Lines of Code
[root]/src/test/dr/evomodel/arg/operators
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 14 (100.0%) | 251 (100.0%) | 17.9 |
| msuchard | 2 (14.3%) | 214 (85.3%) | 107.0 |
| dong.w.xie | 4 (28.6%) | 11 (4.4%) | 2.7 |
| rambaut | 3 (21.4%) | 10 (4.0%) | 3.3 |
| alexei.drummond | 1 (7.1%) | 6 (2.4%) | 6.0 |
| jheled | 2 (14.3%) | 5 (2.0%) | 2.5 |
| bloomquist | 2 (14.3%) | 5 (2.0%) | 2.5 |
Trunk refactoring: organize tree and treelikelihood parsers.
6 lines of code changed in 2 files:
Trunk: hide the confused constructor from MCMC.
1 lines of code changed in 1 file:
Implemented checks to see that all models, likelihood and parameters are being controlled by the MCMC. The checks are made in MCMCParser but the warnings are currently commented out.
8 lines of code changed in 1 file:
Replaced 'preBurnin' with an autoOptimizeDelay (coercionDelay). The rationale for this is that the preBurnin meant that the initial state was not in the log files, it was unecessary and it cause a small inefficiency as the JIT compiler re-optimized after the preburnin chain had finished. We also didn't see warning messages until after the pre-burnin period. There is a new attribute to the MCMC parser - autoOptimizeDelay (to which the old preBurnin attribute now maps so old XML will run).
1 lines of code changed in 1 file:
code police
3 lines of code changed in 1 file:
A small improvment in reducing usage of litteral string constants.
Each constant should be defined in one place and referenced elsewhere.
The best place I found is in the various parsers. This may be wrong but now moving it elsewhere is a simple matter.
2 lines of code changed in 1 file:
Correct JUnit Test to make BEAST complied successfully.
4 lines of code changed in 1 file:
Commented out part that didn't build correctly. Sorry for the trouble.
4 lines of code changed in 1 file:
Fixed bug.
1 lines of code changed in 1 file:
Implemented a dynamic parser loading system. BeastParser loads the 'core' set of parsers and then looks in a properties file for additional classes to load. See 'release_parsers.properties' for the full list. If the class itself is an XMLObjectParser then an instance is created. If it isn't then the system looks for static fields which are instances of XMLObjectParser and adds these.
I have created two lists - 'development_parsers.properties' which contains all the extra parsers that anyone has created. When developing, add your parsers here. 'release_parsers.properties' contains parsers that will be included in the next release of BEAST. If you don't want your stuff in the release version, please remove them from here.
This is a first stage towards a 'plug-in' system. I suggest that we create a new top level package called 'plugins' that people can create packages in. These would contain all the classes for a particular system (possibly in subpackages that mirror the beast hierarchy) and a parsers.properties file that specifies all the parsers. BEAST would then iterate through these packages and pick up the parsers.
1 lines of code changed in 1 file:
Added removeParameter functionality to CompoundParameter to faciliate removal of ARGCompoundParameter and VariableSizeCompoundParameter classes to integrate the ARG code more fully. A small success for simplification against the growing tide of class proliferation!
6 lines of code changed in 1 file:
Fixed ARGAddRemoveOperatorTest so that it actually passes :-)!
7 lines of code changed in 1 file:
Added a flat prior over ARG space.
207 lines of code changed in 1 file: