Directory src/dr/evomodel/indel/

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dong.w.xie 2010-03-02 16:44 Rev.: 3006

Trunk refactoring: finish indel (split parsers).

5 lines of code changed in 6 files:

• src/dr/evomodel/indel: IstvanOperator.java (-44), TKF91Likelihood.java (+2 -48), TKF91Model.java (new)

dong.w.xie 2010-02-17 16:12 Rev.: 2936

Trunk refactoring: make evoxml parsers more organized.

1 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Model.java (+1 -1)

jheled 2009-09-07 13:29 Rev.: 2213

code police

42 lines of code changed in 6 files:

• src/dr/evomodel/indel: HomologyRecursion.java (+9 -11), IntMathVec.java (+23 -21), IstvansProposal.java (new)

jheled 2009-07-31 15:59 Rev.: 1968

automatic intelliJ

2 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Model.java (+2 -2)

alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

5 lines of code changed in 2 files:

• src/dr/evomodel/indel: TKF91Likelihood.java (+1 -1), TKF91Model.java (+4 -3)

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

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

6 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Model.java (+6 -6)

jheled 2009-04-20 09:10 Rev.: 1607

Continued Marc's refactorization. I wonder what other shared functionality we can pull off in there.

0 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Likelihood.java (-24)

jheled 2009-04-19 08:35 Rev.: 1598

add a nethod for getting a meaningfull name of a likelihood. more classes may benefit from overriding the default.

5 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Likelihood.java (+5 -5)

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

2 lines of code changed in 2 files:

• src/dr/evomodel/indel: TKF91Likelihood.java (+1 -1), TKF91Model.java (+1 -2)

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

271 lines of code changed in 2 files:

• src/dr/evomodel/indel: TKF91Likelihood.java (+170 -145), TKF91Model.java (+101 -84)

jheled 2008-11-19 12:11 Rev.: 1318

Code Police

1 lines of code changed in 1 file:

• src/dr/evomodel/indel: IntMathVec.java (+1 -1)

jheled 2008-05-28 09:51 Rev.: 899

Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers

Renamed getSocketChild

Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute

2 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Model.java (+2 -2)

alexei.drummond 2007-08-19 21:01 Rev.: 518

Changed operator weights from ints to doubles (touched a lot of files so I may have missed one or two operators but I was pretty careful). I also took the opportunity to tighten up SimpleMCMCOperator and remove some copy/paste code for handling weights in various operators. This change means that it is a bit easier to adjust the relative rates of operators without having to scale every other operator up when you just want to scale one of the weight=1 operators down. For example: hky.kappa should probably be set to ~ 0.25 for most runs -- it is getting called too often...

195 lines of code changed in 1 file:

• src/dr/evomodel/indel: IstvanOperator.java (+195 -186)

rambaut 2007-08-07 00:23 Rev.: 452

Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.

1 lines of code changed in 2 files:

• src/dr/evomodel/indel: TKF91Likelihood.java (-4), TKF91Model.java (+1 -4)

jheled 2007-07-02 16:20 Rev.: 348

Issue a warning for attributes of elements in BEAST xml files which are not declared by the XML rules. This helps both users (like me) not to get stung by silent ignore of typos, and developers (like me) which need to debug rules for new elements.

Those changes involves fixing some elements rules, and additional cleanup.

1 lines of code changed in 1 file:

• src/dr/evomodel/indel: TKF91Likelihood.java (+1 -1)

jheled 2007-01-19 07:48 Rev.: 150

change units type to an enum
Allow a log file name to be relative to main beast xml file when prefixed with a ./
minor jdoc and 1.5 cleanup

6 lines of code changed in 3 files:

• src/dr/evomodel/indel: IndelModel.java (new), TKF91Model.java (+2 -2)