[med-svn] [beast2-mcmc] 03/09: Merge tag 'upstream/2.3.1+dfsg'
Andreas Tille
tille at debian.org
Mon Sep 28 13:19:23 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository beast2-mcmc.
commit 4bd58c9c55aa256eac838ec8985f4441c077e483
Merge: 13ff174 5db2939
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 28 12:45:29 2015 +0200
Merge tag 'upstream/2.3.1+dfsg'
Upstream version 2.3.1+dfsg
COPYING | 502 +++
README.md | 39 +
build.xml | 705 +++
debian/README.source | 2 -
debian/README.test | 9 -
debian/beast-mcmc-doc.install | 2 -
debian/beast-mcmc-examples.install | 1 -
debian/beast-mcmc.1 | 163 -
debian/beast-mcmc.1.xml | 325 --
debian/beast-mcmc.docs | 2 -
debian/beast-mcmc.install | 3 -
debian/beast-mcmc.manifest | 7 -
debian/beast-mcmc.manpages | 1 -
debian/beast-mcmc.menu | 15 -
debian/beast-mcmc.xpm | 163 -
debian/beauti.1 | 95 -
debian/beauti.1.xml | 185 -
debian/beauti.xpm | 193 -
debian/bin/beast-mcmc | 28 -
debian/bin/beauti | 5 -
debian/bin/loganalyser | 5 -
debian/bin/logcombiner | 7 -
debian/bin/treeannotator | 9 -
debian/bin/treestat | 8 -
debian/changelog | 10 -
debian/compat | 1 -
debian/control | 114 -
debian/copyright | 48 -
debian/get-orig-source | 72 -
debian/libnucleotidelikelihoodcore0.install | 1 -
debian/patches/create_soname.patch | 21 -
debian/patches/enable_hardening.patch | 21 -
.../fix_classpath_in_build_tracer_xml.patch | 141 -
debian/patches/fix_classpath_in_build_xml.patch | 98 -
debian/patches/fix_encoding.patch | 15 -
debian/patches/patch_tex_docs.patch | 67 -
debian/patches/series | 6 -
debian/rules | 75 -
debian/source/format | 1 -
debian/tests/run-unit-test | 11 -
debian/tracer | 11 -
debian/upstream/metadata | 12 -
debian/watch | 2 -
doc/slides.pdf | Bin 0 -> 1182376 bytes
doc/slides/BEAST.png | Bin 0 -> 37369 bytes
doc/slides/BEAST.xdl | 23 +
doc/slides/auckland.png | Bin 0 -> 2723 bytes
doc/slides/beast.gif | Bin 0 -> 124456 bytes
doc/slides/beast.jpg | Bin 0 -> 85832 bytes
doc/slides/beastdoc.png | Bin 0 -> 184998 bytes
doc/slides/beastdoc0.png | Bin 0 -> 191967 bytes
doc/slides/beastdoc1.png | Bin 0 -> 174245 bytes
doc/slides/beastdoc2.png | Bin 0 -> 250479 bytes
doc/slides/beastdoc4.png | Bin 0 -> 186463 bytes
doc/slides/beauti.png | Bin 0 -> 108281 bytes
doc/slides/classes1.png | Bin 0 -> 7407 bytes
doc/slides/classes10.png | Bin 0 -> 16267 bytes
doc/slides/classes11.png | Bin 0 -> 16460 bytes
doc/slides/classes12.png | Bin 0 -> 50743 bytes
doc/slides/classes2.png | Bin 0 -> 12447 bytes
doc/slides/classes3.png | Bin 0 -> 36929 bytes
doc/slides/classes4.png | Bin 0 -> 57859 bytes
doc/slides/classes5.png | Bin 0 -> 6925 bytes
doc/slides/classes5b.png | Bin 0 -> 205742 bytes
doc/slides/classes6.png | Bin 0 -> 33737 bytes
doc/slides/classes7.png | Bin 0 -> 15715 bytes
doc/slides/classes8.png | Bin 0 -> 30244 bytes
doc/slides/classes9.png | Bin 0 -> 48089 bytes
doc/slides/cross.png | Bin 0 -> 18844 bytes
doc/slides/example1.png | Bin 0 -> 34039 bytes
doc/slides/example2.png | Bin 0 -> 45640 bytes
doc/slides/example3.png | Bin 0 -> 104574 bytes
doc/slides/example4.png | Bin 0 -> 113617 bytes
doc/slides/example5.png | Bin 0 -> 150402 bytes
doc/slides/example6.png | Bin 0 -> 186488 bytes
doc/slides/hierarchy1.png | Bin 0 -> 17802 bytes
doc/slides/hierarchy2.png | Bin 0 -> 33344 bytes
doc/slides/hierarchy3.png | Bin 0 -> 7293 bytes
doc/slides/hky.png | Bin 0 -> 73118 bytes
doc/slides/hkymodel.png | Bin 0 -> 36412 bytes
doc/slides/hkymodel2.png | Bin 0 -> 76247 bytes
doc/slides/loggables.png | Bin 0 -> 11692 bytes
doc/slides/modelbuilder.png | Bin 0 -> 143554 bytes
doc/slides/sdk.pdf | Bin 0 -> 897232 bytes
doc/slides/sdk.tex | 640 +++
doc/slides/slides.aux | 102 +
doc/slides/slides.nav | 79 +
doc/slides/slides.out | 5 +
doc/slides/slides.snm | 0
doc/slides/slides.tex | 788 ++++
doc/slides/slides.toc | 7 +
doc/slides/slides101.tex | 1925 ++++++++
doc/slides/speedup.png | Bin 0 -> 7625 bytes
doc/slides/spreadsheet.png | Bin 0 -> 90564 bytes
doc/slides/walk.jpg | Bin 0 -> 242299 bytes
doc/slides/xml.png | Bin 0 -> 33860 bytes
doc/slides/xml1.png | Bin 0 -> 30050 bytes
doc/slides/xml2.png | Bin 0 -> 34919 bytes
doc/slides/xml3.png | Bin 0 -> 58783 bytes
doc/slides/xml4.png | Bin 0 -> 133775 bytes
doc/tutorial.slides.part1.pdf | Bin 0 -> 1745429 bytes
doc/tutorial.slides.part2.pdf | Bin 0 -> 1078490 bytes
doc/tutorial.slides.part3.pdf | Bin 0 -> 893949 bytes
.../DivergenceDating/DivergenceDatingTutorial.bib | 111 +
.../DivergenceDating/DivergenceDatingTutorial.tex | 887 ++++
.../DivergenceDatingTutorialv2.0.3.pdf | Bin 0 -> 1635325 bytes
.../DivergenceDatingTutorialv2.2.0.pdf | Bin 0 -> 1657554 bytes
.../DivergenceDating/figures/AddPartition.png | Bin 0 -> 28398 bytes
.../DivergenceDating/figures/AlignmentViewer.png | Bin 0 -> 57869 bytes
doc/tutorials/DivergenceDating/figures/BEAST.png | Bin 0 -> 97191 bytes
.../figures/BEAUti_DataPartitions.png | Bin 0 -> 85593 bytes
.../figures/BEAUti_DataPartitions_final.png | Bin 0 -> 81853 bytes
.../DivergenceDating/figures/BEAUti_Model.png | Bin 0 -> 77838 bytes
.../DivergenceDating/figures/BEAUti_Prior1.png | Bin 0 -> 103654 bytes
