StatSVN - Directory src/dr/app/beauti/util/

Author	Changes	Lines of Code	Lines per Change
Totals	105 (100.0%)	4806 (100.0%)	45.7
dong.w.xie	67 (63.8%)	3798 (79.0%)	56.6
rambaut	30 (28.6%)	676 (14.1%)	22.5
alexei.drummond	4 (3.8%)	252 (5.2%)	63.0
fbielejec	1 (1.0%)	53 (1.1%)	53.0
jheled	2 (1.9%)	24 (0.5%)	12.0
dong.w.xie@gmail.com	1 (1.0%)	3 (0.1%)	3.0

Most Recent Commits

rambaut 2013-05-13 04:13 Rev.: 5647

Added fasta (and fa and fas) as recognized extensions

2 lines of code changed in 2 files:

src/dr/app/beauti/util: BEAUTiImporter.java (+2 -2)

rambaut 2013-05-11 17:33 Rev.: 5646

Fixed that BEAUti was putting stateTagName attribute into TreeLikelihood elements (even though they should only be there for ancestralStateTreeLikelihoods). Was giving a parser warning when run (no other consequences).

4 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+4 -1)

dong.w.xie@gmail.com 2013-02-25 10:31 Rev.: 5458

trunk: merge Issue 677

3 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+3)

rambaut 2013-01-31 04:42 Rev.: 5367

Porting some fixes from 1.7 branch

3 lines of code changed in 2 files:

src/dr/app/beauti/util: NexusApplicationImporter.java (new)

rambaut 2012-08-09 01:27 Rev.: 5118

Port from 1.7

1 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+1 -1)

rambaut 2012-08-08 21:31 Rev.: 5110

Porting changes from branch 1.7 r5109

2 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+2 -1)

rambaut 2012-03-11 22:59 Rev.: 4813

Porting fix for Issue 605 to trunk

32 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+32 -8)

rambaut 2011-12-04 10:43 Rev.: 4501

Added a dialog box to rename a partition if it has the same name as an existing partition.

127 lines of code changed in 2 files:

src/dr/app/beauti/util: BEAUTiImporter.java (+38 -9), PartitionNameDialog.java (new 89)

dong.w.xie 2011-11-25 13:46 Rev.: 4491

trunk:solve Issue 549: BeautiOptions.updateAll() stop user to customize clock rates

5 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+5 -4)

rambaut 2011-11-22 07:21 Rev.: 4469

Added explicit selection of dN/dS robust counting with additional citation text to keep Marc happy.

7 lines of code changed in 3 files:

src/dr/app/beauti/util: NexusApplicationImporter.java (+1 -1), PanelUtils.java (+6)

rambaut 2011-11-16 21:59 Rev.: 4439

Fixed a few more '!' in user interface messages. Let's keep them for errors that shouldn't happen (i.e., are genuine surprises).

61 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+61 -61)

rambaut 2011-09-16 03:04 Rev.: 4316

Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.

1 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+1 -1)

fbielejec 2011-09-09 01:33 Rev.: 4296

method to return active frame

53 lines of code changed in 1 file:

src/dr/app/beauti/util: PanelUtils.java (+53 -40)

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

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

90 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+90 -99)

alexei.drummond 2011-08-02 14:53 Rev.: 4150

added handling for multi-block partitions

99 lines of code changed in 2 files:

src/dr/app/beauti/util: BEAUTiImporter.java (+28 -3), NexusApplicationImporter.java (+71 -34)

rambaut 2011-06-24 20:49 Rev.: 4062

Some serious cleaning up of how priors are specified. This allows appropriate prior choices for different 'flavours' of parameters (non-negative, zero-one interval, discrete, HPM, CMTC rates). Truncation of the the prior is now a switch and bounds so can be applied to any prior (although the UI is not in place for this yet).

15 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+15 -5)

dong.w.xie 2011-03-31 16:53 Rev.: 3909

Trunk: BEAUti microsat works, but XML is not working in BEAST because of transition probability entry out of bound.

1 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+1)

dong.w.xie 2011-03-28 17:06 Rev.: 3905

Trunk: big update in BEAUti micro-sat.

53 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+53 -72)

dong.w.xie 2011-03-16 16:48 Rev.: 3877

Trunk: big change of implementing clock model group, including to correct some auto GUI event regarding "fix mean" and calibration. Not finished yet.

5 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+5 -6)

dong.w.xie 2011-03-14 16:27 Rev.: 3872

Trunk: more work on micro-sat data in BEAUti.

1 lines of code changed in 2 files:

src/dr/app/beauti/util: CommandLineBeauti.java (+1 -1)

dong.w.xie 2011-03-11 14:03 Rev.: 3867

Trunk: correct a bug in BeautiImpoter that stops BEAUti framework to load micro-sat data, and make framework to recognize data type by searching partitions.

36 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+36 -33)

dong.w.xie 2011-03-11 12:03 Rev.: 3866

Trunk: refactory BEAUti framework.

6 lines of code changed in 1 file:

src/dr/app/beauti/util: NexusApplicationImporter.java (+6 -5)

dong.w.xie 2011-03-11 11:09 Rev.: 3865

Trunk: fix a bug in MicroSatImporter when loading diploid locus data.

34 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+34 -37)

dong.w.xie 2011-03-10 16:30 Rev.: 3864

Trunk: start to make micro-satellite available in BEAUti panels.

2 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+2 -2)

dong.w.xie 2011-03-10 12:11 Rev.: 3863

Trunk: make micro-satellite file successfully loaded in BEAUti data panel.
Start to use jdk1.6 code.

221 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+221 -173)

dong.w.xie 2011-03-09 17:32 Rev.: 3862

Trunk: micro-satellite importer for BEAUti.

3 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+3 -2)

dong.w.xie 2011-03-08 15:15 Rev.: 3860

Trunk: big check-in to add micro-satellite in BEAUti.
1) Because it uses patterns not alignment, PartitionPattern is added, and PartitionData is still used for all previous data type.
2) getDataType is corrected to get actual data type, where traits are generalDataType, and trait name is getting from getDataDescription.
3) add MICRO_SAT data type.

23 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+23)

dong.w.xie 2011-03-01 15:17 Rev.: 3840

Trunk: solve Issue 420: Add error message : Partitions cannot have the same name

7 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+7 -3)

rambaut 2010-10-27 01:30 Rev.: 3680

Many fixes for discrete trait generation.

1 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+1 -3)

rambaut 2010-10-23 03:56 Rev.: 3664

This is a very large commit. It addresses some architectural issues in BEAUti that were going to hinder implementation of continuous traits.

The main thing it does is to isolate creating and importing traits from creating partitions on those traits. A button on the data panel explicitly specifies that a trait should be used as a data partition (i.e., have a TreeLikelihood). This allows traits to be used for other purposes (such as defining Species in *BEAST). This has also allowed considerable simplification of code and tidying up.

There are a number of bug fixes as well over v1.6.0 that I will add to the issue list to keep track of them. Given the complex nature of these changes, I do not think these should be ported to the 1.6.0 branch but perhaps the bugs can be fixed.

These changes will have introduced bugs and possibly cause issues with XML generation that now need to be fixed (I will attempt to catch as many as possible).

85 lines of code changed in 6 files:

src/dr/app/beauti/util: BEAUTiImporter.java (+36 -1), BeastImporter.java (new), BeautiTemplate.java (new), NexusApplicationImporter.java (+1 -1)

dong.w.xie 2010-10-13 15:48 Rev.: 3641

Trunk: merge issue 416, 417 and 418.

23 lines of code changed in 1 file:

src/dr/app/beauti/util: NumberUtil.java (new 23)

dong.w.xie 2010-10-12 09:26 Rev.: 3627

Trunk: merge Issue 413: BEAUti: duplicate class PartitionModelOptions causes
model link conflict.

3 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+3 -3)

dong.w.xie 2010-10-05 14:46 Rev.: 3599

Trunk: merge Issue 410: "Improper priors" on posterior statistics from branch 1.6.

4 lines of code changed in 1 file:

src/dr/app/beauti/util: BeautiTemplate.java (+4 -7)

dong.w.xie 2010-08-25 18:04 Rev.: 3444

Trunk: solve Issue 374: BEAUti: only one taxa set for 3 unlinked partitions

44 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+44 -51)

rambaut 2010-08-18 23:24 Rev.: 3404

Firstly, made writeComment take a VarArg number of strings to allow for multi-line comments. Comments now have a blank line before them to break up the XML visually.

Secondly, removed the 'booleanLikelihood' for LogisticModel as this was nasty. Instead, proper priors need to be put on the t50 parameter (a gamma is given as default). Also added gamma default prior to the doubling time parameter (and picked a larger initial value to help with numerical issues in logistic and expansion model).

Thirdly, normalized the generation of discrete trait models to always use generalSubstitutionModel.

Have generated all these model and tested that they run (but not that they produce reasonable results).

18 lines of code changed in 2 files:

src/dr/app/beauti/util: XMLWriter.java (new)

dong.w.xie 2010-08-13 15:50 Rev.: 3390

Trunk: solve Issue 356: Add instruction to show user how to load specified starting tree from BEAUti

19 lines of code changed in 2 files:

src/dr/app/beauti/util: TextUtil.java (+19 -2)

dong.w.xie 2010-08-13 14:41 Rev.: 3389

Trunk: solve Issue 354: BEAUti: make auto wrap for HTMLEditorKit inside JEditorPane, and Issue 355: get rid of ">" when wrapping text using BEAUti TextUtil

1 lines of code changed in 1 file:

src/dr/app/beauti/util: TextUtil.java (+1 -1)

dong.w.xie 2010-08-13 14:04 Rev.: 3388

Trunk: solve Issue 351: message label on the bottom of BEAUti frame is floating when no space enough

42 lines of code changed in 1 file:

src/dr/app/beauti/util: TextUtil.java (+42)

rambaut 2010-08-05 04:13 Rev.: 3364

This is rather a large update as I was making changes in a branch and have merged them back in. This allows any trait name to be created (not just 'Location' and 'Species'). The idea is that the discrete model is not phylogoegraphy specific - you can model any discrete change. Have added a check box to say use *BEAST - at this point you should create a Species trait. Have cleaned up a few othe UI issues. Almost certainly there will be XML generation issues as a result and we should concentrate on testing and fixing these.

179 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+179 -54)

dong.w.xie 2010-06-24 11:51 Rev.: 3283

TRUNK: merge Issue 323: BEAUti: reload xml having alignments with different taxa

6 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+6 -2)

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