Directory src/dr/evolution/util/

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rambaut 2013-05-10 03:29 Rev.: 5642

Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.

27 lines of code changed in 2 files:

• src/dr/evolution/util: Date.java (+27 -5)

fbielejec 2013-03-22 20:36 Rev.: 5523

missing hashCode method

5 lines of code changed in 2 files:

• src/dr/evolution/util: Taxon.java (new)

rambaut 2012-08-08 10:19 Rev.: 5107

Porting 'evaluateLate' interface method from 1.7 branch.

0 lines of code changed in 1 file:

• src/dr/evolution/util: Taxon.java (-2)

rambaut 2012-08-01 04:12 Rev.: 5079

Fixed a (hopefully) final issue with sampling dates.

4 lines of code changed in 1 file:

• src/dr/evolution/util: Taxon.java (+4)

rambaut 2012-07-19 04:41 Rev.: 5073

Overhauled the date system so that the 'height' timescale is now universal to all taxa. Previously there was an issue if you create independent trees on different taxon sets, they would have their own 'zero' point depending on their most recently sampled taxon. Now, when you call 'setDate' for a taxon (as done by the TaxonParser) it keeps track of the globally most recent sample (in a static variable) and can give the global height from a given date object using a static function. Taxon objects also have a 'getHeight' methods that uses this system. The two main sources of trees (CoalescentSimulator and NewickParser) now use these heights (simplifying their own code). Runs benchmarks correctly but keep an eye out for issues.

122 lines of code changed in 2 files:

• src/dr/evolution/util: Date.java (+9), Taxon.java (+113 -75)

rambaut 2012-05-17 20:47 Rev.: 4979

Fix for issue with multi-threading not working. The issue was that -threads 0 was being treated as no-multithreading where as it should specify an automatic thread pool size (having no -threads option gives a thread 0 value). For best performance the default should be not to use the thread command line option (but -threads 1 should be used to turn off multithreading). This also affected -beagle_instances as these use the threadpool.

1 lines of code changed in 2 files:

• src/dr/evolution/util: Taxa.java (+1)

rambaut 2012-01-04 02:27 Rev.: 4569

Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.

3 lines of code changed in 2 files:

• src/dr/evolution/util: Units.java (new)

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.

26 lines of code changed in 4 files:

• src/dr/evolution/util: Taxa.java (+5 -1), Taxon.java (+7 -2), TaxonList.java (+14)

dong.w.xie 2011-08-23 14:41 Rev.: 4230

trunk: merge Issue 495 from branch 1.6

15 lines of code changed in 1 file:

• src/dr/evolution/util: TaxonList.java (+15 -1)

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).

4 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+4 -19)

dong.w.xie 2010-08-17 16:23 Rev.: 3402

Trunk: solve Issue 298: BEAUti should validate a user specified tree that is only bifurcating at the root

24 lines of code changed in 1 file:

• src/dr/evolution/util: Units.java (+24 -11)

rambaut 2010-04-29 02:53 Rev.: 3143

Fixed an issue with BEAUti importing calendar dates from an existing XML file. The way the date was converted (using the birthdate of the well-known offspring of a polular deity) was inducing precision problems resulting in inaccurate dates expressed as decimal years (in the order of a month).

21 lines of code changed in 3 files:

• src/dr/evolution/util: Date.java (+20 -5), TimeScale.java (new)

dong.w.xie 2010-02-16 15:30 Rev.: 2924

Trunk refactoring: RandomTaxaSampleParser.

0 lines of code changed in 1 file:

• src/dr/evolution/util: RandomTaxaSample.java (del)

dong.w.xie 2009-12-10 16:04 Rev.: 2686

Trunk: merge from branch 1.5 in

21 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+21 -4)

jheled 2009-09-09 08:26 Rev.: 2227

generify and auto intelliJ

1 lines of code changed in 1 file:

• src/dr/evolution/util: Taxon.java (+1 -1)

jheled 2009-09-08 11:29 Rev.: 2224

generify via auto intelliJ

2 lines of code changed in 1 file:

• src/dr/evolution/util: Taxon.java (+2 -5)

jheled 2009-09-07 14:23 Rev.: 2218

automatic idea changes and generify

10 lines of code changed in 2 files:

• src/dr/evolution/util: Taxa.java (+7 -5), Taxon.java (+3 -3)

jheled 2009-07-21 13:26 Rev.: 1889

Intellij auto changes

33 lines of code changed in 1 file:

• src/dr/evolution/util: RandomTaxaSample.java (new 33)

dong.w.xie 2009-04-30 13:53 Rev.: 1654

Add boolean containsAttribute(String name) to check whether Taxon contains the attribute by given its name, if attributes == null, return false.

12 lines of code changed in 1 file:

• src/dr/evolution/util: Taxon.java (+12)

rambaut 2009-04-26 05:52 Rev.: 1637

Made some improvements to TaxonList and Taxa to make them work better with collections. For a start TaxonList is now Iterable so can be used in a for(Taxon taxon : taxonList) construct. In the long run we would be better dropping TaxonList and just replacing it with List<Taxon>.

106 lines of code changed in 3 files:

• src/dr/evolution/util: RandomTaxaSample.java (+33 -33), Taxa.java (+65 -2), TaxonList.java (+8 -2)

rambaut 2009-04-08 04:33 Rev.: 1539

Made it easier to set up CTMC of locations by allowing GeneralDataTypeParser to take Identifyable objects as states (such as a set of Location objects). The AttributePatternsParser can then extract the states from attributes of the taxa.

110 lines of code changed in 2 files:

• src/dr/evolution/util: Location.java (new 92), Taxon.java (+18)

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

automatic idea changes

1 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+1 -1)

bloomquist 2008-08-13 07:27 Rev.: 1118

Added a feature to print out the random sample in RandomTaxaSample.java in xml format. Also added a logChoose function to the Binomial class for overflow reasons.

57 lines of code changed in 1 file:

• src/dr/evolution/util: RandomTaxaSample.java (+57 -2)

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

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

83 lines of code changed in 1 file:

• src/dr/evolution/util: RandomTaxaSample.java (+83)

rambaut 2007-08-16 03:38 Rev.: 504

Fixed Taxa so it can only add taxa that are not already present. Hence removed unionTaxons and renamed addTaxons and removeTaxons to addTaxa and removeTaxa. This means that taxa

21 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+21 -22)

jheled 2007-08-08 20:10 Rev.: 468

add support for non monophyletic constraints. The logic is not proven to be 100% but hopefully will take care of almost all reasonable usage.

9 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+9)

jheled 2007-08-05 20:15 Rev.: 445

new version for mrca constraints and test files

22 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+22 -5)

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/evolution/util: Units.java (+1 -1)

jheled 2007-06-28 16:06 Rev.: 334

generify and remove dead code

20 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+20 -20)

rambaut 2007-06-01 10:56 Rev.: 286

Fixed a couple of errors due to an incomplete port of fixes from the 1.4 branch.

18 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+18 -2)

rambaut 2007-04-25 03:40 Rev.: 248

Ported improvements and bug fixes from the 1.4.x branch into Trunk.

18 lines of code changed in 1 file:

• src/dr/evolution/util: Taxa.java (+18)

jheled 2007-01-25 10:36 Rev.: 172

comments & cosmetic changes

2 lines of code changed in 1 file:

• src/dr/evolution/util: TaxonList.java (+2 -2)

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

54 lines of code changed in 3 files:

• src/dr/evolution/util: Date.java (+14 -14), TimeScale.java (+25 -25), Units.java (+15 -42)