.../DivergenceDating/figures/BEAUti_Prior2.png | Bin 0 -> 143335 bytes
.../DivergenceDating/figures/BEAUti_TaxonSets.png | Bin 0 -> 36639 bytes
.../DivergenceDating/figures/DensiTree.png | Bin 0 -> 456235 bytes
doc/tutorials/DivergenceDating/figures/FigTree.png | Bin 0 -> 173462 bytes
.../DivergenceDating/figures/GammaPrior.png | Bin 0 -> 108120 bytes
doc/tutorials/DivergenceDating/figures/Tracer1.png | Bin 0 -> 209867 bytes
.../figures/Tracer_divergences.png | Bin 0 -> 211521 bytes
.../figures/Tracer_marginalDensity.png | Bin 0 -> 213196 bytes
.../DivergenceDating/figures/TreeAnnotator1.png | Bin 0 -> 56395 bytes
.../DivergenceDating/figures/cloneFrom.png | Bin 0 -> 58426 bytes
.../figures/primatePriorPosteriorKappa.pdf | Bin 0 -> 41604 bytes
.../figures/primatePriorPosteriorShape.pdf | Bin 0 -> 39283 bytes
doc/tutorials/DivergenceDating/figures/warning.png | Bin 0 -> 28695 bytes
.../primatePriorPosteriorKappa.tex | 4721 ++++++++++++++++++++
.../primatePriorPosteriorShape.tex | 4347 ++++++++++++++++++
doc/tutorials/GeneralNotes.pdf | Bin 0 -> 73526 bytes
doc/tutorials/GeneralNotes.tex | 112 +
doc/tutorials/MEPs/MEPs.bib | 38 +
doc/tutorials/MEPs/MEPs.tex | 446 ++
doc/tutorials/MEPs/MEPsv2.0.2.pdf | Bin 0 -> 1871736 bytes
doc/tutorials/MEPs/MEPsv2.2.0.pdf | Bin 0 -> 2088707 bytes
doc/tutorials/MEPs/figures/BEAST.png | Bin 0 -> 98888 bytes
doc/tutorials/MEPs/figures/BEAUti_GuessDates.png | Bin 0 -> 55742 bytes
doc/tutorials/MEPs/figures/BEAUti_Site_Model.png | Bin 0 -> 78844 bytes
doc/tutorials/MEPs/figures/BEAUti_dates.png | Bin 0 -> 101034 bytes
doc/tutorials/MEPs/figures/BEAUti_init.png | Bin 0 -> 90169 bytes
doc/tutorials/MEPs/figures/BEAUti_mcmc.png | Bin 0 -> 79270 bytes
doc/tutorials/MEPs/figures/BEAUti_mcmc_long.png | Bin 0 -> 91702 bytes
doc/tutorials/MEPs/figures/BEAUti_partition.png | Bin 0 -> 80531 bytes
doc/tutorials/MEPs/figures/BEAUti_priors.png | Bin 0 -> 107294 bytes
doc/tutorials/MEPs/figures/BEAUti_priors2.png | Bin 0 -> 115604 bytes
doc/tutorials/MEPs/figures/BEAUti_split.png | Bin 0 -> 34673 bytes
doc/tutorials/MEPs/figures/DensiTree.pdf | Bin 0 -> 570696 bytes
doc/tutorials/MEPs/figures/RSV2_mcc_tree.pdf | Bin 0 -> 51129 bytes
doc/tutorials/MEPs/figures/Tracer1.png | Bin 0 -> 269966 bytes
doc/tutorials/MEPs/figures/Tracer2.png | Bin 0 -> 174702 bytes
doc/tutorials/MEPs/figures/Tracer_density.png | Bin 0 -> 164375 bytes
.../MEPs/figures/Tracer_relativeRates.png | Bin 0 -> 181824 bytes
doc/tutorials/MEPs/figures/cloneFrom.png | Bin 0 -> 62134 bytes
doc/tutorials/MEPs/figures/tracerBSP1.png | Bin 0 -> 212236 bytes
doc/tutorials/MEPs/figures/tracerBSP2.png | Bin 0 -> 89012 bytes
doc/tutorials/MEPs/figures/tracerBSP3.png | Bin 0 -> 56117 bytes
doc/tutorials/README.txt | 39 +
doc/tutorials/STACEY/STACEY_tutorial.bib | 67 +
doc/tutorials/STACEY/STACEY_tutorial.tex | 540 +++
.../STARBEAST/StarBEASTTutorialv2.0.3.pdf | Bin 0 -> 1579669 bytes
doc/tutorials/STARBEAST/StarBEAST_tutorial.bib | 32 +
doc/tutorials/STARBEAST/StarBEAST_tutorial.tex | 534 +++
.../STARBEAST/StarBEAST_tutorialv2.2.0.pdf | Bin 0 -> 1950172 bytes
doc/tutorials/STARBEAST/figures/BEAST.png | Bin 0 -> 98804 bytes
.../STARBEAST/figures/BEAUti_ClockModel1.png | Bin 0 -> 63087 bytes
.../STARBEAST/figures/BEAUti_ClockModel2.png | Bin 0 -> 62715 bytes
.../STARBEAST/figures/BEAUti_ClockModel3.png | Bin 0 -> 62542 bytes
.../STARBEAST/figures/BEAUti_DataPartitions.png | Bin 0 -> 77348 bytes
.../STARBEAST/figures/BEAUti_Guess_Taxonsets.png | Bin 0 -> 122252 bytes
doc/tutorials/STARBEAST/figures/BEAUti_MCMC.png | Bin 0 -> 102713 bytes
doc/tutorials/STARBEAST/figures/BEAUti_MSP.png | Bin 0 -> 79386 bytes
doc/tutorials/STARBEAST/figures/BEAUti_Prior.png | Bin 0 -> 92972 bytes
.../STARBEAST/figures/BEAUti_Site_Model.png | Bin 0 -> 77597 bytes
.../STARBEAST/figures/BEAUti_selectTemplate.png | Bin 0 -> 81742 bytes
doc/tutorials/STARBEAST/figures/DensiTree.png | Bin 0 -> 592745 bytes
doc/tutorials/STARBEAST/figures/Tracer1.png | Bin 0 -> 176273 bytes
doc/tutorials/STARBEAST/figures/Tracer2.png | Bin 0 -> 213917 bytes
doc/tutorials/STARBEAST/figures/TreeAnnotator.png | Bin 0 -> 56661 bytes
doc/tutorials/STARBEAST/figures/cloneFrom.png | Bin 0 -> 60373 bytes
doc/tutorials/STARBEAST/figures/figtree.png | Bin 0 -> 168456 bytes
doc/tutorials/STARBEAST/figures/gopher.pdf | Bin 0 -> 760041 bytes
.../STARBEAST/figures/species_population1.pdf | Bin 0 -> 23134 bytes
.../STARBEAST/figures/species_population2.pdf | Bin 0 -> 27089 bytes
.../STARBEAST/figures/species_population3.pdf | Bin 0 -> 172057 bytes
.../STARBEAST/figures/species_population4.pdf | Bin 0 -> 26652 bytes
.../STARBEAST/figures/species_population5.pdf | Bin 0 -> 26642 bytes
doc/tutorials/tex2html.sh | 29 +
examples/beast2vs1/beast1/testBSP1.xml | 317 ++
examples/beast2vs1/beast1/testBSPNoClock.xml | 239 +
examples/beast2vs1/beast1/testBirthDeathAsYule.xml | 296 ++
.../beast1/testBirthDeathModel_10taxa.xml | 111 +
examples/beast2vs1/beast1/testCalibration.xml | 241 +
examples/beast2vs1/beast1/testCoalescent.xml | 174 +
.../beast2vs1/beast1/testCoalescentNoClock.xml | 222 +
