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| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 146 (100.0%) | 5095 (100.0%) | 34.8 |
| rambaut | 81 (55.5%) | 2887 (56.7%) | 35.6 |
| dong.w.xie | 37 (25.3%) | 994 (19.5%) | 26.8 |
| alexei.drummond | 4 (2.7%) | 853 (16.7%) | 213.2 |
| Sibon.Li@gmail.com | 4 (2.7%) | 241 (4.7%) | 60.2 |
| jheled | 9 (6.2%) | 85 (1.7%) | 9.4 |
| dong.w.xie@gmail.com | 7 (4.8%) | 15 (0.3%) | 2.1 |
| tbcbedford@gmail.com | 3 (2.1%) | 11 (0.2%) | 3.6 |
| msuchard | 1 (0.7%) | 9 (0.2%) | 9.0 |
tracer: big correction of tracer code for my previous development on "Conditional Posterior Distributions", which fixed bugs in GUI especially in Filter, and use EDT thread.
2 lines of code changed in 4 files:
tracer: doWork in EBSP needs to be reviewed, it seems a copy of BSP.
13 lines of code changed in 3 files:
Updated InstantiableTracerApp to include an option to load a System exitable instance of Tracer
54 lines of code changed in 2 files:
RandomDiscretizedBranchRates has been renamed to the more meaningful ContinuousBranchRates. RandomDiscretizedBranchRatesParser has been kept and throws an error in the unlikely case that someone actually has been using this implementation.
34 lines of code changed in 1 file:
Added InstantiableTracerApp, which allows a threaded call of Tracer (that won't terminate the JVM)
153 lines of code changed in 1 file:
Porting 'evaluateLate' interface method from 1.7 branch.
1 lines of code changed in 1 file:
Created a new GUI app for plotting antigenic maps (and other multivariate traits). Starting to diverge from tracer.
1 lines of code changed in 1 file:
Created a new GUI app for plotting antigenic maps (and other multivariate traits). Currently just a copy of Tracer.
1 lines of code changed in 1 file:
Model comparison now defaults to comparing all open trace files, rather than all selected trace files. To me this seems like a more expected behavior. I tried to implement a checkbox in the dialog box for "Use selected trace files only". However, this was difficult because the List<TraceList> that's passed in from TracerFrame doesn't have information about what is currently selected.
8 lines of code changed in 1 file:
Moving naming from "Bayes Factors" to "Model Comparison"
3 lines of code changed in 2 files:
trunk: add EBSP analysis in Tracer, but doWork() not working yet.
68 lines of code changed in 4 files:
Fix for issue 464: http://code.google.com/p/beast-mcmc/issues/detail?id=464
Set the default locale to US at the beginning of the main() of each of the applications. We don't currently do any localization and the use of a comma as a decimal in some places but not other for those languages that use this was causing major incompatibilities.
5 lines of code changed in 1 file:
Visual tweaks.
31 lines of code changed in 1 file:
Trace type buttons weren't working...
12 lines of code changed in 1 file:
Working towards Tracer 1.6. Switched trace 'types' (in the GUI) to 'real', 'integer' and 'categorical' as the previous ones were in programmers' jargon. These buttons also are now disabled when no trace is selected. Also disabled the confirmation box for setting types - if you press the button, then you probably intended to do it (this is a static switch at the top of the TracerFrame.java).
Cleaned up some issues with the generification of 'Variate' - in particular some methods in the plotting were not being overridden.
In 'distribution' tab, for real traces, KDEs are now the default. Histogram estimates can also be shown.
Options for plotting are now stored for specific traces (for example, if you set a manual range for a trace it is now remembered and used for this trace only).
Cleaned up some odd code in Skyline plotting (causing an erroneous warning box to appear).
Removed a few exclamation marks from dialog box messages and cleaned up the text.
49 lines of code changed in 2 files:
Trunk: make micro-satellite file successfully loaded in BEAUti data panel.
Start to use jdk1.6 code.
1 lines of code changed in 1 file:
Trunk new Trace: fix some bugs.
11 lines of code changed in 1 file:
Trunk new Trace: if combined traces exists, the change type function should apply to all log files including combined traces as well.
39 lines of code changed in 1 file:
Trunk new Trace: if combined traces exists, the filter has to be applied to all log files including combined traces, as Alexei advised.
25 lines of code changed in 1 file:
Trunk new Trace: finally fix the bug of FilterPanels not showing in FilterJDialog.
37 lines of code changed in 1 file:
Trunk new Trace: fix filter not working bug.
0 lines of code changed in 1 file:
Trunk new Tracer: fix the bug of missing possible values displayed in FilterDiscretePanel after filter applied.
29 lines of code changed in 1 file:
Trunk new Trace: make trace type change function working.
93 lines of code changed in 1 file:
Trunk new Trace: struggling with filter applied situation.
6 lines of code changed in 1 file:
Trunk new Trace: update Find Conditional Posterior Distributions... jdialog and jpanel and jtable, but panelParent cannot be repainted.
15 lines of code changed in 1 file:
Trunk new Trace: remove filter comb, add Find Conditional Posterior Distributions... in Analysis menu, create regarding jdialog and jpanel and jtable.
122 lines of code changed in 3 files:
Trunk new Trace: 1) Try to replace Double[] as List<Double>, which save some memory, but it still crashes after loading a big log; 2) use traceType to detemine type, instead of prime type (T) of List<T> in Trace, and integer is stored as List<Double> currently for simlple solution of plotting.
9 lines of code changed in 1 file:
Trunk: starts using List instead array in Trace, and return List for getValues.
13 lines of code changed in 1 file:
Trunk: new Tracer dev: solve some generic type casting problems.
1 lines of code changed in 1 file:
Trunk: new Tracer dev: make it complied, but there is still casting problem.
35 lines of code changed in 1 file:
Trunk: solve Issue 322: Tracer: stack buttons to save space
29 lines of code changed in 1 file:
Switched all uses of org.virion.jam.* to jam.* (org.virion.jam.* is not being updated or fixed). This has touched alot of files but mainly just in the import statements.
24 lines of code changed in 11 files:
Ignore nonesense ESS on constant values. integer ESS values in panel.
11 lines of code changed in 1 file:
Tracer now uses a Gaussian KDE that performs very nicely
9 lines of code changed in 1 file:
TRUNK: new tracer: fixing changing trace type bug.
2 lines of code changed in 1 file:
TRUNK: new tracer dev: fix remove all filters bug.
91 lines of code changed in 1 file:
TRUNK: new tracer: fixing status message bug after filter applied.
60 lines of code changed in 1 file:
TRUNK: new tracer dev: fix filter plotting bug in all panels.
3 lines of code changed in 1 file:
TRUNK: new tracer dev: bug fixing again.
1 lines of code changed in 1 file:
TRUNK: new tracer dev: add filter status message.
2 lines of code changed in 1 file:
(45 more)