Directory src/dr/app/util/

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msuchard 2012-07-12 05:50 Rev.: 5063

Default behavior brings up GUI panel instead of just the open file panel

339 lines of code changed in 2 files:

• src/dr/app/util: Arguments.java (+339 -332)

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

1 lines of code changed in 2 files:

• src/dr/app/util: Utils.java (new)

rambaut 2011-07-23 04:00 Rev.: 4116

uncommitting an erroneous revision

285 lines of code changed in 5 files:

• src/dr/app/util: Arguments.java (+27 -4), ErrorLogHandler.java (del), MessageLogHandler.java (del), Utils.java (+258 -4), Version.java (del)

rambaut 2011-07-22 08:49 Rev.: 4115

Added a UI for BEAST on GUI platforms. Not completely linked yet.

147 lines of code changed in 5 files:

• src/dr/app/util: Arguments.java (+4 -27), ErrorLogHandler.java (new 71), MessageLogHandler.java (new 45), Utils.java (+4 -258), Version.java (new 23)

dong.w.xie 2011-06-09 17:13 Rev.: 4021

Trunk: allow to select directory

1 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+1)

dong.w.xie 2011-06-01 17:30 Rev.: 3995

Trunk: more updates for GetDateFromTree and LogAnalyser

30 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+30 -7)

jheled 2010-11-09 11:52 Rev.: 3701

Allows any number of tempratures in command line

79 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+79 -44)

rambaut 2010-09-09 23:49 Rev.: 3517

Now I really think it builds OK. Sorry if anyone got messed up by that.

173 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+173)

rambaut 2010-09-09 23:33 Rev.: 3515

A few more bits of clean up.

3 lines of code changed in 4 files:

• src/dr/app/util: Arguments.java (+1 -1), OSType.java (new), Utils.java (+1 -1)

rambaut 2010-09-09 23:04 Rev.: 3513

95 lines of code changed in 3 files:

• src/dr/app/util: Arguments.java (+80 -80), OSType.java (+14 -14), Utils.java (+1 -174)

msuchard 2010-08-25 06:50 Rev.: 3437

Fixing (? I think) command-line bug that entered in r3435. Please code review. At a minimum, BEAST now runs for me.

2 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+2 -1)

rambaut 2010-08-25 01:21 Rev.: 3435

Slight adjustment of how command line arguments work. Previously they could be partially specified (thus '-work' instead of '-working') but this means that you can't have an argument that is a substring of another (thus '-beagle' and '-beagle_cpu') without specifiying the shorter one first. Now you have to specify the full option.

2 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+2 -1)

dong.w.xie 2010-03-19 13:27 Rev.: 3059

TRUNK: contine to dev new trait in BEAUti.

42 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+42 -26)

dong.w.xie 2010-03-18 17:33 Rev.: 3054

TRUNK: initial dev for new trait in BEAUti.

121 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+121 -91)

dong.w.xie 2009-08-11 11:17 Rev.: 2053

Add OSType in dr.app.util to detect OS, and replace all old isMacOS into new one.

99 lines of code changed in 2 files:

• src/dr/app/util: OSType.java (+75), Utils.java (+24 -24)

rambaut 2009-08-04 00:16 Rev.: 2006

Fixed issue 105: http://code.google.com/p/beast-mcmc/issues/detail?id=105
and addressed 106 (made the dialog box say it is a 'Warning') rather than an error.

3 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+3 -2)

msuchard 2009-07-27 07:24 Rev.: 1921

2D contouring now appears to work better in Java than in R (and much faster). TimeSlicer appropriately rescales the Brownian precision to give accurate inference ... the animations are going to look *awesome*.

1 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+1 -1)

jheled 2009-07-17 16:29 Rev.: 1868

fix failure due to incorrrect parameter name
Use file chooser for save as well. Start file chooser in current directory.

38 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+38 -9)

dong.w.xie 2009-06-12 10:38 Rev.: 1773

Finally fix the compile error r1770 this time

1 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+1 -1)

jheled 2009-05-01 09:27 Rev.: 1659

More validity checks for traits file loading

5 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+5 -1)

jheled 2009-04-30 13:27 Rev.: 1653

Load traits from a file for beauti. File is tab delimeted.
The first line contains the lables, including the first column.
If the first column is a trait name, it is followed by the trait value and a list of taxa.

95 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+95 -89)

dong.w.xie 2009-04-29 16:50 Rev.: 1650

Add parser in Utils and change importTraitsFromFile to distinguish Joseph and Andrew's trait file format (not finished yet).

53 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+53 -2)

jheled 2009-04-25 18:16 Rev.: 1632

Change comment in readFileIntoMap to reflect the generic nature of the function. clean up code a little.

37 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+37 -38)

dong.w.xie 2009-04-24 17:01 Rev.: 1630

More work on Multispecies Coalescent for BEAUTI, try to implement mapping between species and taxa.

47 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+47 -1)

jheled 2008-11-24 15:22 Rev.: 1326

Comments, nitpicking

7 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+7 -1)

rambaut 2008-07-23 11:42 Rev.: 1009

Started work on a new version of BEAUti to be released as part of v1.5. This allows multiple data partitions. It compiles and runs but will be full of bugs (particularly for code generation). Work continues...

12 lines of code changed in 1 file:

• src/dr/app/util: Utils.java (+12 -12)

alexei.drummond 2007-04-29 14:25 Rev.: 255

Ported the Bayes factor approximation code from C++ that Marc Suchard shared with me to Java -- lets plug this in to Tracer and automatically calculate the Bayes factor and bootstrap estimated uncertainty for the treeLikelihood statistic... This will facilitate easy model comparison of different substitution models

57 lines of code changed in 1 file:

• src/dr/app/util: Arguments.java (+57 -59)