Directory src/dr/evolution/io/

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dong.w.xie@gmail.com 2013-02-22 11:25 Rev.: 5454

trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.

8 lines of code changed in 2 files:

• src/dr/evolution/io: MicroSatImporter.java (new)

rambaut 2013-02-15 12:47 Rev.: 5406

Ported recent updates from 1.7 branch

17 lines of code changed in 2 files:

• src/dr/evolution/io: NexusImporter.java (new)

alexei.drummond 2012-12-20 10:37 Rev.: 5288

Added warning about single-child internal nodes that is suppressed in TreeStat but active in BEAST-MCMC and other programs.

9 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+9 -3)

alexei.drummond 2012-12-20 08:51 Rev.: 5285

Relaxed nexus importer to allow internal nodes with 1 or more children. This is to allow TreeStat to analyze direct ancestor trees and migration trees where migrations events are defined by internal nodes.

11 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+11 -7)

msuchard 2012-12-20 07:49 Rev.: 5284

Modified NexusImporter to handle nested arrays. May cause unforeseen bugs in important other traits.

31 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+31 -2)

msuchard 2012-06-23 08:34 Rev.: 5042

Standardizing format for change events; these should always be an array of arrays because the number of events is variable.

8 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+8 -8)

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.

5 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+5 -5)

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

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

3 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+3 -3)

rambaut 2011-08-23 18:18 Rev.: 4231

Very minor language improvements.

1 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+1 -1)

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

trunk: merge Issue 495 from branch 1.6

6 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+6 -1)

dong.w.xie 2011-05-24 17:23 Rev.: 3987

Trunk: update get date from tree

0 lines of code changed in 1 file:

• src/dr/evolution/io: GetDateFromTree.java (del)

dong.w.xie 2011-05-23 18:50 Rev.: 3986

Trunk: update get date from tree

12 lines of code changed in 1 file:

• src/dr/evolution/io: GetDateFromTree.java (new 12)

dong.w.xie 2011-05-20 11:10 Rev.: 3983

Trunk: a tool to get date value from given tree

78 lines of code changed in 1 file:

• src/dr/evolution/io: GetDateFromTree.java (+78)

rambaut 2011-04-28 04:27 Rev.: 3964

2 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+2 -2)

dong.w.xie 2011-04-01 17:53 Rev.: 3920

Trunk: A new XML for Calibration with Yule.

3 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+3 -1)

dong.w.xie 2011-04-01 13:20 Rev.: 3918

Trunk: finish micro-sat finailly.

53 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+53 -17)

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.

6 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+6)

dong.w.xie 2011-03-30 16:45 Rev.: 3907

Trunk: continue to work on BEAUti microsat, but writing different taxa function still has a bug.

3 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+3 -3)

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

Trunk: big update in BEAUti micro-sat.

9 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+9 -4)

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

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

9 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+9 -3)

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

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

40 lines of code changed in 3 files:

• src/dr/evolution/io: MicroSatImporter.java (+39 -22), PatternImporter.java (new)

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.

26 lines of code changed in 2 files:

• src/dr/evolution/io: MicroSatImporter.java (+23 -12), PatternImporter.java (+3 -2)

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

Trunk: micro-satellite importer for BEAUti.

139 lines of code changed in 2 files:

• src/dr/evolution/io: MicroSatImporter.java (+120 -7), PatternImporter.java (+19)

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.

25 lines of code changed in 1 file:

• src/dr/evolution/io: MicroSatImporter.java (+25)

alexei.drummond 2010-04-13 17:29 Rev.: 3116

Small fixes to migrate conversion program

21 lines of code changed in 2 files:

• src/dr/evolution/io: MigrateTreeImporter.java (+21 -19)

alexei.drummond 2010-04-13 12:10 Rev.: 3115

Converter for Migrate trees that converts migrations to population reconstructions at internal nodes

316 lines of code changed in 4 files:

• src/dr/evolution/io: MigrateTreeImporter.java (+288), NewickImporter.java (+11 -10), NexusImporter.java (+17 -17)

rambaut 2010-03-18 18:32 Rev.: 3055

Added ability to import FASTA format files in BEAUti. Should probably allow extraction of individual fields from label line.

206 lines of code changed in 3 files:

• src/dr/evolution/io: FastaImporter.java (new 108), Importer.java (+98 -98)

rambaut 2009-11-29 08:53 Rev.: 2625

New version of Path-O-Gen v1.2 released.

13 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+13 -3)

rambaut 2009-11-26 04:04 Rev.: 2612

Another little tree processing main.

11 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+11)

rambaut 2009-11-05 03:21 Rev.: 2507

A fix for the empiricalTreeDistributionModel. If the NEXUS tree file uses a translation list then these numbers are used as node numbers.

17 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+17 -1)

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

generify and auto intelliJ

1 lines of code changed in 1 file:

• src/dr/evolution/io: NewickImporter.java (+1 -1)

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

automatic idea changes and generify

14 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+14 -17)

jheled 2009-08-17 16:56 Rev.: 2088

Give more info upon error

2 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+2 -1)

alexei.drummond 2009-07-13 22:26 Rev.: 1844

Refactoring to remove illegal dependencies. No classes in dr.evolution.* packages should depend on classes in dr.evomodel.* or dr.inference.* or dr.evomodelxml. Also converted dr.evolution.coalescent.IntervalType to enum and minor other tidy ups.

196 lines of code changed in 1 file:

• src/dr/evolution/io: TreeTrace.java (new 196)

jheled 2009-05-24 19:21 Rev.: 1741

Parse comments in Newick parser as well

16 lines of code changed in 1 file:

• src/dr/evolution/io: NewickImporter.java (+16 -8)

rambaut 2009-02-11 05:01 Rev.: 1424

Work on Path-O-Gen

2 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+2)

rambaut 2009-02-10 22:23 Rev.: 1422

Work on Path-O-Gen

9 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+9 -8)

jheled 2008-11-17 13:09 Rev.: 1309

Handle root attributes correctly. (e.g. tree [comment] = [&R] [&W xxx] (( ...))

38 lines of code changed in 2 files:

• src/dr/evolution/io: Importer.java (+2 -1), NexusImporter.java (+36 -12)

rambaut 2008-11-16 00:12 Rev.: 1306

Added a statistic to TreeStat to obtain the mean of an attribute across a clade.

3 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+3 -4)

rambaut 2008-08-15 11:08 Rev.: 1133

Started work on a TreesPanel. Moved tree prior stuff here. Allow selection of user tree (from those loaded). Other features to be added soon is the ability to do a root to tip plot to check temporal signal. Other tweaks and fixes.

1 lines of code changed in 1 file:

• src/dr/evolution/io: NexusImporter.java (+1 -1)

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