Directory src/dr/inference/loggers/

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rambaut 2012-08-11 08:53 Rev.: 5122

Fix for Issue 655: Operator log sometimes attempts to write to locked folder causing exception. Needs testing and porting to 1.7 branch.

0 lines of code changed in 1 file:

• src/dr/inference/loggers: TreeLogger.java (del)

msuchard 2012-03-07 12:09 Rev.: 4780

Reverting inadvertent changes from Julia

6 lines of code changed in 2 files:

• src/dr/inference/loggers: MCLogger.java (new)

julia.pal.r@gmail.com 2012-03-07 11:42 Rev.: 4779

Not finished but descent version of GPOperator - fixing imports :S

3 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+3)

rambaut 2011-11-16 03:13 Rev.: 4430

Loggers weren't logging if they overrode the base class log(int state) - because it had been changed to log(long state). Put a final int version in the base class to prevent overriding.

9 lines of code changed in 3 files:

• src/dr/inference/loggers: MCLogger.java (+4), MLLogger.java (new)

rambaut 2011-11-15 09:26 Rev.: 4424

Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.

6 lines of code changed in 3 files:

• src/dr/inference/loggers: Logger.java (new), MCLogger.java (+4 -4)

graham853@gmail.com 2011-09-02 21:18 Rev.: 4279

Remove debugging class intended for my use only.

0 lines of code changed in 1 file:

• src/dr/inference/loggers: AlloppDBUGTUNELogger.java (del)

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

54 lines of code changed in 1 file:

• src/dr/inference/loggers: AlloppDBUGTUNELogger.java (new 54)

jheled@gmail.com 2011-06-24 21:43 Rev.: 4065

Report speed per 10^9 for fast runs

9 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+9 -4)

dong.w.xie 2011-02-17 15:31 Rev.: 3805

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.

2 lines of code changed in 2 files:

• src/dr/inference/loggers: ArrayLogFormatter.java (+2 -1)

dong.w.xie 2011-02-16 16:32 Rev.: 3804

Trunk: starts using List instead array in Trace, and return List for getValues.

1 lines of code changed in 1 file:

• src/dr/inference/loggers: ArrayLogFormatter.java (+1 -2)

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.

5 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+5 -27)

dong.w.xie 2010-06-01 13:01 Rev.: 3204

TRUNK: new tracer dev merged from branch TRACER_NEW_DEV.

3 lines of code changed in 1 file:

• src/dr/inference/loggers: ArrayLogFormatter.java (+3 -1)

dong.w.xie 2010-03-16 10:44 Rev.: 3044

TRUNK: merge Issue 288 from branch 1.5.

5 lines of code changed in 2 files:

• src/dr/inference/loggers: NumberColumn.java (new)

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

Trunk refactoring: finish Logger (split parsers).

266 lines of code changed in 4 files:

• src/dr/inference/loggers: Columns.java (new), MLLogger.java (-81), TreeLogger.java (new 266)

msuchard 2009-11-12 05:49 Rev.: 2531

Fixed in case users wrap a parameter in a column and forget to provide a label

1 lines of code changed in 1 file:

• src/dr/inference/loggers: Columns.java (+1 -1)

rambaut 2009-10-26 23:50 Rev.: 2471

Added a delay to the PerformanceReport in MCLogger. This is to skip the states when the JIT compiler is still optimizing. Currently this is set (in LoggerParser) to 5 x logEvery.

34 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+34 -10)

jheled 2009-09-07 08:16 Rev.: 2207

comments changes

2 lines of code changed in 4 files:

• src/dr/inference/loggers: BooleanColumn.java (+1 -1), PercentColumn.java (+1 -1)

jheled 2009-07-24 11:15 Rev.: 1909

Intellij auto changes

2 lines of code changed in 2 files:

• src/dr/inference/loggers: BooleanColumn.java (+1 -1), PercentColumn.java (+1 -1)

alexei.drummond 2009-07-18 18:12 Rev.: 1871

First step in development of a generic version of Parameter, called Variable for now. Parameter now implements Variable<Double> but eventually all dr.inference.* will be based on Variable rather than Parameter. At least that is the idea anyway...

37 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+37 -16)

alexei.drummond 2009-07-17 01:13 Rev.: 1863

Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...

1 lines of code changed in 1 file:

• src/dr/inference/loggers: TreeLogger.java (+1 -1)

alexei.drummond 2009-07-15 16:25 Rev.: 1860

refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying

2 lines of code changed in 6 files:

• src/dr/inference/loggers: Convergence.java (del), ConvergenceListener.java (del), ConvergenceLogger.java (del), MLLogger.java (+1 -1), TreeLogger.java (+1 -1), TreeSpaceLogger.java (del)

jheled 2009-04-19 08:17 Rev.: 1596

comment out unused code

267 lines of code changed in 1 file:

• src/dr/inference/loggers: TreeLogger.java (+267 -266)

jheled 2009-03-27 09:51 Rev.: 1518

ongoing sp tree development

6 lines of code changed in 1 file:

