Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 95 (100.0%) | 6525 (100.0%) | 68.6 |
| rambaut | 65 (68.4%) | 6367 (97.6%) | 97.9 |
| dong.w.xie | 23 (24.2%) | 150 (2.3%) | 6.5 |
| tbcbedford@gmail.com | 3 (3.2%) | 4 (0.1%) | 1.3 |
| msuchard | 2 (2.1%) | 2 (0.0%) | 1.0 |
| baele.guy@gmail.com | 2 (2.1%) | 2 (0.0%) | 1.0 |
Finished tipdate precision for Pathogen. Now shows these as error bars (the points are given a date that is midpoint within the specified precision).
115 lines of code changed in 1 file:
Pathogen - you can now copy names of selected taxa to the clipboard.
49 lines of code changed in 8 files:
Log transformed kernel density estimation can also be used in Tracer
2 lines of code changed in 2 files:
Porting fixes from 1.7.3 back into the trunk
0 lines of code changed in 2 files:
Removed unwanted import.
0 lines of code changed in 2 files:
Tweaking colors to make Tracer plots less garish. Feel free to roll this back if you're unhappy.
Before: http://imgur.com/1BpFx,UQkAl#0
After: http://imgur.com/1BpFx,UQkAl#1
4 lines of code changed in 3 files:
Fixes to HPM specification in BEAUti
2 lines of code changed in 2 files:
Cleaned up PriorDialog to better render distributions if possible.
478 lines of code changed in 6 files:
Visual tweaks.
57 lines of code changed in 2 files:
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.
195 lines of code changed in 18 files:
Trunk new Trace: remove static convert method from Trace.
1 lines of code changed in 1 file:
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.
52 lines of code changed in 9 files:
Trunk: starts using List instead array in Trace, and return List for getValues.
3 lines of code changed in 1 file:
Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.
92 lines of code changed in 11 files:
Trunk: new Tracer dev: make it complied, but there is still casting problem.
2 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.
5473 lines of code changed in 26 files: