/trunk Developers: dong.w.xie

Login name:
dong.w.xie
Total Commits:
5,844 (24.2%)
Lines of Code:
310,067 (27.2%)
Most Recent Commit:
2012-02-15 11:30
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 5844 (100.0%) 310067 (100.0%) 53.0
release/common/examples/ 154 (2.6%) 26557 (8.6%) 172.4
doc/Virus Practical Tex/ 15 (0.3%) 23720 (7.6%) 1581.3
release/common/doc/ 6 (0.1%) 21003 (6.8%) 3500.5
src/dr/app/beauti/options/ 709 (12.1%) 18276 (5.9%) 25.7
examples/unrelease/ 130 (2.2%) 17429 (5.6%) 134.0
src/dr/app/beauti/generator/ 647 (11.1%) 15037 (4.8%) 23.2
doc/EBSP/mystery-run-1/ 28 (0.5%) 13895 (4.5%) 496.2
native/expokit/ 21 (0.4%) 9592 (3.1%) 456.7
doc/tutorial/DivergenceDating/1.2_Primates/ 4 (0.1%) 8520 (2.7%) 2130.0
doc/tutorial/BSP/ 7 (0.1%) 6877 (2.2%) 982.4
examples/incorrect/ 23 (0.4%) 6239 (2.0%) 271.2
release/common/examples/beauti1.5/starBEAST/ 8 (0.1%) 4767 (1.5%) 595.8
examples/beauti1.6/starBEAST/ 16 (0.3%) 4573 (1.5%) 285.8
release/common/examples/starBEAST/ 18 (0.3%) 4371 (1.4%) 242.8
examples/beauti1.5/starBEAST/ 24 (0.4%) 4371 (1.4%) 182.1
native/ 31 (0.5%) 4006 (1.3%) 129.2
src/dr/app/beauti/util/ 67 (1.1%) 3798 (1.2%) 56.6
release/common/examples/treePriors/ 40 (0.7%) 3542 (1.1%) 88.5
src/dr/app/beauti/taxonsetspanel/ 24 (0.4%) 3035 (1.0%) 126.4
examples/release/clockModels/ 15 (0.3%) 2936 (0.9%) 195.7
src/dr/app/tracer/traces/ 109 (1.9%) 2933 (0.9%) 26.9
release/common/examples/treePrior+clockModel/ 36 (0.6%) 2887 (0.9%) 80.1
examples/beauti1.5/treePrior+clockModel/ 19 (0.3%) 2887 (0.9%) 151.9
release/common/examples/beauti1.5/treePrior+clockModel/ 18 (0.3%) 2876 (0.9%) 159.7
examples/beauti1.6/codon/ 12 (0.2%) 2860 (0.9%) 238.3
src/dr/evomodelxml/coalescent/ 42 (0.7%) 2825 (0.9%) 67.2
/ 77 (1.3%) 2799 (0.9%) 36.3
src/dr/app/beauti/treespanel/ 145 (2.5%) 2674 (0.9%) 18.4
src/dr/app/tools/ 44 (0.8%) 2458 (0.8%) 55.8
src/dr/app/beauti/ 146 (2.5%) 2427 (0.8%) 16.6
src/dr/inference/trace/ 128 (2.2%) 2335 (0.8%) 18.2
src/dr/evomodelxml/substmodel/ 35 (0.6%) 2291 (0.7%) 65.4
src/dr/app/beauti/datapanel/ 91 (1.6%) 2290 (0.7%) 25.1
src/dr/app/beauti/priorsPanel/ 73 (1.2%) 2121 (0.7%) 29.0
examples/release/ 24 (0.4%) 1932 (0.6%) 80.5
src/dr/app/beauti/siteModelsPanel/ 49 (0.8%) 1882 (0.6%) 38.4
src/dr/inferencexml/distribution/ 21 (0.4%) 1878 (0.6%) 89.4
src/dr/evomodelxml/tree/ 25 (0.4%) 1769 (0.6%) 70.7
src/test/dr/integration/ 32 (0.5%) 1711 (0.6%) 53.4
src/dr/inferencexml/model/ 31 (0.5%) 1639 (0.5%) 52.8
doc/StarBEAST/ 6 (0.1%) 1587 (0.5%) 264.5
src/dr/inferencexml/operators/ 34 (0.6%) 1549 (0.5%) 45.5
src/dr/evomodelxml/ 69 (1.2%) 1527 (0.5%) 22.1
src/dr/app/beast/ 122 (2.1%) 1372 (0.4%) 11.2
src/dr/app/beauti/clockModelsPanel/ 43 (0.7%) 1321 (0.4%) 30.7
examples/release/treePriors/ 30 (0.5%) 1291 (0.4%) 43.0
src/dr/app/SnAPhyl/ 21 (0.4%) 1256 (0.4%) 59.8
src/dr/evomodelxml/speciation/ 35 (0.6%) 1220 (0.4%) 34.8
src/dr/app/tracer/analysis/ 42 (0.7%) 1216 (0.4%) 28.9
doc/tutorial/DivergenceDating/1.2_Primates/latex/ 3 (0.1%) 1171 (0.4%) 390.3
src/dr/evomodelxml/operators/ 22 (0.4%) 1142 (0.4%) 51.9
release/common/examples/Phylogeography/ 2 (0.0%) 1137 (0.4%) 568.5
release/common/examples/beauti1.5/Virus Practical/RSVA/ 6 (0.1%) 1077 (0.3%) 179.5
doc/tutorial/StarBEAST/ 4 (0.1%) 1058 (0.3%) 264.5
src/dr/app/beauti/traitspanel/ 69 (1.2%) 1053 (0.3%) 15.2
src/dr/app/beauti/mcmcpanel/ 21 (0.4%) 1050 (0.3%) 50.0
examples/release/microsatellite/ 1 (0.0%) 1012 (0.3%) 1012.0
doc/tutorial/Virus_Practical_1_6_1/ 2 (0.0%) 1007 (0.3%) 503.5
src/dr/app/tracer/application/ 37 (0.6%) 994 (0.3%) 26.8
src/dr/app/beauti/enumTypes/ 46 (0.8%) 994 (0.3%) 21.6
src/dr/evomodelxml/branchratemodel/ 14 (0.2%) 947 (0.3%) 67.6
src/test/dr/evomodel/branchratemodel/ 28 (0.5%) 920 (0.3%) 32.8
native/deprecated/ 3 (0.1%) 870 (0.3%) 290.0
src/dr/app/beauti/tipdatepanel/ 28 (0.5%) 863 (0.3%) 30.8
src/dr/app/SnAPhyl/datapanel/ 13 (0.2%) 860 (0.3%) 66.1
release/common/examples/calibrations/ 18 (0.3%) 827 (0.3%) 45.9
doc/tutorial/DivergenceDating/1.2_Primates/latex/figures/ 29 (0.5%) 825 (0.3%) 28.4
doc/tutorial/EBSP/flu/figures/ 14 (0.2%) 814 (0.3%) 58.1
src/test/dr/evomodel/treelikelihood/ 13 (0.2%) 750 (0.2%) 57.6
src/test/dr/evomodel/operators/ 27 (0.5%) 728 (0.2%) 26.9
release/common/examples/beauti1.5/Virus Practical/FPV/ 6 (0.1%) 703 (0.2%) 117.1
src/test/dr/beauti/ 27 (0.5%) 690 (0.2%) 25.5
src/dr/inferencexml/loggers/ 6 (0.1%) 673 (0.2%) 112.1
release/Launch4j/lib/ 26 (0.4%) 668 (0.2%) 25.6
src/dr/evomodel/speciation/ModelAveragingResearch/ 6 (0.1%) 654 (0.2%) 109.0
src/test/dr/evomodel/substmodel/ 17 (0.3%) 646 (0.2%) 38.0
release/common/ 20 (0.3%) 632 (0.2%) 31.6
src/dr/app/beauti/operatorspanel/ 8 (0.1%) 614 (0.2%) 76.7
examples/release/substModels/ 4 (0.1%) 607 (0.2%) 151.7
src/dr/app/SnAPhyl/util/ 8 (0.1%) 603 (0.2%) 75.3
release/ 13 (0.2%) 598 (0.2%) 46.0
doc/tutorial/DivergenceDating/1.1a_Primates/latex/ 1 (0.0%) 585 (0.2%) 585.0
doc/tutorial/Virus_Practical_1_6_1/figures3/ 44 (0.8%) 577 (0.2%) 13.1
src/test/dr/app/beauti/ 3 (0.1%) 568 (0.2%) 189.3
src/dr/gui/chart/ 11 (0.2%) 548 (0.2%) 49.8
doc/tutorial/EBSP/flu/ 2 (0.0%) 512 (0.2%) 256.0
src/dr/app/oldbeauti/ 44 (0.8%) 500 (0.2%) 11.3
release/common/examples/beauti1.5/ 24 (0.4%) 495 (0.2%) 20.6
examples/beauti1.6/ 16 (0.3%) 495 (0.2%) 30.9
src/dr/inferencexml/ 22 (0.4%) 492 (0.2%) 22.3
src/test/dr/inference/trace/ 11 (0.2%) 486 (0.2%) 44.1
src/dr/inference/model/ 53 (0.9%) 486 (0.2%) 9.1
src/test/dr/calibration/ 4 (0.1%) 478 (0.2%) 119.5
release/common/examples/beauti1.5/Virus Practical/Flu/ 4 (0.1%) 461 (0.1%) 115.2
src/dr/app/SnAPhyl/priorsPanel/ 11 (0.2%) 457 (0.1%) 41.5
release/common/examples/beauti1.5/Gopher Data/ 14 (0.2%) 449 (0.1%) 32.0
release/common/examples/Data/Gopher Data/ 23 (0.4%) 449 (0.1%) 19.5
release/common/examples/Data/ 20 (0.3%) 434 (0.1%) 21.7
examples/Data/ 16 (0.3%) 434 (0.1%) 27.1
doc/tutorial/DivergenceDating/1.1a_Primates/ 2 (0.0%) 423 (0.1%) 211.5
examples/incorrect/treePriors/ 2 (0.0%) 422 (0.1%) 211.0
src/dr/app/beauti/modelsPanel/ 25 (0.4%) 415 (0.1%) 16.6
examples/ 74 (1.3%) 414 (0.1%) 5.5
src/dr/evolution/io/ 18 (0.3%) 409 (0.1%) 22.7
src/dr/app/SnAPhyl/mcmcpanel/ 6 (0.1%) 405 (0.1%) 67.5
src/dr/evomodel/operators/ 37 (0.6%) 402 (0.1%) 10.8
src/dr/evoxml/util/ 4 (0.1%) 400 (0.1%) 100.0
src/dr/app/util/ 9 (0.2%) 394 (0.1%) 43.7
src/dr/evomodelxml/treelikelihood/ 9 (0.2%) 390 (0.1%) 43.3
src/dr/evomodel/substmodel/ 66 (1.1%) 348 (0.1%) 5.2
src/dr/inferencexml/trace/ 12 (0.2%) 343 (0.1%) 28.5
src/dr/evomodel/speciation/ 36 (0.6%) 343 (0.1%) 9.5
release/Launch4j/bin/ 6 (0.1%) 340 (0.1%) 56.6
src/dr/evomodelxml/MSSD/ 5 (0.1%) 339 (0.1%) 67.8
doc/EBSP/scripts/ 4 (0.1%) 339 (0.1%) 84.7
src/dr/evomodelxml/coalescent/operators/ 4 (0.1%) 336 (0.1%) 84.0
src/dr/evoxml/ 28 (0.5%) 328 (0.1%) 11.7
src/dr/evomodelxml/sitemodel/ 4 (0.1%) 325 (0.1%) 81.2
src/dr/xml/ 24 (0.4%) 315 (0.1%) 13.1
src/dr/app/SnAPhyl/operatorspanel/ 5 (0.1%) 305 (0.1%) 61.0
src/dr/inference/loggers/ 10 (0.2%) 277 (0.1%) 27.7
examples/release/calibrations/ 19 (0.3%) 241 (0.1%) 12.6
src/dr/evomodel/coalescent/ 81 (1.4%) 188 (0.1%) 2.3
src/dr/inference/operators/ 72 (1.2%) 186 (0.1%) 2.5
src/dr/evolution/datatype/ 38 (0.7%) 182 (0.1%) 4.7
src/test/dr/inference/mcmc/ 8 (0.1%) 177 (0.1%) 22.1
src/dr/evomodelxml/indel/ 3 (0.1%) 164 (0.1%) 54.6
src/dr/app/beauti/types/ 22 (0.4%) 156 (0.1%) 7.0
src/dr/app/gui/chart/ 23 (0.4%) 150 (0.0%) 6.5
src/dr/evomodelxml/clock/ 2 (0.0%) 149 (0.0%) 74.5
src/dr/app/SnAPhyl/initializationpanel/ 2 (0.0%) 136 (0.0%) 68.0
src/test/dr/inference/prior/ 3 (0.1%) 134 (0.0%) 44.6
doc/PackageStructure/ 4 (0.1%) 125 (0.0%) 31.2
doc/EBSP/mystery-mammal/ 6 (0.1%) 120 (0.0%) 20.0
src/dr/stats/ 3 (0.1%) 110 (0.0%) 36.6
src/dr/app/pathogen/ 12 (0.2%) 106 (0.0%) 8.8
src/test/dr/evolution/ 1 (0.0%) 101 (0.0%) 101.0
src/dr/evomodel/branchratemodel/ 14 (0.2%) 83 (0.0%) 5.9
src/dr/evolution/util/ 5 (0.1%) 72 (0.0%) 14.4
src/dr/evomodel/treelikelihood/ 15 (0.3%) 70 (0.0%) 4.6
src/dr/app/beauti/components/ 26 (0.4%) 54 (0.0%) 2.0
release/Windows/ 15 (0.3%) 53 (0.0%) 3.5
examples/release/Data/ 2 (0.0%) 51 (0.0%) 25.5
src/test/dr/evomodel/speciation/ 21 (0.4%) 50 (0.0%) 2.3
examples/beauti1.5/Virus Practical/RSVA/ 6 (0.1%) 47 (0.0%) 7.8
src/dr/app/beauti/components/sequenceerror/ 3 (0.1%) 42 (0.0%) 14.0
src/dr/evolution/alignment/ 2 (0.0%) 36 (0.0%) 18.0
examples/beauti1.5/Virus Practical/Flu/ 4 (0.1%) 33 (0.0%) 8.2
src/dr/evomodel/tree/ 39 (0.7%) 32 (0.0%) 0.8
release/Linux/scripts/ 6 (0.1%) 32 (0.0%) 5.3
release/Launch4j/ 8 (0.1%) 32 (0.0%) 4.0
src/dr/util/ 6 (0.1%) 27 (0.0%) 4.5
release/Mac/scripts/ 1 (0.0%) 27 (0.0%) 27.0
release/Launch4j/manifest/ 4 (0.1%) 26 (0.0%) 6.5
src/dr/inference/mcmc/ 3 (0.1%) 25 (0.0%) 8.3
release/Launch4j/w32api/ 16 (0.3%) 25 (0.0%) 1.5
doc/tutorial/DivergenceDating/ 1 (0.0%) 24 (0.0%) 24.0
release/Launch4j/head/ 2 (0.0%) 23 (0.0%) 11.5
src/dr/inference/distribution/ 18 (0.3%) 22 (0.0%) 1.2
src/dr/math/distributions/ 8 (0.1%) 21 (0.0%) 2.6
src/dr/math/ 1 (0.0%) 21 (0.0%) 21.0
src/dr/evolution/tree/ 3 (0.1%) 20 (0.0%) 6.6
src/dr/app/coalgen/ 5 (0.1%) 18 (0.0%) 3.6
src/dr/app/beauti/components/ancestralstates/ 2 (0.0%) 18 (0.0%) 9.0
src/dr/evomodel/MSSD/ 8 (0.1%) 17 (0.0%) 2.1
src/dr/app/beagle/evomodel/parsers/ 5 (0.1%) 16 (0.0%) 3.2
src/dr/app/treestat/ 3 (0.1%) 15 (0.0%) 5.0
examples/beauti1.5/Virus Practical/FPV/ 6 (0.1%) 15 (0.0%) 2.5
src/dr/app/beauti/ancestralStatesPanel/ 3 (0.1%) 12 (0.0%) 4.0
src/test/dr/evomodel/arg/operators/ 4 (0.1%) 11 (0.0%) 2.7
src/dr/gui/tree/ 2 (0.0%) 9 (0.0%) 4.5
src/dr/app/gui/table/ 2 (0.0%) 9 (0.0%) 4.5
release/common/native/ 32 (0.5%) 8 (0.0%) 0.2
examples/treePriors/ 16 (0.3%) 8 (0.0%) 0.5
src/dr/evomodel/sitemodel/ 8 (0.1%) 7 (0.0%) 0.8
src/dr/evomodel/coalescent/operators/ 8 (0.1%) 7 (0.0%) 0.8
src/dr/evomodel/indel/ 7 (0.1%) 6 (0.0%) 0.8
src/dr/evolution/ 4 (0.1%) 6 (0.0%) 1.5
src/dr/geo/ 3 (0.1%) 5 (0.0%) 1.6
src/dr/evomodel/clock/ 4 (0.1%) 5 (0.0%) 1.2
src/dr/evolution/coalescent/ 2 (0.0%) 5 (0.0%) 2.5
src/dr/app/vcs/ 2 (0.0%) 5 (0.0%) 2.5
release/Windows/scripts/ 1 (0.0%) 5 (0.0%) 5.0
examples/Phylogeography/ 7 (0.1%) 5 (0.0%) 0.7
src/dr/evomodel/arg/operators/ 5 (0.1%) 4 (0.0%) 0.8
src/dr/evomodel/arg/ 6 (0.1%) 4 (0.0%) 0.6
src/dr/evomodel/approxPopTree/ 2 (0.0%) 3 (0.0%) 1.5
src/test/dr/math/ 2 (0.0%) 2 (0.0%) 1.0
src/dr/evomodel/transmission/ 3 (0.1%) 2 (0.0%) 0.6
src/dr/app/treestat/statistics/ 2 (0.0%) 1 (0.0%) 0.5
src/dr/app/treespace/ 1 (0.0%) 1 (0.0%) 1.0
src/dr/app/gui/components/ 1 (0.0%) 1 (0.0%) 1.0
src/dr/app/beauti/components/tipdatesampling/ 1 (0.0%) 1 (0.0%) 1.0
src/dr/app/beauti/components/discrete/ 1 (0.0%) 1 (0.0%) 1.0
src/test/dr/inference/distribution/ 1 (0.0%) 0 (0.0%) 0.0
src/test/dr/inference/ 1 (0.0%) 0 (0.0%) 0.0
src/test/dr/evomodel/ 1 (0.0%) 0 (0.0%) 0.0
src/dr/inference/xml/ 1 (0.0%) 0 (0.0%) 0.0
src/dr/inference/ml/ 1 (0.0%) 0 (0.0%) 0.0
src/dr/evomodel/tree/randomlocalmodel/ 1 (0.0%) 0 (0.0%) 0.0
src/dr/app/java16compat/ 1 (0.0%) 0 (0.0%) 0.0
src/dr/app/SnAPhyl/images/ 8 (0.1%) 0 (0.0%) 0.0
release/extra_lib/ 3 (0.1%) 0 (0.0%) 0.0
release/common/icons/ 3 (0.1%) 0 (0.0%) 0.0
release/common/examples/Virus Practical/RSVA/ 3 (0.1%) 0 (0.0%) 0.0
release/common/examples/Virus Practical/Flu/ 2 (0.0%) 0 (0.0%) 0.0
release/common/examples/Virus Practical/FPV/ 3 (0.1%) 0 (0.0%) 0.0
release/Windows/lib/ 4 (0.1%) 0 (0.0%) 0.0
release/Mac/ 1 (0.0%) 0 (0.0%) 0.0
release/Linux/lib/ 4 (0.1%) 0 (0.0%) 0.0
icons/ 11 (0.2%) 0 (0.0%) 0.0
examples/treeOpsTest/ 3 (0.1%) 0 (0.0%) 0.0
examples/release/starBEAST/ 1 (0.0%) 0 (0.0%) 0.0
examples/calibrations/ 9 (0.2%) 0 (0.0%) 0.0
examples/beauti1.6/treePrior+clockModel/ 18 (0.3%) 0 (0.0%) 0.0
examples/beauti1.5/Gopher data/ 16 (0.3%) 0 (0.0%) 0.0
examples/beauti1.5/ 8 (0.1%) 0 (0.0%) 0.0
examples/Phylogeography/continuous/ 4 (0.1%) 0 (0.0%) 0.0
doc/tutorial/Virus_Practical_1_6_1/figures2/ 9 (0.2%) 0 (0.0%) 0.0
doc/tutorial/Virus_Practical_1_6_1/figures1/ 17 (0.3%) 0 (0.0%) 0.0
doc/tutorial/Virus Practical Tex/figures3/ 25 (0.4%) 0 (0.0%) 0.0
doc/tutorial/DivergenceDating/1.1a_Primates/latex/figures/ 19 (0.3%) 0 (0.0%) 0.0
doc/tutorial/BSP/figures3/ 10 (0.2%) 0 (0.0%) 0.0
doc/Virus Practical Tex/figures3/ 18 (0.3%) 0 (0.0%) 0.0
doc/Virus Practical Tex/figures2/ 30 (0.5%) 0 (0.0%) 0.0
doc/Virus Practical Tex/figures1/ 64 (1.1%) 0 (0.0%) 0.0
doc/StarBEAST/figures/ 40 (0.7%) 0 (0.0%) 0.0
doc/EBSP/ 4 (0.1%) 0 (0.0%) 0.0
doc/ 4 (0.1%) 0 (0.0%) 0.0
bin/ 10 (0.2%) 0 (0.0%) 0.0

Activity of dong.w.xie

Most Recent Commits

dong.w.xie 2012-02-15 11:30 Rev.: 4696

trunk: update version history

16 lines of code changed in 1 file:

  • release/common: VERSION HISTORY.txt (+16 -1)
dong.w.xie 2012-02-15 09:36 Rev.: 4694

trunk: add xml test batch file

5 lines of code changed in 1 file:

  • examples: test.sh (new 5)
dong.w.xie 2011-12-22 10:19 Rev.: 4564

trunk: update README

4 lines of code changed in 1 file:

  • release/common: README.txt (+4)
dong.w.xie 2011-12-21 15:04 Rev.: 4556

trunk: update version history

40 lines of code changed in 1 file:

  • release/common: VERSION HISTORY.txt (+40 -1)
dong.w.xie 2011-12-20 12:43 Rev.: 4555

trunk: add microsatellite data and xml example

1035 lines of code changed in 2 files:

  • examples/release/Data: microsatellite_data.txt (new 23)
  • examples/release/microsatellite: microsatellite.xml (new 1012)
dong.w.xie 2011-12-20 12:25 Rev.: 4554

trunk:solve Issue 548: Beauti does not generate functional xml for msat data analysis

53 lines of code changed in 6 files:

  • src/dr/app/beauti/generator: InitialTreeGenerator.java (+2 -2), TreeLikelihoodGenerator.java (+2 -9)
  • src/dr/app/beauti/options: AbstractPartitionData.java (+2 -23), BeautiOptions.java (+16 -3), PartitionData.java (+23), PartitionPattern.java (+8)
dong.w.xie 2011-12-15 15:13 Rev.: 4546

trunk:solve Issue 565: hasIdenticalTaxa(List<AbstractPartitionData> partitionDataList) gives wrong boolean

6 lines of code changed in 2 files:

  • src/dr/app/beauti: BeautiFrame.java (+1 -1)
  • src/dr/app/beauti/options: BeautiOptions.java (+5 -3)
dong.w.xie 2011-12-15 13:38 Rev.: 4545

trunk:solve Issue 446: no indication that Checkboxes and rate text boxes are not editable in Clock Group table

18 lines of code changed in 1 file:

  • src/dr/app/beauti/clockModelsPanel: OldClockModelsPanel.java (+18 -6)
dong.w.xie 2011-12-13 11:07 Rev.: 4540

trunk:solve Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on node ages, and add a nexus example with user specified starting tree

78 lines of code changed in 5 files:

  • examples/release/Data: Primates_starting_tree.nex (new 28)
  • src/dr/app/beauti/generator: BeastGenerator.java (+2 -1), InitialTreeGenerator.java (+15 -15)
  • src/dr/app/beauti/options: PartitionTreeModel.java (+4 -1)
  • src/dr/app/beauti/treespanel: PartitionTreeModelPanel.java (+29 -19)
dong.w.xie 2011-12-12 12:10 Rev.: 4539

trunk: tidy up native/ folder but it needs Andrew to update all Makefiles before deleting compile scripts

1305 lines of code changed in 14 files:

  • build.xml (+435 -428)
  • native: Makefile (del), NewNativeLikelihoodCore.c (del), NewNativeLikelihoodCore.h (del)
  • native/deprecated: Makefile (new 40), NewNativeLikelihoodCore.c (new 713), NewNativeLikelihoodCore.h (new 117)
  • native/expokit: Makefile (del), SparseMatrixExponential.cpp (del), SparseMatrixExponential.h (del), blas.f (del), dgexpv-beast.f (del), dgpadm.f (del), lapack.f (del)
dong.w.xie 2011-12-12 10:30 Rev.: 4535

trunk: revert r4509 but keep the changes in r4529

8 lines of code changed in 1 file:

  • src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+8 -8)
dong.w.xie 2011-12-09 10:03 Rev.: 4526

trunk:solve Issue 562: BEAUTi : Birth Death Epidemiology Model update

130 lines of code changed in 3 files:

  • src/dr/app/beauti/generator: TreePriorGenerator.java (+78 -65)
  • src/dr/app/beauti/options: PartitionTreePrior.java (+51 -34)
  • src/dr/evomodelxml/speciation: BirthDeathEpidemiologyModelParser.java (+1 -1)
dong.w.xie 2011-12-07 15:37 Rev.: 4523

trunk: remove wrong dependency to dr.evomodel.newtreelikelihood.TreeLikelihood which is not used by main BEAST

4 lines of code changed in 2 files:

  • src/dr/app/beagle/evomodel/parsers: TreeLikelihoodParser.java (+1 -2)
  • src/dr/app/beauti/generator: TreeLikelihoodGenerator.java (+3 -3)
dong.w.xie 2011-12-07 11:13 Rev.: 4521

trunk: move the remaining native folder under the root of project for easy finding.

13601 lines of code changed in 46 files:

  • build.xml (+3 -3), build_BEAST_Backup_2009_10_27.xml (new)
  • native: AminoAcidLikelihoodCore.c (new 2405), AminoAcidLikelihoodCore.h (new 57), GeneralLikelihoodCore.c (new 266), GeneralLikelihoodCore.h (new 52), NativeMemoryLikelihoodCore.c (new 509), NativeMemoryLikelihoodCore.h (new 97), NativeSubstitutionModel.c (new 177), NativeSubstitutionModel.h (new 45), NucleotideLikelihoodCore.c (new 330), NucleotideLikelihoodCore.h (new 61), compileNativeWin32.bat (new 4)
  • native/expokit: Makefile (new 54), SparseMatrixExponential.cpp (new 120), SparseMatrixExponential.h (new 42), blas.f (new 4762), dgexpv-beast.f (new 850), dgpadm.f (new 340), lapack.f (new 3424)
  • release/common/native: AminoAcidLikelihoodCore.c (del), AminoAcidLikelihoodCore.h (del), GeneralLikelihoodCore.c (del), GeneralLikelihoodCore.h (del), Makefile (del), Makefile.OSX (del), Makefile.OSX.icc (del), Makefile.amd64 (del), Makefile.ia64 (del), Makefile.icc (del), Makefile.linux (del), Makefile.solaris (del), Makefile.sunos (del), NativeMemoryLikelihoodCore.c (del), NativeMemoryLikelihoodCore.h (del), NativeSubstitutionModel.c (del), NativeSubstitutionModel.h (del), NewNativeLikelihoodCore.c (del), NewNativeLikelihoodCore.h (del), NucleotideLikelihoodCore.c (del), NucleotideLikelihoodCore.h (del), compileNativeLinux.sh (del), compileNativeMacOSX.sh (del), compileNativeWin32.bat (del), expokit (del)
dong.w.xie 2011-12-07 11:07 Rev.: 4520

trunk: delete duplicate native folder

0 lines of code changed in 24 files:

  • native: AminoAcidLikelihoodCore.c (del), AminoAcidLikelihoodCore.h (del), GeneralLikelihoodCore.c (del), GeneralLikelihoodCore.h (del), Makefile (del), NativeMemoryLikelihoodCore.c (del), NativeMemoryLikelihoodCore.h (del), NativeSubstitutionModel.c (del), NativeSubstitutionModel.h (del), NewNativeLikelihoodCore.c (del), NewNativeLikelihoodCore.h (del), NucleotideLikelihoodCore.c (del), NucleotideLikelihoodCore.h (del), compileNativeLinux.sh (del), compileNativeMacOSX.sh (del), compileNativeWin32.bat (del)
  • native/expokit: Makefile (del), SparseMatrixExponential.cpp (del), SparseMatrixExponential.h (del), blas.f (del), dgexpv-beast.f (del), dgpadm.f (del), lapack.f (del)
  • release/common/native: expokit (new)
dong.w.xie 2011-12-07 10:58 Rev.: 4519

trunk:solve Issue 559: BEAUti throws exception if adding any additional partition with different taxa when already having data partitions

1 lines of code changed in 1 file:

  • src/dr/app/beauti: BeautiFrame.java (+1)
dong.w.xie 2011-12-07 10:45 Rev.: 4517

trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa

75 lines of code changed in 10 files:

  • src/dr/app/beauti: BeautiFrame.java (+1 -1)
  • src/dr/app/beauti/datapanel: DataPanel.java (+5 -5)
  • src/dr/app/beauti/generator: BeastGenerator.java (+1 -1), BranchRatesModelGenerator.java (+1 -1), InitialTreeGenerator.java (+1 -1), PatternListGenerator.java (+1 -1), TreePriorGenerator.java (+1 -1)
  • src/dr/app/beauti/options: AbstractPartitionData.java (+4), BeautiOptions.java (+60 -37)
dong.w.xie 2011-12-06 16:09 Rev.: 4511

more

3 lines of code changed in 1 file:

  • native: compileNativeLinux.sh (new 3)
dong.w.xie 2011-12-06 16:01 Rev.: 4510

trunk: make consistent between 2 native folder, we need to delete one

5 lines of code changed in 4 files:

  • release/common/native: Makefile (new), compileNativeMacOSX.sh (new)
dong.w.xie 2011-12-06 15:04 Rev.: 4509

trunk: correct getPrefix in AncestralStatesComponentGenerator

10 lines of code changed in 1 file:

  • src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+10 -9)

(883 more)

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