.java (new 109)

msuchard 2009-03-25 02:03 Rev.: 1512

The CUDA version of BEAGLE requires that each getLogLikelihood() be called from the same thread each time (known incompatibility); CompoundLikelihood uses a pool, while ThreadedCompoundLikelihood has static allocation. Fixed missing files in build_development.xml

5 lines of code changed in 2 files:

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

rambaut 2009-03-24 23:20 Rev.: 1511

Created a BEAGLE specific parser for <likelihood> that puts child TreeLikelihoods into threads.

77 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: CompoundLikelihoodParser.java (+77)

rambaut 2009-03-20 05:08 Rev.: 1504

Towards a working beagle library

123 lines of code changed in 1 file:

src/dr/evomodel/beagle/parsers: GTRParser.java (+123)

rambaut 2009-03-19 05:23 Rev.: 1502

Towards a working beagle library

26 lines of code changed in 2 files:

src/dr/evomodel/beagle/parsers: GammaSiteModelParser.java (+13 -2), TreeLikelihoodParser.java (+13 -3)

rambaut 2009-03-19 02:15 Rev.: 1501

I have moved all the new stuff for the 'BEAGLE' library into its own package. I am producing a set of parsers that override the default ones to use the new classes. I envisage that at some point we will want to move to the new SubstModel hierarchy as it is much cleaner. But to avoid breaking anything whilst this develops, I am compartmentalizing them.

340 lines of code changed in 4 files:

src/dr/evomodel/beagle/parsers: FrequencyModelParser.java (new 110), GammaSiteModelParser.java (+101), HKYParser.java (new 59), TreeLikelihoodParser.java (+70)