Directory src/dr/inferencexml/loggers/

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rambaut 2012-03-04 01:01 Rev.: 4761

Removing wrongly located files.

0 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (del)

sibon.li 2012-03-03 21:38 Rev.: 4758

Commented out all of my last commit until issues resolved

167 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (new 167)

sibon.li 2012-03-03 16:23 Rev.: 4755

Added classes to enable implicit convergence assessment checks using BLUE

166 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (+166 -165)

sibon.li 2012-02-28 12:09 Rev.: 4743

Correction, parsers pending updates to other files. Currently commented out

166 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (+166 -166)

sibon.li 2012-02-28 12:05 Rev.: 4742

Added two new parsers for BLUE integration

169 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (+169)

graham853@gmail.com 2011-09-02 21:19 Rev.: 4280

Remove debugging class intended for my use only.

0 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: AlloppDBUGTUNELoggerParser.java (del)

graham853@gmail.com 2011-09-02 00:01 Rev.: 4277

60 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: AlloppDBUGTUNELoggerParser.java (new 60)

rambaut 2010-08-19 21:31 Rev.: 3411

LoggerParser uses a special function to get the log file which may set different paths (for example to a working directory). Thus just checking that fileName exists may not work. So moved the check for existing file into XMLParser.getFilePrintWriter(). This has the added benefit that all loggers use this function and thus all have the overwriting behaviour.

Also added a check box to the BEAST options dialog box.

4 lines of code changed in 4 files:

• src/dr/inferencexml/loggers: LoggerParser.java (+3 -28), MLLoggerParser.java (new)

rambaut 2010-08-19 20:56 Rev.: 3410

Reduced verbosity - 'allowOverwrite' attribute is now just 'overwrite'

1 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: LoggerParser.java (+1 -1)

rambaut 2010-08-19 20:50 Rev.: 3408

Added a command line option to BEAST '-overwrite' which will allow overwriting of log files (overriding any attribute in the XML). This works by setting a System property 'allow.overwrite=true'. This can also be set (true or false) using the JVM option -Dallow.overwrite=XXXX

10 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: LoggerParser.java (+10 -2)

dong.w.xie 2010-08-19 11:17 Rev.: 3405

Trunk: solve Issue 305: BEAST should warn/halt if log files already exist

15 lines of code changed in 1 file:

• src/dr/inferencexml/loggers: LoggerParser.java (+15)

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

0 lines of code changed in 2 files:

• src/dr/inferencexml/loggers: DemographicLoggerParser.java (del), TreeLoggerParser.java (del)

dong.w.xie 2010-03-02 10:24 Rev.: 3002

Trunk refactoring: finish Logger (split parsers).

658 lines of code changed in 5 files:

• src/dr/inferencexml/loggers: ColumnsParser.java (new 126), DemographicLoggerParser.java (new 60), LoggerParser.java (+170), MLLoggerParser.java (+88), TreeLoggerParser.java (new 214)