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| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 102 (100.0%) | 4332 (100.0%) | 42.4 |
| rambaut | 85 (83.3%) | 4014 (92.7%) | 47.2 |
| alexei.drummond | 5 (4.9%) | 212 (4.9%) | 42.4 |
| dong.w.xie | 12 (11.8%) | 106 (2.4%) | 8.8 |
Added local root search to Pathogen.
140 lines of code changed in 4 files:
Finished tipdate precision for Pathogen. Now shows these as error bars (the points are given a date that is midpoint within the specified precision).
39 lines of code changed in 4 files:
Adding date precision to the BEAUti/Pathogen date guessing panel
24 lines of code changed in 1 file:
Pathogen - you can now copy names of selected taxa to the clipboard.
11 lines of code changed in 1 file:
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.
177 lines of code changed in 3 files:
Added a hack to get rough time-tree out of Pathogen
59 lines of code changed in 3 files:
Porting 'evaluateLate' interface method from 1.7 branch.
0 lines of code changed in 1 file:
Fixed issue with trees with polytomies having bad branch lengths.
1 lines of code changed in 1 file:
Fixed issue with trees with polytomies having bad branch lengths.
2 lines of code changed in 1 file:
Added node-density feature to Pathogen
77 lines of code changed in 2 files:
uncommitting an erroneous revision
0 lines of code changed in 3 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.
12 lines of code changed in 2 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.
21 lines of code changed in 2 files:
Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.
67 lines of code changed in 2 files:
Pathogen updates
1 lines of code changed in 2 files:
A bit of a hack but if the RegEx function of DateGuesser doesn't like the number it tries to parse it as a calendar date.
3 lines of code changed in 1 file:
Fixed an error loading non-binary trees (i.e., most unrooted trees).
2 lines of code changed in 1 file:
Final tweaks to new version of Pathogen
34 lines of code changed in 2 files:
Pathogen loads Newick tree files now.
35 lines of code changed in 1 file:
Updated revision number of Pathogen
2 lines of code changed in 1 file:
Added common ancestor lines to pathogen. These help explore the outliers.
20 lines of code changed in 2 files:
Experimenting with Path-O-Gen
205 lines of code changed in 3 files:
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.
25 lines of code changed in 8 files:
TRUNK: new tracer dev merged from branch TRACER_NEW_DEV.
2 lines of code changed in 1 file:
Fixed an issue with root optimization for some trees in PathOGen.
823 lines of code changed in 5 files:
New version of Path-O-Gen v1.2 released.
90 lines of code changed in 1 file:
Correct ANT for Pathogen Hudson project, and remove warning
0 lines of code changed in 2 files:
TreeModel that draws a random tree from a set loaded from NEXUS file.
53 lines of code changed in 2 files:
BEAUTi:
1) part of code for Issue 171: Version update reminder in BEAUTi;
2) remove all "/" in the end of URL, which cause error for Wiki.
9 lines of code changed in 1 file:
Add OSType in dr.app.util to detect OS, and replace all old isMacOS into new one.
5 lines of code changed in 2 files:
Updated the credits for the upcoming release of BEAST. Note the list of developers in 'BeastVersion.java' is not complete. Please review and revise.
15 lines of code changed in 1 file:
Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.
153 lines of code changed in 2 files:
Refactory BEAUTI package structure, add few panel packages and util package.
1 lines of code changed in 1 file:
Create dr.app.beauti.tipdatepanel package to make clear structure.
1 lines of code changed in 1 file:
New Uniform Root Prior
124 lines of code changed in 1 file:
Pathogen improvements
1 lines of code changed in 1 file:
Pathogen improvements
9 lines of code changed in 1 file:
Pathogen work.
17 lines of code changed in 2 files:
Added a cutdown version of FigTree as a library to the BEAST lib folder (and as a consequence had to add the jam.jar library). This is so the program 'Path-O-Gen' can use it but it may be useful elsewhere. To get dr/app/pathogen/ to compile you will need to add figtreepanel.jar to your dependencies. To get Path-O-Gen to run, you will need to add jam.jar to the class path.
18 lines of code changed in 1 file:
First version of 'Path-O-Gen' complete.
266 lines of code changed in 4 files:
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