Lines of Code
[root]/src/dr/app/beagle/evomodel/treelikelihood
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 232 (100.0%) | 12747 (100.0%) | 54.9 |
| rambaut | 91 (39.2%) | 7393 (58.0%) | 81.2 |
| msuchard | 123 (53.0%) | 5042 (39.6%) | 40.9 |
| fbielejec | 15 (6.5%) | 300 (2.4%) | 20.0 |
| jheled | 1 (0.4%) | 11 (0.1%) | 11.0 |
| sibon.li | 2 (0.9%) | 1 (0.0%) | 0.5 |
Debugging flag to check for thread-level parallelization of likelihood evaluations
5 lines of code changed in 2 files:
Reconstructions from AncestralStateBeagleTreeLikelihood now follow useAmbiguities=true/false setting.
9 lines of code changed in 4 files:
no need for site count, this information can be parsed from partitions
3 lines of code changed in 1 file:
split the condition to avoid compiler warnings
24 lines of code changed in 2 files:
Added a flag to debug and profile epoch models in series; option should probably be elevated to a system property.
53 lines of code changed in 1 file:
The code as written requires at least eigenCount extra buffers to be able to guarantee to convolve matrices along a branch. Put a check in for this if convolution is being used. Also fixed a possible error where we run out of buffers midway through compiling a set of convolutions for a branch. Now if it knows it will not have enough buffers, it computes the current list and then continues, rather than waiting until it runs out.
36 lines of code changed in 1 file:
minor changes to Utils and partition element parser
1 lines of code changed in 1 file:
starting to work on reportable timers for update and convolve operations
64 lines of code changed in 2 files:
I think the convolution buffer issue is now fixed. Had to create a single extra reserve buffer that was used to free up the convolution list when all the other buffers had been used. Now runs - can't promise correctness so probably ought to be compared to older implementation.
59 lines of code changed in 1 file:
Towards making the spare buffer stack working. The convolveMatrices() was not completing the convolution operation that it had interrupted to free up some buffers. There is still a bug though - if this method runs out of buffers on the first convolution then it has nothing to free up. More thinking required.
8 lines of code changed in 1 file:
Can now set BEAGLE extra buffer count from system properties
20 lines of code changed in 2 files:
Some buffers not returned to pool; but error still persists in code.
14 lines of code changed in 1 file:
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.
2 lines of code changed in 1 file:
Standardizing output for markov jumps
55 lines of code changed in 2 files:
SubstitutionModelDelegate returns the root substitution model's frequencies.
2 lines of code changed in 1 file:
A better solution to the multithreading issue with trees that avoids thread syncs. The problem was only for empirical trees for which the branch lengths were known but not the node heights. Thus it had to compute the node heights when asked and this caused the thread conflict. Now the EmpiricalTrees object forces a node height calculation prior to evaluation.
2 lines of code changed in 1 file:
There was an issue when multiple BTL tried to get node heights from the same tree in different threads giving negative branch length errors. Synchronizing on the tree fixes this - might have other implications.
10 lines of code changed in 1 file:
Removing a debug exit()
5 lines of code changed in 1 file:
Fixed bug in SubstitutionModelDelegate; new and old BeagleTreeLikelihood now return same values.
15 lines of code changed in 1 file:
New BeagleTreeLikelihood was not updating correctly for a rescale after an underflow.
1 lines of code changed in 1 file:
Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.
124 lines of code changed in 2 files:
Old TL/ASTL/MJTL in parser list.
2 lines of code changed in 1 file:
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.
584 lines of code changed in 1 file:
Inserting the old ASTL back in to the deep inheritance chain of OTL. MJTL next.
533 lines of code changed in 1 file:
switching the simulator to new interfaces
31 lines of code changed in 2 files:
Renamed NewTreeLikelihood to BeagleTreeLikelihood
1282 lines of code changed in 5 files:
Renamed BeagleTreeLikelihood to OldBeagleTreeLikelihood
1322 lines of code changed in 5 files:
Updated copyright messages.
108 lines of code changed in 15 files:
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.
64 lines of code changed in 5 files:
Debuggin'
4 lines of code changed in 2 files:
Parsers for the new epoch implementations.
2 lines of code changed in 1 file:
Implemented eventuality where the delegate runs out of spare buffers - it now shunts of what it has so far and then continues.
99 lines of code changed in 1 file:
NewBeagleTreeLikelihood evaluation seems to work for Epoch models.
30 lines of code changed in 2 files:
Stuff
35 lines of code changed in 1 file:
Test main for NewBeagleTreeLikelihood
91 lines of code changed in 1 file:
Finished first implementation of new SubstitutionModelDelegate for BranchModels (which allow changing substitution model by branch).
1410 lines of code changed in 3 files:
Porting fixes from 1.7.3 back into the trunk
12 lines of code changed in 1 file:
Fixed more -1s in thread-pools and add limited dialogue support for SSE (which sidesteps known bug in SSE phylogeography)
7 lines of code changed in 1 file:
Reducing over-logging on underflows
1 lines of code changed in 1 file:
Added BEAGLE rescaling options to BEAST UI dialog. Added command line option to control the rescaling frequency in dynamic scaling.
18 lines of code changed in 1 file:
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