.../beast2vs1/beast1/testCoalescentNoClock1.xml | 213 +
examples/beast2vs1/beast1/testEBSP.xml | 836 ++++
.../beast2vs1/beast1/testExponentialGrowth.xml | 232 +
examples/beast2vs1/beast1/testMCMC.xml | 175 +
examples/beast2vs1/beast1/testMultiSubstModel.xml | 358 ++
examples/beast2vs1/beast1/testRandomLocalClock.xml | 274 ++
examples/beast2vs1/beast1/testSRD06CP12_3.xml | 324 ++
examples/beast2vs1/beast1/testSiteModelAlpha.xml | 318 ++
.../beast2vs1/beast1/testStarBEASTConstant.xml | 707 +++
examples/beast2vs1/beast1/testStarBEASTLinear.xml | 707 +++
.../beast1/testStarBEASTLinearConstRoot.xml | 707 +++
.../beast2vs1/beast1/testStrictClockNoDate.xml | 234 +
.../beast2vs1/beast1/testStrictClockNoDate2.xml | 228 +
.../beast1/testStrictClockTipDatesSampling.xml | 372 ++
.../beast2vs1/beast1/testStrictClockTipTime.xml | 330 ++
.../beast1/testUCRelaxedClockLogNormal.xml | 274 ++
examples/beast2vs1/beast1/testYule.xml | 215 +
examples/beast2vs1/beast1/testYuleModel_10taxa.xml | 108 +
examples/beast2vs1/testBSP1.xml | 197 +
examples/beast2vs1/testBSPNoClock.xml | 136 +
examples/beast2vs1/testBirthDeathAsYule.xml | 162 +
examples/beast2vs1/testBirthDeathModel_10taxa.xml | 59 +
examples/beast2vs1/testCalibration.xml | 124 +
examples/beast2vs1/testCalibrationMono.xml | 128 +
examples/beast2vs1/testCoalescent2.xml | 103 +
examples/beast2vs1/testCoalescentNoClock.xml | 128 +
examples/beast2vs1/testCoalescentNoClock1.xml | 117 +
examples/beast2vs1/testCoalescentTipDates.xml | 70 +
examples/beast2vs1/testCoalescentTipDates1.xml | 70 +
.../beast2vs1/testCoalescentTipDatesSampling.xml | 101 +
examples/beast2vs1/testEBSP.xml | 317 ++
examples/beast2vs1/testExponentialGrowth.xml | 147 +
examples/beast2vs1/testHKY.xml | 89 +
examples/beast2vs1/testMultiSubstModel.xml | 141 +
examples/beast2vs1/testRandomLocalClock.xml | 148 +
examples/beast2vs1/testSRD06CP12_3.xml | 171 +
examples/beast2vs1/testSiteModelAlpha.xml | 197 +
examples/beast2vs1/testStarBEAST.xml | 473 ++
examples/beast2vs1/testStarBEASTConstant.xml | 482 ++
examples/beast2vs1/testStarBEASTLinear.xml | 491 ++
.../beast2vs1/testStarBEASTLinearConstRoot.xml | 490 ++
examples/beast2vs1/testStarBeast2.xml | 354 ++
examples/beast2vs1/testStrictClock.xml | 134 +
examples/beast2vs1/testStrictClock2.xml | 128 +
.../beast2vs1/testStrictClockTipDatesSampling.xml | 227 +
examples/beast2vs1/testStrictClockTipTime.xml | 174 +
examples/beast2vs1/testTipDates.xml | 162 +
examples/beast2vs1/testUCRelaxedClockLogNormal.xml | 148 +
examples/beast2vs1/testYuleModel_10taxa.xml | 55 +
examples/benchmark/1/experiment.sh | 24 +
examples/benchmark/1/testHKY1044.xml | 397 ++
examples/benchmark/1/testHKY1366.xml | 352 ++
examples/benchmark/1/testHKY1510.xml | 327 ++
examples/benchmark/1/testHKY1748.xml | 482 ++
examples/benchmark/1/testHKY1749.xml | 517 +++
examples/benchmark/1/testHKY1809.xml | 442 ++
examples/benchmark/1/testHKY336.xml | 282 ++
examples/benchmark/1/testHKY3475.xml | 397 ++
examples/benchmark/1/testHKY501.xml | 292 ++
examples/benchmark/1/testHKY520.xml | 482 ++
examples/benchmark/1/testHKY755.xml | 467 ++
examples/benchmark/1/testHKY767.xml | 502 +++
examples/benchmark/II/experiment.sh | 24 +
examples/benchmark/II/testHKY1044.xml | 283 ++
examples/benchmark/II/testHKY1366.xml | 247 +
examples/benchmark/II/testHKY1510.xml | 227 +
examples/benchmark/II/testHKY1748.xml | 351 ++
examples/benchmark/II/testHKY1749.xml | 379 ++
examples/benchmark/II/testHKY1809.xml | 319 ++
examples/benchmark/II/testHKY336.xml | 191 +
examples/benchmark/II/testHKY3475.xml | 283 ++
examples/benchmark/II/testHKY501.xml | 199 +
examples/benchmark/II/testHKY520.xml | 351 ++
examples/benchmark/II/testHKY755.xml | 339 ++
examples/benchmark/II/testHKY767.xml | 367 ++
examples/benchmark/mrbayes/experiment.sh | 24 +
examples/benchmark/mrbayes/run1044.nex | 6 +
examples/benchmark/mrbayes/run1366.nex | 6 +
examples/benchmark/mrbayes/run1510.nex | 6 +
examples/benchmark/mrbayes/run1748.nex | 6 +
examples/benchmark/mrbayes/run1749.nex | 6 +
examples/benchmark/mrbayes/run1809.nex | 6 +
examples/benchmark/mrbayes/run336.nex | 6 +
examples/benchmark/mrbayes/run3475.nex | 6 +
examples/benchmark/mrbayes/run501.nex | 6 +
examples/benchmark/mrbayes/run520.nex | 6 +
examples/benchmark/mrbayes/run755.nex | 6 +
examples/benchmark/mrbayes/run767.nex | 6 +
examples/benchmark/mrbayes/testHKY1044.nex | 67 +
examples/benchmark/mrbayes/testHKY1366.nex | 58 +
examples/benchmark/mrbayes/testHKY1510.nex | 53 +
examples/benchmark/mrbayes/testHKY1748.nex | 84 +
examples/benchmark/mrbayes/testHKY1749.nex | 91 +
examples/benchmark/mrbayes/testHKY1809.nex | 76 +
examples/benchmark/mrbayes/testHKY336.nex | 44 +
examples/benchmark/mrbayes/testHKY3475.nex | 67 +
examples/benchmark/mrbayes/testHKY501.nex | 47 +
examples/benchmark/mrbayes/testHKY520.nex | 84 +
examples/benchmark/mrbayes/testHKY755.nex | 81 +
examples/benchmark/mrbayes/testHKY767.nex | 88 +
examples/bitflip.xml | 22 +
examples/nexus/26.nex | 63 +
examples/nexus/29.nex | 64 +
examples/nexus/47.nex | 67 +
examples/nexus/53.nex | 63 +
examples/nexus/59.nex | 64 +
examples/nexus/64.nex | 64 +
examples/nexus/72.nex | 64 +
examples/nexus/Darwins-finches.nex | 46 +
examples/nexus/Dengue4.env.nex | 54 +
examples/nexus/FPV.nex | 15 +
examples/nexus/Flu.nex | 1 +
examples/nexus/M243.nex | 214 +
examples/nexus/ML_analysis.nex | Bin 0 -> 2990 bytes
examples/nexus/MP_analysis.nex | 1 +
examples/nexus/Primates.nex | 24 +
examples/nexus/RSV2.nex | 141 +
examples/nexus/Shankarappa.Patient9.nex | 259 ++
examples/nexus/angiosperms.nex | 1 +
examples/nexus/anolis.nex | 37 +
examples/nexus/avian-ovomucoids.nex | 1 +
examples/nexus/dna.nex | 142 +
examples/nexus/gopher.nex | 63 +
examples/nexus/humanChimpSNP.nex | 19 +
examples/nexus/old.nex | 25 +
examples/nexus/primate-mtDNA-interleaved.nex | 1 +
examples/nexus/primate-mtDNA.nex | 1 +
examples/nexus/protein.nex | 54 +
examples/nexus/seaview.nxs | 606 +++
examples/nexus/traitlab.nex | 35 +
examples/starbeastinit/sbi-01.xml | 170 +
examples/starbeastinit/sbi-02.xml | 170 +
examples/starbeastinit/sbi-03.xml | 210 +
examples/testBSP.xml | 205 +
examples/testCalYule_5t_2c.xml | 55 +
examples/testCalibration.xml | 146 +
examples/testClassicRootCalibrationPrior.xml | 78 +
examples/testCoalescent.xml | 126 +
examples/testConditionalRootCalibrationPrior.xml | 78 +
examples/testEBSP.xml | 601 +++
examples/testExponentialGrowth.xml | 213 +
examples/testGTR.xml | 211 +
examples/testHKY.json | 87 +
examples/testHKY.xml | 104 +
examples/testJukesCantor.xml | 85 +
examples/testJukesCantorShort.xml | 84 +
examples/testJukesCantorShortUncertain.xml | 95 +
examples/testJukesCantorShortUncertain2.xml | 96 +
examples/testJukesCantorShortUncertain2MLE.xml | 87 +
.../testMultipleAlignments_randomTaxaOrder.xml | 332 ++
examples/testPlates.xml | 128 +
examples/testRNA.xml | 212 +
examples/testRandomLocalClock.xml | 120 +
examples/testRelaxedClock.xml | 163 +
examples/testRestrictedGTR.xml | 179 +
examples/testSRD06.xml | 127 +
examples/testSYM.xml | 207 +
examples/testSeqGen.xml | 89 +
examples/testSimulatedAlignment.xml | 126 +
examples/testSliceHKY.xml | 127 +
examples/testStarBeast.xml | 349 ++
examples/testTIM.xml | 188 +
examples/testTN93.xml | 161 +
examples/testTVM.xml | 197 +
examples/testTipDates.xml | 199 +
examples/testTipDates2.xml | 113 +
examples/testTwoCalibrationsPrior.xml | 91 +
examples/testYuleCalibrated.xml | 151 +
examples/testYuleOneSite.xml | 90 +
examples/testYuleUncalibrated.xml | 150 +
packages.xml | 71 +
release/Linux/bin/addonmanager | 33 +
release/Linux/bin/appstore | 33 +
release/Linux/bin/beast | 32 +
release/Linux/bin/beauti | 33 +
release/Linux/bin/densitree | 33 +
release/Linux/bin/logcombiner | 33 +
release/Linux/bin/treeannotator | 33 +
release/Mac/createdmg.sh | 58 +
release/Mac/install.png | Bin 0 -> 17518 bytes
release/Windows/AppStore_launch4j.xml | 21 +
release/Windows/BEAST_launch4j.xml | 21 +
release/Windows/BEAUti_launch4j.xml | 21 +
release/Windows/LogCombiner_launch4j.xml | 21 +
release/Windows/TreeAnnotator_launch4j.xml | 20 +
release/common/LICENSE.txt | 504 +++
release/common/README.txt | 203 +
release/common/VERSION HISTORY.txt | 167 +
release/common/icons/beast.icns | Bin 0 -> 49344 bytes
release/common/icons/beast.ico | Bin 0 -> 82726 bytes
release/common/icons/beast.png | Bin 0 -> 27970 bytes
release/common/icons/beauti.icns | Bin 0 -> 54504 bytes
release/common/icons/beauti.ico | Bin 0 -> 82726 bytes
release/common/icons/beauti.png | Bin 0 -> 20131 bytes
release/common/icons/utility.icns | Bin 0 -> 59742 bytes
release/common/icons/utility.ico | Bin 0 -> 82726 bytes
release/common/icons/utility.png | Bin 0 -> 29413 bytes
release/common/tools/DensiTree.icns | Bin 0 -> 10326 bytes
release/common/tools/DensiTree.ico | Bin 0 -> 7406 bytes
release/common/tools/DensiTree.png | Bin 0 -> 1608 bytes
release/common/tools/DensiTree_launch4j.xml | 16 +
scripts/doc.pl | 88 +
src/beast/app/BEASTVersion.java | 150 +
src/beast/app/BeastMCMC.java | 533 +++
src/beast/app/DocMaker.java | 567 +++
src/beast/app/ModelBuilder.java | 88 +
src/beast/app/beastapp/BeastDialog.java | 252 ++
src/beast/app/beastapp/BeastLauncher.java | 152 +
src/beast/app/beastapp/BeastMain.java | 622 +++
src/beast/app/beastapp/WholeNumberField.java | 202 +
src/beast/app/beastapp/images/beast.png | Bin 0 -> 27970 bytes
src/beast/app/beauti/0.png | Bin 0 -> 15719 bytes
src/beast/app/beauti/1.png | Bin 0 -> 9583 bytes
src/beast/app/beauti/10.png | Bin 0 -> 25275 bytes
src/beast/app/beauti/11.png | Bin 0 -> 28777 bytes
src/beast/app/beauti/12.png | Bin 0 -> 24213 bytes
src/beast/app/beauti/13.png | Bin 0 -> 25275 bytes
src/beast/app/beauti/2.png | Bin 0 -> 27335 bytes
src/beast/app/beauti/3.png | Bin 0 -> 27686 bytes
src/beast/app/beauti/4.png | Bin 0 -> 22591 bytes
src/beast/app/beauti/5.png | Bin 0 -> 27214 bytes
src/beast/app/beauti/6.png | Bin 0 -> 9063 bytes
src/beast/app/beauti/7.png | Bin 0 -> 27158 bytes
src/beast/app/beauti/8.png | Bin 0 -> 9256 bytes
src/beast/app/beauti/9.png | Bin 0 -> 9389 bytes
src/beast/app/beauti/AlignmentListInputEditor.java | 1223 +++++
src/beast/app/beauti/AlignmentViewer.java | 286 ++
src/beast/app/beauti/Beauti.java | 1293 ++++++
src/beast/app/beauti/BeautiAlignmentProvider.java | 376 ++
src/beast/app/beauti/BeautiConfig.java | 303 ++
src/beast/app/beauti/BeautiConnector.java | 252 ++
src/beast/app/beauti/BeautiDoc.java | 2367 ++++++++++
src/beast/app/beauti/BeautiDocListener.java | 9 +
src/beast/app/beauti/BeautiLauncher.java | 23 +
src/beast/app/beauti/BeautiPanel.java | 463 ++
src/beast/app/beauti/BeautiPanelConfig.java | 355 ++
src/beast/app/beauti/BeautiSubTemplate.java | 442 ++
.../app/beauti/ClockModelListInputEditor.java | 182 +
src/beast/app/beauti/ClonePartitionPanel.java | 72 +
src/beast/app/beauti/Fragment.java | 18 +
src/beast/app/beauti/FrequenciesInputEditor.java | 111 +
...eTreeForSpeciesTreeDistributionInputEditor.java | 107 +
src/beast/app/beauti/GuessPatternDialog.java | 634 +++
src/beast/app/beauti/JPackageDialog.java | 428 ++
src/beast/app/beauti/JPackageRepositoryDialog.java | 184 +
src/beast/app/beauti/LoggerListInputEditor.java | 61 +
src/beast/app/beauti/MRCAPriorInputEditor.java | 184 +
src/beast/app/beauti/OperatorListInputEditor.java | 168 +
.../beauti/ParametricDistributionInputEditor.java | 345 ++
src/beast/app/beauti/PartitionContext.java | 70 +
src/beast/app/beauti/PriorInputEditor.java | 126 +
src/beast/app/beauti/PriorListInputEditor.java | 272 ++
src/beast/app/beauti/SiteModelInputEditor.java | 343 ++
.../app/beauti/SpeciesTreePriorInputEditor.java | 38 +
src/beast/app/beauti/StateNodeListInputEditor.java | 36 +
src/beast/app/beauti/TaxonSetDialog.java | 309 ++
src/beast/app/beauti/TaxonSetInputEditor.java | 585 +++
src/beast/app/beauti/TipDatesInputEditor.java | 613 +++
.../app/beauti/TreeDistributionInputEditor.java | 155 +
src/beast/app/beauti/cancel.png | Bin 0 -> 4750 bytes
src/beast/app/beauti/finish.png | Bin 0 -> 4484 bytes
.../app/beauti/guiutil/S11InitialSelection.java | 153 +
src/beast/app/beauti/link.png | Bin 0 -> 379 bytes
src/beast/app/beauti/unlink.png | Bin 0 -> 409 bytes
src/beast/app/beauti/woosh.wav | Bin 0 -> 15298 bytes
src/beast/app/draw/Arrow.java | 264 ++
src/beast/app/draw/BEASTObjectDialog.java | 208 +
src/beast/app/draw/BEASTObjectInputEditor.java | 481 ++
src/beast/app/draw/BEASTObjectPanel.java | 474 ++
src/beast/app/draw/BEASTObjectSet.java | 20 +
src/beast/app/draw/BEASTObjectShape.java | 264 ++
src/beast/app/draw/BooleanInputEditor.java | 61 +
src/beast/app/draw/Document.java | 1937 ++++++++
src/beast/app/draw/DoubleInputEditor.java | 17 +
src/beast/app/draw/DoubleListInputEditor.java | 406 ++
src/beast/app/draw/EnumInputEditor.java | 76 +
src/beast/app/draw/ExtensionFileFilter.java | 95 +
src/beast/app/draw/HelpBrowser.java | 200 +
src/beast/app/draw/InputEditor.java | 472 ++
src/beast/app/draw/InputEditorFactory.java | 349 ++
src/beast/app/draw/InputShape.java | 188 +
src/beast/app/draw/IntegerInputEditor.java | 18 +
src/beast/app/draw/ListInputEditor.java | 472 ++
src/beast/app/draw/ModelBuilder.java | 2157 +++++++++
src/beast/app/draw/MyAction.java | 67 +
src/beast/app/draw/ParameterInputEditor.java | 281 ++
src/beast/app/draw/Selection.java | 169 +
src/beast/app/draw/Shape.java | 410 ++
src/beast/app/draw/SmallButton.java | 45 +
src/beast/app/draw/SmallButtonOld.java | 106 +
src/beast/app/draw/SmallLabel.java | 66 +
src/beast/app/draw/StringInputEditor.java | 28 +
src/beast/app/draw/TrackPoint.java | 36 +
src/beast/app/draw/icons/GenerationD.png | Bin 0 -> 2051 bytes
src/beast/app/draw/icons/add.png | Bin 0 -> 161 bytes
src/beast/app/draw/icons/alignbottom.png | Bin 0 -> 195 bytes
src/beast/app/draw/icons/alignleft.png | Bin 0 -> 191 bytes
src/beast/app/draw/icons/alignright.png | Bin 0 -> 202 bytes
src/beast/app/draw/icons/aligntop.png | Bin 0 -> 201 bytes
src/beast/app/draw/icons/arrow.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/arrow.png | Bin 0 -> 267 bytes
src/beast/app/draw/icons/beast.png | Bin 0 -> 27970 bytes
src/beast/app/draw/icons/beauti.png | Bin 0 -> 20131 bytes
src/beast/app/draw/icons/bigger.png | Bin 0 -> 236 bytes
src/beast/app/draw/icons/bold.png | Bin 0 -> 1000 bytes
src/beast/app/draw/icons/center.png | Bin 0 -> 570 bytes
src/beast/app/draw/icons/centerhorizontal.png | Bin 0 -> 186 bytes
src/beast/app/draw/icons/centervertical.png | Bin 0 -> 193 bytes
src/beast/app/draw/icons/color.png | Bin 0 -> 642 bytes
src/beast/app/draw/icons/constant.png | Bin 0 -> 273 bytes
src/beast/app/draw/icons/copy.png | Bin 0 -> 204 bytes
src/beast/app/draw/icons/cut.png | Bin 0 -> 179 bytes
src/beast/app/draw/icons/del.png | Bin 0 -> 144 bytes
src/beast/app/draw/icons/down.png | Bin 0 -> 302 bytes
src/beast/app/draw/icons/edit.png | Bin 0 -> 394 bytes
src/beast/app/draw/icons/ellipse.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/ellipse.png | Bin 0 -> 274 bytes
src/beast/app/draw/icons/font.png | Bin 0 -> 261 bytes
src/beast/app/draw/icons/function.png | Bin 0 -> 227 bytes
src/beast/app/draw/icons/help.png | Bin 0 -> 239 bytes
src/beast/app/draw/icons/italic.png | Bin 0 -> 799 bytes
src/beast/app/draw/icons/left.png | Bin 0 -> 336 bytes
src/beast/app/draw/icons/line.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/line.png | Bin 0 -> 259 bytes
src/beast/app/draw/icons/new.png | Bin 0 -> 216 bytes
src/beast/app/draw/icons/open.png | Bin 0 -> 203 bytes
src/beast/app/draw/icons/paste.png | Bin 0 -> 221 bytes
src/beast/app/draw/icons/poly.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/poly.png | Bin 0 -> 281 bytes
src/beast/app/draw/icons/print.png | Bin 0 -> 269 bytes
src/beast/app/draw/icons/rect.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/rect.png | Bin 0 -> 245 bytes
src/beast/app/draw/icons/redo.png | Bin 0 -> 223 bytes
src/beast/app/draw/icons/right.png | Bin 0 -> 340 bytes
src/beast/app/draw/icons/rrect.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/rrect.png | Bin 0 -> 260 bytes
src/beast/app/draw/icons/save.png | Bin 0 -> 176 bytes
src/beast/app/draw/icons/select.bmp | Bin 0 -> 1194 bytes
src/beast/app/draw/icons/select.gif | Bin 0 -> 868 bytes
src/beast/app/draw/icons/select.jpg | Bin 0 -> 773 bytes
src/beast/app/draw/icons/select.png | Bin 0 -> 266 bytes
src/beast/app/draw/icons/smaller.png | Bin 0 -> 216 bytes
src/beast/app/draw/icons/spacehorizontal.png | Bin 0 -> 190 bytes
src/beast/app/draw/icons/spacevertical.png | Bin 0 -> 183 bytes
src/beast/app/draw/icons/tcolor.png | Bin 0 -> 956 bytes
src/beast/app/draw/icons/undo.png | Bin 0 -> 218 bytes
src/beast/app/seqgen/MergeDataWith.java | 76 +
src/beast/app/seqgen/SequenceSimulator.java | 321 ++
src/beast/app/seqgen/SimulatedAlignment.java | 221 +
src/beast/app/tools/AppStore.java | 479 ++
src/beast/app/tools/AppStoreLauncher.java | 19 +
src/beast/app/tools/EBSPAnalyser.java | 447 ++
src/beast/app/tools/LogCombiner.java | 495 ++
src/beast/app/tools/LogCombinerDialog.java | 390 ++
src/beast/app/tools/LogCombinerLauncher.java | 17 +
src/beast/app/tools/TableEditorStopper.java | 80 +
src/beast/app/tools/images/EBSPAnalyser.png | Bin 0 -> 35295 bytes
src/beast/app/tools/images/logcombiner.png | Bin 0 -> 19198 bytes
src/beast/app/tools/images/utility.png | Bin 0 -> 29413 bytes
src/beast/app/treeannotator/CladeSystem.java | 386 ++
src/beast/app/treeannotator/ContourAttrib.java | 79 +
src/beast/app/treeannotator/ContourGenerator.java | 896 ++++
src/beast/app/treeannotator/ContourMaker.java | 11 +
src/beast/app/treeannotator/ContourPath.java | 129 +
src/beast/app/treeannotator/ContourWithSynder.java | 61 +
src/beast/app/treeannotator/FileDrop.java | 900 ++++
.../treeannotator/KernelDensityEstimator2D.java | 280 ++
src/beast/app/treeannotator/RealNumberField.java | 332 ++
src/beast/app/treeannotator/SnyderContour.java | 496 ++
src/beast/app/treeannotator/TreeAnnotator.java | 1536 +++++++
.../app/treeannotator/TreeAnnotatorDialog.java | 241 +
.../app/treeannotator/TreeAnnotatorLauncher.java | 22 +
src/beast/app/treeannotator/TreeSetParser.java | 618 +++
src/beast/app/util/Arguments.java | 611 +++
src/beast/app/util/ErrorLogHandler.java | 71 +
src/beast/app/util/FileDrop.java | 895 ++++
src/beast/app/util/MessageLogHandler.java | 46 +
src/beast/app/util/Utils.java | 310 ++
src/beast/app/util/Utils6.java | 98 +
src/beast/app/util/Version.java | 34 +
src/beast/app/util/WholeNumberField.java | 202 +
src/beast/app/util/images/beast.png | Bin 0 -> 27970 bytes
src/beast/core/BEASTInterface.java | 377 ++
src/beast/core/BEASTObject.java | 76 +
src/beast/core/BEASTObjectAnnotation.java | 12 +
src/beast/core/CalculationNode.java | 129 +
src/beast/core/Citation.java | 56 +
src/beast/core/Description.java | 61 +
src/beast/core/Distribution.java | 172 +
src/beast/core/Evaluator.java | 9 +
src/beast/core/Function.java | 29 +
src/beast/core/Input.java | 732 +++
src/beast/core/Loggable.java | 39 +
src/beast/core/Logger.java | 592 +++
src/beast/core/MCMC.java | 575 +++
src/beast/core/Operator.java | 309 ++
src/beast/core/OperatorSchedule.java | 325 ++
src/beast/core/Param.java | 43 +
src/beast/core/Runnable.java | 45 +
src/beast/core/State.java | 632 +++
src/beast/core/StateNode.java | 227 +
src/beast/core/StateNodeInitialiser.java | 36 +
src/beast/core/parameter/BooleanParameter.java | 117 +
src/beast/core/parameter/BooleanParameterList.java | 44 +
src/beast/core/parameter/CompoundValuable.java | 104 +
src/beast/core/parameter/GeneralParameterList.java | 654 +++
src/beast/core/parameter/IntegerParameter.java | 112 +
src/beast/core/parameter/IntegerParameterList.java | 49 +
src/beast/core/parameter/Map.java | 93 +
src/beast/core/parameter/Parameter.java | 472 ++
src/beast/core/parameter/RealParameter.java | 119 +
src/beast/core/parameter/RealParameterList.java | 49 +
src/beast/core/util/CompoundDistribution.java | 238 +
src/beast/core/util/ESS.java | 260 ++
src/beast/core/util/Evaluator.java | 9 +
src/beast/core/util/Log.java | 115 +
src/beast/core/util/Sum.java | 121 +
src/beast/evolution/alignment/Alignment.java | 737 +++
.../evolution/alignment/AscertainedAlignment.java | 95 +
.../evolution/alignment/FilteredAlignment.java | 332 ++
src/beast/evolution/alignment/Sequence.java | 165 +
src/beast/evolution/alignment/Taxon.java | 89 +
src/beast/evolution/alignment/TaxonSet.java | 171 +
.../evolution/alignment/distance/Distance.java | 90 +
.../evolution/alignment/distance/F84Distance.java | 137 +
.../alignment/distance/HammingDistance.java | 21 +
.../alignment/distance/JukesCantorDistance.java | 81 +
.../evolution/alignment/distance/SMMDistance.java | 31 +
.../evolution/branchratemodel/BranchRateModel.java | 23 +
.../branchratemodel/RandomLocalClockModel.java | 172 +
.../evolution/branchratemodel/RateStatistic.java | 191 +
.../branchratemodel/StrictClockModel.java | 51 +
.../branchratemodel/UCRelaxedClockModel.java | 406 ++
src/beast/evolution/datatype/Aminoacid.java | 33 +
src/beast/evolution/datatype/Binary.java | 38 +
src/beast/evolution/datatype/DataType.java | 291 ++
src/beast/evolution/datatype/IntegerData.java | 34 +
src/beast/evolution/datatype/Nucleotide.java | 42 +
src/beast/evolution/datatype/StandardData.java | 188 +
src/beast/evolution/datatype/TwoStateCovarion.java | 35 +
src/beast/evolution/datatype/UserDataType.java | 110 +
.../evolution/likelihood/BeagleTreeLikelihood.java | 1032 +++++
.../evolution/likelihood/BeerLikelihoodCore.java | 891 ++++
.../evolution/likelihood/BeerLikelihoodCore4.java | 311 ++
.../likelihood/GenericTreeLikelihood.java | 50 +
src/beast/evolution/likelihood/LikelihoodCore.java | 181 +
src/beast/evolution/likelihood/TreeLikelihood.java | 542 +++
src/beast/evolution/operators/BitFlipOperator.java | 99 +
.../operators/CompoundParameterHelper.java | 81 +
.../evolution/operators/DeltaExchangeOperator.java | 344 ++
src/beast/evolution/operators/Exchange.java | 244 +
.../evolution/operators/IntRandomWalkOperator.java | 57 +
.../evolution/operators/IntUniformOperator.java | 43 +
src/beast/evolution/operators/JointOperator.java | 78 +
src/beast/evolution/operators/NodeReheight.java | 301 ++
.../operators/RealRandomWalkOperator.java | 110 +
src/beast/evolution/operators/ScaleOperator.java | 317 ++
src/beast/evolution/operators/SliceOperator.java | 246 +
src/beast/evolution/operators/SubtreeSlide.java | 287 ++
src/beast/evolution/operators/SwapOperator.java | 63 +
.../evolution/operators/TipDatesRandomWalker.java | 186 +
src/beast/evolution/operators/TipDatesScaler.java | 125 +
src/beast/evolution/operators/TreeOperator.java | 69 +
src/beast/evolution/operators/Uniform.java | 108 +
src/beast/evolution/operators/UniformOperator.java | 60 +
src/beast/evolution/operators/UpDownOperator.java | 192 +
src/beast/evolution/operators/WilsonBalding.java | 198 +
src/beast/evolution/sitemodel/SiteModel.java | 612 +++
.../evolution/sitemodel/SiteModelInterface.java | 188 +
.../speciation/BirthDeathGernhard08Model.java | 138 +
.../speciation/CalibratedBirthDeathModel.java | 1046 +++++
.../speciation/CalibratedYuleInitialTree.java | 79 +
.../evolution/speciation/CalibratedYuleModel.java | 892 ++++
.../speciation/CalibrationLineagesIterator.java | 296 ++
.../evolution/speciation/CalibrationPoint.java | 55 +
.../GeneTreeForSpeciesTreeDistribution.java | 401 ++
src/beast/evolution/speciation/RandomGeneTree.java | 54 +
.../speciation/SpeciesTreeDistribution.java | 101 +
.../evolution/speciation/SpeciesTreeLogger.java | 177 +
.../evolution/speciation/SpeciesTreePrior.java | 194 +
.../evolution/speciation/StarBeastStartState.java | 416 ++
src/beast/evolution/speciation/TreeTopFinder.java | 61 +
src/beast/evolution/speciation/YuleModel.java | 171 +
.../substitutionmodel/BinaryCovarion.java | 333 ++
.../evolution/substitutionmodel/Blosum62.java | 272 ++
src/beast/evolution/substitutionmodel/CPREV.java | 271 ++
src/beast/evolution/substitutionmodel/Dayhoff.java | 274 ++
.../substitutionmodel/DefaultEigenSystem.java | 659 +++
.../substitutionmodel/EigenDecomposition.java | 108 +
.../evolution/substitutionmodel/EigenSystem.java | 14 +
.../EmpiricalSubstitutionModel.java | 132 +
.../evolution/substitutionmodel/Frequencies.java | 259 ++
src/beast/evolution/substitutionmodel/GTR.java | 94 +
.../GeneralSubstitutionModel.java | 273 ++
src/beast/evolution/substitutionmodel/HKY.java | 270 ++
src/beast/evolution/substitutionmodel/JTT.java | 273 ++
.../evolution/substitutionmodel/JukesCantor.java | 72 +
src/beast/evolution/substitutionmodel/MTREV.java | 279 ++
.../substitutionmodel/MutationDeathModel.java | 103 +
src/beast/evolution/substitutionmodel/SYM.java | 108 +
.../substitutionmodel/SubstitutionModel.java | 172 +
src/beast/evolution/substitutionmodel/TIM.java | 91 +
src/beast/evolution/substitutionmodel/TN93.java | 389 ++
src/beast/evolution/substitutionmodel/TVM.java | 95 +
src/beast/evolution/substitutionmodel/WAG.java | 727 +++
src/beast/evolution/tree/CladeSet.java | 261 ++
src/beast/evolution/tree/Node.java | 813 ++++
src/beast/evolution/tree/RandomTree.java | 700 +++
src/beast/evolution/tree/TraitSet.java | 256 ++
src/beast/evolution/tree/Tree.java | 956 ++++
src/beast/evolution/tree/TreeDistribution.java | 53 +
src/beast/evolution/tree/TreeHeightLogger.java | 59 +
src/beast/evolution/tree/TreeInterface.java | 65 +
src/beast/evolution/tree/TreeTraceAnalysis.java | 309 ++
src/beast/evolution/tree/TreeUtils.java | 400 ++
.../evolution/tree/TreeWithMetaDataLogger.java | 166 +
