StatSVN - Directory src/dr/evomodel/newsubstmodel/

Lines of Code

src/dr/evomodel/newsubstmodel/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	36 (100.0%)	2029 (100.0%)	56.3
rambaut	25 (69.4%)	1908 (94.0%)	76.3
msuchard	6 (16.7%)	112 (5.5%)	18.6
alexei.drummond	5 (13.9%)	9 (0.4%)	1.8

Most Recent Commits

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.

0 lines of code changed in 8 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (del), DefaultEigenSystem.java (del), EigenDecomposition.java (del), EigenSystem.java (del), FrequencyModel.java (del), GeneralSubstitutionModel.java (del), HKY.java (del), SubstitutionModel.java (del)

msuchard 2009-03-16 11:26 Rev.: 1496

Added analytic eigendecomposition of HKY model for BEAGLE likelihood evaluator

112 lines of code changed in 6 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (new), EigenDecomposition.java (+1), HKY.java (new)

rambaut 2009-02-27 23:31 Rev.: 1461

Finished up the design of the newsubstmodel package. Not currently used. To be used by newtreelikelihood.

89 lines of code changed in 8 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (+20 -85), DefaultEigenSystem.java (new), EigenDecomposition.java (+60), EigenSystem.java (+1 -19), SubstitutionModel.java (+1 -12)

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

2 lines of code changed in 3 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (+1 -2), FrequencyModel.java (+1 -2)

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

7 lines of code changed in 2 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (+4 -2), FrequencyModel.java (+3 -1)

rambaut 2008-11-06 10:51 Rev.: 1282

Fixed a couple of build errors

5 lines of code changed in 2 files:

src/dr/evomodel/newsubstmodel: GeneralSubstitutionModel.java (+5 -6)

rambaut 2008-11-05 12:01 Rev.: 1279

Started work on an overhaul of SubstitutionModel. This is motivated by newtreelikelihood and the GPU work but is also aiming to simplify the very complex hierarchy in subtmodel. SubstitutionModel is the interface, BaseSubstitutionModel is a base for most models. HKY no longer uses the analytical form. The Eigen system is now provided as a plug in so better methods can be switched in.

1814 lines of code changed in 7 files:

src/dr/evomodel/newsubstmodel: BaseSubstitutionModel.java (+385), DefaultEigenSystem.java (+694), EigenSystem.java (+56), FrequencyModel.java (+249), GeneralSubstitutionModel.java (+200), HKY.java (+151), SubstitutionModel.java (+79)