[root]/src/dr/app/beauti/components
ancestralstates
(3 files, 79 lines)
continuous
(4 files, 54 lines)
discrete
(4 files, 38 lines)
dnds
(0 files, 0 lines)
dollo
(3 files, 68 lines)
hpm
(4 files, 38 lines)
sequenceerror
(3 files, 36 lines)
tipdatesampling
(3 files, 63 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 75 (100.0%) | 1282 (100.0%) | 17.0 |
| rambaut | 44 (58.7%) | 1171 (91.3%) | 26.6 |
| jheled | 5 (6.7%) | 57 (4.4%) | 11.4 |
| dong.w.xie | 26 (34.7%) | 54 (4.2%) | 2.0 |
Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.
0 lines of code changed in 9 files:
Various bits
5 lines of code changed in 1 file:
Some serious cleaning up of how priors are specified. This allows appropriate prior choices for different 'flavours' of parameters (non-negative, zero-one interval, discrete, HPM, CMTC rates). Truncation of the the prior is now a switch and bounds so can be applied to any prior (although the UI is not in place for this yet).
12 lines of code changed in 2 files:
A tweak to the previous fix for issue 436 - ensure that the sequence error model doesn't generate if there is not exactly 1 data partition.
18 lines of code changed in 1 file:
Trunk: more for Issue 409: BEAUti should explicitly generate uniform priors.
11 lines of code changed in 2 files:
This is a very large commit. It addresses some architectural issues in BEAUti that were going to hinder implementation of continuous traits.
The main thing it does is to isolate creating and importing traits from creating partitions on those traits. A button on the data panel explicitly specifies that a trait should be used as a data partition (i.e., have a TreeLikelihood). This allows traits to be used for other purposes (such as defining Species in *BEAST). This has also allowed considerable simplification of code and tidying up.
There are a number of bug fixes as well over v1.6.0 that I will add to the issue list to keep track of them. Given the complex nature of these changes, I do not think these should be ported to the 1.6.0 branch but perhaps the bugs can be fixed.
These changes will have introduced bugs and possibly cause issues with XML generation that now need to be fixed (I will attempt to catch as many as possible).
9 lines of code changed in 6 files:
Created an HypermutantAlignment that flags hypermutation contexts for use in the APOBECErrorModel. It does this by replacing 'A's by an ambiguity code for A/G if it is in the correct context in the alignment. These can then be compressed into unique site patterns so that speed is not affected.
Extracted a common abstract base class with ConvertAlignment which wraps an alignment.
36 lines of code changed in 1 file:
TRUNK: modification of Discrete Trait in BEAUti, and change default prior of all clock rates into Gamma(0.001, 1000)
1 lines of code changed in 1 file:
Minor tweaks to APOBEC model.
7 lines of code changed in 1 file:
Added a few models of sequence (tip) error to model the action of hypermutation by APOBEC editing in HIV.
100 lines of code changed in 2 files:
TRUNK: BEAUti make taxonList static.
1 lines of code changed in 1 file:
Updated phylogeography discrete trait example XML. Also, a framework for implementing this in BEAUti.
168 lines of code changed in 3 files:
Trunk refactoring: finish tree likihood model (split parsers)..
5 lines of code changed in 1 file:
BEAUTi: solve Issue 131: rewrite Parameter and Operator class by Builder pattern, and all referring methods.
2 lines of code changed in 1 file:
BEAUTi: continue the code using Builder parttern in Parameter, and tidy up createParameter... methods
6 lines of code changed in 2 files:
BEAUTi: continue Builder parttern in Parameter.
4 lines of code changed in 1 file:
BEAUTi: start to create Builder parttern in Parameter, and simplify prior's parameters.
1 lines of code changed in 1 file:
Fixed an issue with the generation of the SequenceErrorModel. Altered the screen log to only give the 'rate of evolution' under the rate column.
2 lines of code changed in 1 file:
BEAUTi big refactory: move all enum into dr.app.beauti.enumTypes to spearate logic from GUI.
Note: some BEAST classes are using BEAUTi enum.
8 lines of code changed in 6 files:
BEAUTi: refactory for Issue #114: Beauti Priors panel for starbeast.
4 lines of code changed in 2 files:
Refactory BEAUTI package structure, add few panel packages and util package.
3 lines of code changed in 3 files:
Simplify BEAUTI code to use writer.writeIDref replace writeTag(..., idref , ...).
5 lines of code changed in 2 files:
Add species parameters and operator in Priors and Operators panel in Beauti.
2 lines of code changed in 2 files:
more common strings fun.
create method for writing an idref
3 lines of code changed in 1 file:
Fixed an issue with a null pointer in SequenceErrorModel.
44 lines of code changed in 2 files:
factor out common strings
33 lines of code changed in 2 files:
Refactored the component stuff into into a factory pattern to make things neater. Compiles, runs and generate code that runs in BEAST (for both SequenceErrorModel and TipDateSampling - but haven't tested all combinations).
279 lines of code changed in 6 files:
Fix bug that cannot start Beauti because of null point exception in setOption.
1 lines of code changed in 1 file:
More of the same - string constants
21 lines of code changed in 2 files:
This may seem like a rather large load of edits but it is just to get the 'plugin' model generator working better. All the Generators are now created in BeastGenerator's constructor. I am going to implement a factory system for the plug in modules but thought I would submit my changes now before things move on too much. I updated before committing so hopefully no painful merges for anyone.
144 lines of code changed in 3 files:
Further work on BEAUti. Added options to allow sampling of tip dates.
96 lines of code changed in 2 files:
Lots of work on BEAUti
Started work on a modularization of BEAST generation (look in beauti.components). Lots of insertion points are defined throughout the BEAST file (relative to all the standard content) and a component can offer to write content to each or any of these. Instances of each component are created in BeautiFrame constructor. Started converting some of the monolithic generation into components (see SequenceErrorModel for an example).
Implemented the ability to import an existing BEAST file but at the moment the taxa, dates and sequences are all that are picked up.
Started work on a 'locations' tab but am currently uncertain whether this shouldn't just be a general traits tab.
Save/Apply templates menu options are hidden as we don't have an implementation yet.
251 lines of code changed in 4 files: