July 2008 Commit Log

Number of Commits:
87
Number of Active Developers:
5
alexei.drummond 2008-07-31 01:34 Rev.: 1075

really fixed MrBayes parsing -- getting sloppy with my commits :-(

2 lines of code changed in 2 files:

alexei.drummond 2008-07-31 01:25 Rev.: 1074

fixed MrBayes parsing

40 lines of code changed in 1 file:

alexei.drummond 2008-07-30 23:41 Rev.: 1073

fixes to gtr element generation

36 lines of code changed in 3 files:

alexei.drummond 2008-07-30 23:10 Rev.: 1072

allow charset commands inside PAUP block

8 lines of code changed in 2 files:

alexei.drummond 2008-07-30 22:59 Rev.: 1071

allow charset commands inside PAUP block

46 lines of code changed in 4 files:

alexei.drummond 2008-07-30 20:50 Rev.: 1070

multi-partition BEAUti with different codon position rates now works for me...

191 lines of code changed in 6 files:

alexei.drummond 2008-07-30 19:40 Rev.: 1069

22 lines of code changed in 1 file:

alexei.drummond 2008-07-30 19:17 Rev.: 1068

refactoring in BEAUti

122 lines of code changed in 7 files:

rambaut 2008-07-30 09:30 Rev.: 1067

Now generates 3500 BEAST files!

459 lines of code changed in 2 files:

alexei.drummond 2008-07-30 05:30 Rev.: 1066

still working on multi-partition user interface -- something wrong with operators on base frequencies parameter at the moment..

261 lines of code changed in 11 files:

alexei.drummond 2008-07-30 02:17 Rev.: 1065

continued work on Multi-partition Beauti

71 lines of code changed in 7 files:

rambaut 2008-07-29 23:44 Rev.: 1064

Overhauled the parameter and element naming system. PartitionModel can now give a prefix (its name and codon partition but drops the name if there is only one partition).

836 lines of code changed in 10 files:

rambaut 2008-07-29 21:52 Rev.: 1063

Fixing element names

128 lines of code changed in 2 files:

alexei.drummond 2008-07-29 21:37 Rev.: 1062

added allMus parameter to log

21 lines of code changed in 2 files:

alexei.drummond 2008-07-29 21:15 Rev.: 1061

fixed getSiteCount() method in DataPartition

1 lines of code changed in 1 file:

rambaut 2008-07-29 12:55 Rev.: 1060

Fixed getSiteCount in DataPartition

28 lines of code changed in 3 files:

alexei.drummond 2008-07-29 12:43 Rev.: 1059

fixed getSiteCount() method in DataPartition

1 lines of code changed in 1 file:

rambaut 2008-07-29 12:33 Rev.: 1058

Generates and runs!!! But perhaps not for all combinations.

326 lines of code changed in 8 files:

rambaut 2008-07-29 11:04 Rev.: 1057

Compiles and generates for multiple partitions. Resulting BEAST file doesn't work because it doesn't have an alignment with id="alignment" from which to get empirical frequencies. We need to compile the patterns for each partition model from the alignments that assigned to that model. We can then use this resulting pattern list.

66 lines of code changed in 6 files:

rambaut 2008-07-29 10:11 Rev.: 1056

Compiling again. Sorry.

1 lines of code changed in 1 file:

rambaut 2008-07-29 10:03 Rev.: 1055

Broken, but just for a moment

7 lines of code changed in 2 files:

rambaut 2008-07-29 04:13 Rev.: 1054

Some progress. Now creates a set of 'mu' parameters across all active partition models. The current stumbling block is that the deltaExchange operator requires the weight of each partition. This is currently supposed to be provided by 'BeautiOptions.getActivePartitionWeights()' but I haven't finished implementing it yet.

293 lines of code changed in 7 files:

alexei.drummond 2008-07-29 02:22 Rev.: 1053

fixed mean rate is global (in GUI) -- needs fixing behind scenes -- added an "unlink relative rates across partitions" checkbox that is also only cosmetic as the moment.

36 lines of code changed in 3 files:

alexei.drummond 2008-07-28 09:58 Rev.: 1052

fixed mean rate

34 lines of code changed in 6 files:

alexei.drummond 2008-07-28 09:11 Rev.: 1051

added ClockType enum

73 lines of code changed in 10 files:

alexei.drummond 2008-07-28 08:32 Rev.: 1050

nicer pattern names

14 lines of code changed in 1 file:

rambaut 2008-07-27 11:00 Rev.: 1049

Popup model choice in the data table seem to render and operate as expected.

20 lines of code changed in 3 files:

rambaut 2008-07-27 10:35 Rev.: 1048

Gave the tree prior enums a name which means they can be used directly in a JComboBox. It will make it more robust to changes of order.

54 lines of code changed in 3 files:

alexei.drummond 2008-07-27 09:59 Rev.: 1047

2 lines of code changed in 1 file:

rambaut 2008-07-27 09:59 Rev.: 1046

Added pop-down model choice in data table.

50 lines of code changed in 4 files:

alexei.drummond 2008-07-27 09:50 Rev.: 1045

XML runs with single shared siteModel but still many bugs :-)

115 lines of code changed in 5 files:

alexei.drummond 2008-07-27 08:48 Rev.: 1044

3 lines of code changed in 1 file:

alexei.drummond 2008-07-27 08:45 Rev.: 1043

provides each alignment with unique id, and only writes XML of each alignment once, regardless of number of partitions.

34 lines of code changed in 1 file:

alexei.drummond 2008-07-26 22:38 Rev.: 1042

Painted a few more details of the new BEAUti. It now generates a BEAST XML from a Nexus file with charPartitions defined, but the BEAST XML doesn't run yet :-)

971 lines of code changed in 22 files:

alexei.drummond 2008-07-26 05:06 Rev.: 1037

The broad brush strokes of a new BeastGenerator have now been painted. Some details are lacking but it compiles :-)

3608 lines of code changed in 20 files:

rambaut 2008-07-25 11:20 Rev.: 1033

More tweaking

4 lines of code changed in 1 file:

rambaut 2008-07-25 11:17 Rev.: 1032

Partitions are now read from the Assumptions block of a NEXUS file. These are not really dealt with properly yet. PAUP and MrBayes blocks also read. A few other tweaks.

227 lines of code changed in 5 files:

rambaut 2008-07-25 08:07 Rev.: 1031

Reattaching the monkey's head.

3673 lines of code changed in 13 files:

alexei.drummond 2008-07-24 10:03 Rev.: 1029

tidying

22 lines of code changed in 1 file:

alexei.drummond 2008-07-24 10:01 Rev.: 1028

operators and prior panels now seem to work again

65 lines of code changed in 5 files:

rambaut 2008-07-24 04:39 Rev.: 1027


13 lines of code changed in 2 files:

alexei.drummond 2008-07-24 04:37 Rev.: 1026

58 lines of code changed in 3 files:

rambaut 2008-07-24 04:23 Rev.: 1025


113 lines of code changed in 4 files:

alexei.drummond 2008-07-24 03:52 Rev.: 1024

1 lines of code changed in 1 file:

rambaut 2008-07-24 03:45


3034 lines of code changed in 3 files:

alexei.drummond 2008-07-24 03:44

38 lines of code changed in 3 files:

rambaut 2008-07-24 03:36


392 lines of code changed in 5 files:

alexei.drummond 2008-07-24 03:34 Rev.: 1016

15 lines of code changed in 1 file:

alexei.drummond 2008-07-24 03:29

48 lines of code changed in 3 files:

alexei.drummond 2008-07-24 03:20 Rev.: 1012

Multi-partition BEAUti here we come!!

91 lines of code changed in 1 file:

rambaut 2008-07-24 03:15 Rev.: 1011

691 lines of code changed in 3 files:

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

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

3833 lines of code changed in 36 files:

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...

2319 lines of code changed in 12 files:

rambaut 2008-07-23 04:52 Rev.: 1007

A few tweaks.

553 lines of code changed in 7 files:

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.

1405 lines of code changed in 32 files:

alexei.drummond 2008-07-22 03:50 Rev.: 999

tidying

29 lines of code changed in 4 files:

alexei.drummond 2008-07-22 03:08 Rev.: 998

separated out speciation prior parsers and set yule model XML to silently use birth-death model with zero death rate.

84 lines of code changed in 2 files:

alexei.drummond 2008-07-22 03:03 Rev.: 997

separated out speciation prior parsers and set yule model XML to silently use birth-death model with zero death rate.

113 lines of code changed in 5 files:

jheled 2008-07-17 21:33 Rev.: 996

scale and weight has been swapped in the last update. switch back to correct assignment.

2 lines of code changed in 1 file:

jheled 2008-07-17 20:50 Rev.: 995

Map names only if NEXUS format (thanks Alexei)

2 lines of code changed in 1 file:

jheled 2008-07-17 20:42 Rev.: 994

Fix issue 56 (incorrect generation of nexus file). Also revert default of taxa names in trees to numbers.

18 lines of code changed in 2 files:

alexei.drummond 2008-07-17 20:30 Rev.: 993

137 lines of code changed in 2 files:

alexei.drummond 2008-07-15 05:25 Rev.: 992

Made a very large improvement to CompoundParameter performance by using more memory and removing findParameter method... It should make a big difference for trait models on trees, especially when you aren't calculating the likelihood of an alignment. On a 400 taxa example I looked at it sped things up by a factor of 6. Also a few other small fixes...

2066 lines of code changed in 5 files:

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 ""

81 lines of code changed in 3 files:

bloomquist 2008-07-14 10:06 Rev.: 990

Had to go back to a previous version of the Logger. Current approach not appropriate.

216 lines of code changed in 1 file:

alexei.drummond 2008-07-12 01:49 Rev.: 989

Be very afraid: I have tidied up double and string attribute parsing in various classes. Hopefully no logic was changed, and I avoided code that couldn't be understood in a brief moment.

2347 lines of code changed in 36 files:

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...

1530 lines of code changed in 24 files:

alexei.drummond 2008-07-10 21:59 Rev.: 987

Tidied up boolean attribute parsing in various classes

3503 lines of code changed in 34 files:

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

Output performance message only to screen logs

19 lines of code changed in 5 files:

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...

2541 lines of code changed in 14 files:

alexei.drummond 2008-07-10 01:14 Rev.: 984

tidying

37 lines of code changed in 1 file:

jheled 2008-07-10 00:15 Rev.: 983

oldCoal usage cleanup

2 lines of code changed in 1 file:

alexei.drummond 2008-07-10 00:08 Rev.: 982

fixed spelling :-0)

4 lines of code changed in 1 file:

jheled 2008-07-09 23:31 Rev.: 981

oldCoal usage cleanup

34 lines of code changed in 5 files:

jheled 2008-07-09 23:00 Rev.: 980

Allow any tree in target, not just tree models

132 lines of code changed in 1 file:

jheled 2008-07-09 22:56 Rev.: 979

Restore broken EBSP

89 lines of code changed in 3 files:

alexei.drummond 2008-07-07 22:26 Rev.: 978

Actually it was just a display error - but was still causing confusion

1 lines of code changed in 1 file:

alexei.drummond 2008-07-07 22:21

The appears to be a bug in SitePatternsParser. If to="x" is specified as an attribute then the site pattern is actually created up to an including site number x-1 (counting the first site as 1). This is inconsistent with the handling of the "from" attribute. It also causes an inconsistency between the XML and the output of BEAST when the file is run. This should be added to the list of fixes in next BEAST release.

31 lines of code changed in 2 files:

bloomquist 2008-07-05 05:35 Rev.: 975

Added class to randomly sample n taxa from a collection of N taxa.

85 lines of code changed in 2 files:

rambaut 2008-07-05 03:13 Rev.: 974

Fixed problem with DateParser not recognizing calendar dates.

405 lines of code changed in 1 file:

alexei.drummond 2008-07-04 03:55 Rev.: 973

fixed annoying GUI bug in choosing the number of steps in the Bayesian skyline plot

109 lines of code changed in 1 file:

Sibon.Li@gmail.com 2008-07-02 16:06 Rev.: 972

Updated testLikelihood.xml - GTR, GTR+i and GTR+g+i added. Updated likelihood values from PAUP. PAUP nexus file now added to the bottom.

386 lines of code changed in 1 file:

rambaut 2008-07-02 02:30 Rev.: 971

Updated build number

1 lines of code changed in 1 file:

rambaut 2008-07-02 02:28 Rev.: 970

Logged a warning when scaling is turned on.

2 lines of code changed in 1 file:

rambaut 2008-07-02 02:25 Rev.: 969

OK. Automatic scaling is now working. If the initial evaluation of the log likelihood returns -Inf then it turns on. It will impact performance but is better than not working at all. There are a number of improvements that could be made: one is to switch it off again once the tree is significantly improved. The other is to only rescale on certain nodes.

I tested it by comparing with the ArbitraryPrecisionLikelihoodCore (see ExperimentalTreeLikelihood) which is a form of GeneralLikelihoodCore that uses BigDecimal to a specified precision.

751 lines of code changed in 13 files:

rambaut 2008-07-01 23:19 Rev.: 968

More work on the scaling issue. Removed CodonLikelihoodCore because it does nothing that GeneralLikelihoodCore doesn't do but is out of date.

870 lines of code changed in 15 files:

rambaut 2008-07-01 03:23 Rev.: 967

Am working on a partial likelihood scaling mechanism that will allow us to calculate likelihoods of very bad trees and very big trees. The aim is that this is dynamic and switches off if no longer needed. It is crude at the moment but compiles and runs (and shouldn't affect anything that doesn't explicitly ask for it).

566 lines of code changed in 21 files:

June 2008 »

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