• src/dr/inference/loggers: TreeLogger.java (+6 -15)

jheled 2009-03-27 09:49 Rev.: 1517

automatic idea changes

2 lines of code changed in 1 file:

• src/dr/inference/loggers: MLLogger.java (+2 -2)

Sebastian.Hoehna 2009-03-04 09:54 Rev.: 1477

Some work on convergence measurements

827 lines of code changed in 5 files:

• src/dr/inference/loggers: Convergence.java (new 222), ConvergenceListener.java (new 34), ConvergenceLogger.java (new 55), TreeLogger.java (+275), TreeSpaceLogger.java (new 241)

jheled 2008-12-03 19:38 Rev.: 1353

supervised automatic code improvments (Intellij)

1 lines of code changed in 1 file:

• src/dr/inference/loggers: NumberColumn.java (+1 -1)

bloomquist 2008-11-26 08:29 Rev.: 1330

Added a method to MCLogger that stores the fileName.

26 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+26 -3)

rambaut 2008-10-25 05:52 Rev.: 1256

Alex and I have been experimenting with a path sampling approach to estimating marginal likelihoods. See eXML in examples/testPathSampling.xml. Not sure it works.

8 lines of code changed in 1 file:

• src/dr/inference/loggers: MCLogger.java (+8)

Sebastian.Hoehna 2008-09-03 17:44 Rev.: 1176

Some work on the tree operators.

4 lines of code changed in 1 file:

• src/dr/inference/loggers: ConvergenceLogger.java (+4 -1)

msuchard 2008-09-03 04:48 Rev.: 1174

Implemented BSSVS for possible complex substitution matrices.

8 lines of code changed in 2 files:

• src/dr/inference/loggers: MatrixEntryColumn.java (new)

msuchard 2008-09-01 09:12 Rev.: 1173

ComplexeSubstitutionModel will exponentiate any real matrix regardless if the infinitesimal generator contains complex eigenvalues (common in irreversible chains).

27 lines of code changed in 1 file:

• src/dr/inference/loggers: MatrixEntryColumn.java (+27)

alexei.drummond 2008-08-17 08:03 Rev.: 1150

moved Sebastian's TreeLogger out of inference/loggers. The inference package should not contain any dependencies on evolution or evomodel.

76 lines of code changed in 3 files:

• src/dr/inference/loggers: LogColumn.java (new), TreeLogger.java (del)

Sebastian.Hoehna 2008-08-15 18:44 Rev.: 1138

Some new operators, but still under development. A little tigying up in the old stuff and some minor corrections.

1 lines of code changed in 1 file:

• src/dr/inference/loggers: ConvergenceLogger.java (+1 -2)

Sebastian.Hoehna 2008-08-15 11:50 Rev.: 1134

Some convergence listener, logger and a tree logger which doesn't use the output file.

1209 lines of code changed in 3 files:

• src/dr/inference/loggers: ConvergenceListener.java (+271), ConvergenceLogger.java (+405), TreeLogger.java (new 533)

alexei.drummond 2008-07-24 03:10 Rev.: 1010

Multi-partition BEAUti here we come!! 205 errors to fix before anybody notices this commit...

41 lines of code changed in 3 files:

• src/dr/inference/loggers: ArrayLogFormatter.java (+35 -2), TabDelimitedFormatter.java (+6 -1)

alexei.drummond 2008-07-22 22:05 Rev.: 1002

renamed mispelled method (setSumDeviation), added CoercionMode enum and refactored autoOptimize parsing accordingly. Added ability to log to memory and import newick from string.

94 lines of code changed in 4 files:

• src/dr/inference/loggers: ArrayLogFormatter.java (+39), LogFormatter.java (+12 -19), TabDelimitedFormatter.java (+43 -42)

alexei.drummond 2008-07-14 19:10 Rev.: 991

Issue 55. I had attempted to pass a null as the default value in the new getAttribute method of XMLObject, which is not allowed. Fixed by passing ""

1 lines of code changed in 1 file:

• src/dr/inference/loggers: Columns.java (+1 -1)

alexei.drummond 2008-07-12 01:14 Rev.: 988

Be scared: I have tidied up integer attribute parsing in various classes. Also operator weights were integers in some places -- they should all be doubles now...

80 lines of code changed in 2 files:

• src/dr/inference/loggers: Columns.java (+78 -88), MLLogger.java (+2 -6)

jheled 2008-07-10 18:27 Rev.: 986

Output performance message only to screen logs

16 lines of code changed in 2 files:

• src/dr/inference/loggers: MCLogger.java (+15 -10), MLLogger.java (+1 -1)

alexei.drummond 2008-07-10 04:26 Rev.: 985

I plan to move all XML parsers of evomodel objects to new package evomodelxml. This is preparation for a completely new input file format that will be shared between BEAUti 2.0 and BEAST 2.0. I don't want any of this nasty old XML that is so hard to maintain to be left in evomodel package when I am finished...

118 lines of code changed in 2 files:

• src/dr/inference/loggers: MCLogger.java (-193), MLLogger.java (+118 -135)

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