.../evolution/tree/coalescent/BayesianSkyline.java | 351 ++
.../evolution/tree/coalescent/Coalescent.java | 148 +
.../coalescent/CompoundPopulationFunction.java | 619 +++
.../tree/coalescent/ConstantPopulation.java | 141 +
.../tree/coalescent/ExponentialGrowth.java | 212 +
.../evolution/tree/coalescent/IntervalList.java | 157 +
.../evolution/tree/coalescent/IntervalType.java | 75 +
.../tree/coalescent/PopulationFunction.java | 256 ++
.../evolution/tree/coalescent/SampleOffValues.java | 87 +
.../tree/coalescent/ScaledPopulationFunction.java | 56 +
.../evolution/tree/coalescent/TreeIntervals.java | 491 ++
src/beast/math/Binomial.java | 102 +
src/beast/math/GammaFunction.java | 205 +
src/beast/math/MachineAccuracy.java | 82 +
src/beast/math/distributions/Beta.java | 53 +
src/beast/math/distributions/ChiSquare.java | 48 +
src/beast/math/distributions/Dirichlet.java | 82 +
src/beast/math/distributions/Exponential.java | 53 +
src/beast/math/distributions/Gamma.java | 57 +
src/beast/math/distributions/InverseGamma.java | 98 +
.../math/distributions/LaplaceDistribution.java | 95 +
.../distributions/LogNormalDistributionModel.java | 136 +
src/beast/math/distributions/MRCAPrior.java | 316 ++
.../distributions/MarkovChainDistribution.java | 123 +
src/beast/math/distributions/Normal.java | 67 +
src/beast/math/distributions/OneOnX.java | 57 +
.../math/distributions/ParametricDistribution.java | 201 +
src/beast/math/distributions/Poisson.java | 61 +
src/beast/math/distributions/Prior.java | 78 +
src/beast/math/distributions/Uniform.java | 122 +
src/beast/math/statistic/DiscreteStatistics.java | 394 ++
src/beast/math/statistic/RPNcalculator.java | 157 +
.../math/statistic/RPNexpressionCalculator.java | 199 +
src/beast/util/AddOnManager.java | 1186 +++++
src/beast/util/ClusterTree.java | 809 ++++
src/beast/util/CollectionUtils.java | 56 +
src/beast/util/CredibleSet.java | 58 +
src/beast/util/FrequencySet.java | 185 +
src/beast/util/HeapSort.java | 383 ++
src/beast/util/JSONParser.java | 1122 +++++
src/beast/util/JSONParserException.java | 137 +
src/beast/util/JSONProducer.java | 449 ++
src/beast/util/LogAnalyser.java | 525 +++
src/beast/util/LogComparator.java | 168 +
src/beast/util/MersenneTwisterFast.java | 780 ++++
src/beast/util/NexusParser.java | 1017 +++++
src/beast/util/NexusParserListener.java | 16 +
src/beast/util/OutputUtils.java | 65 +
src/beast/util/Package.java | 162 +
src/beast/util/PackageDependency.java | 71 +
src/beast/util/Randomizer.java | 494 ++
src/beast/util/TreeParser.java | 630 +++
src/beast/util/XMLParser.java | 1035 +++++
src/beast/util/XMLParserException.java | 112 +
src/beast/util/XMLParserUtils.java | 158 +
src/beast/util/XMLProducer.java | 1019 +++++
src/beast/util/treeparser/Newick.g4 | 38 +
src/beast/util/treeparser/NewickBaseVisitor.java | 77 +
src/beast/util/treeparser/NewickLexer.java | 136 +
src/beast/util/treeparser/NewickParser.java | 627 +++
src/beast/util/treeparser/NewickVisitor.java | 67 +
.../apache/commons/math/ConvergenceException.java | 73 +
.../apache/commons/math/ConvergingAlgorithm.java | 138 +
.../commons/math/ConvergingAlgorithmImpl.java | 155 +
.../commons/math/FunctionEvaluationException.java | 169 +
.../commons/math/MathConfigurationException.java | 74 +
src/org/apache/commons/math/MathException.java | 202 +
.../apache/commons/math/MathRuntimeException.java | 541 +++
.../math/MaxEvaluationsExceededException.java | 75 +
.../math/MaxIterationsExceededException.java | 75 +
.../commons/math/analysis/BinaryFunction.java | 134 +
.../math/analysis/BivariateRealFunction.java | 41 +
.../commons/math/analysis/ComposableFunction.java | 577 +++
.../DifferentiableUnivariateRealFunction.java | 34 +
.../math/analysis/MultivariateRealFunction.java | 41 +
.../math/analysis/UnivariateRealFunction.java | 37 +
.../analysis/integration/RombergIntegrator.java | 126 +
.../analysis/integration/TrapezoidIntegrator.java | 150 +
.../integration/UnivariateRealIntegrator.java | 107 +
.../integration/UnivariateRealIntegratorImpl.java | 197 +
.../math/analysis/solvers/BisectionSolver.java | 116 +
.../commons/math/analysis/solvers/BrentSolver.java | 362 ++
.../math/analysis/solvers/MullerSolver.java | 370 ++
.../math/analysis/solvers/NewtonSolver.java | 141 +
.../math/analysis/solvers/RiddersSolver.java | 207 +
.../math/analysis/solvers/SecantSolver.java | 190 +
.../analysis/solvers/UnivariateRealSolver.java | 168 +
.../solvers/UnivariateRealSolverFactory.java | 96 +
.../solvers/UnivariateRealSolverFactoryImpl.java | 74 +
.../analysis/solvers/UnivariateRealSolverImpl.java | 280 ++
.../solvers/UnivariateRealSolverUtils.java | 254 ++
.../AbstractContinuousDistribution.java | 199 +
.../math/distribution/AbstractDistribution.java | 70 +
.../distribution/AbstractIntegerDistribution.java | 266 ++
.../math/distribution/BetaDistribution.java | 70 +
.../math/distribution/BetaDistributionImpl.java | 255 ++
.../math/distribution/BinomialDistribution.java | 64 +
.../distribution/BinomialDistributionImpl.java | 229 +
.../math/distribution/CauchyDistribution.java | 67 +
.../math/distribution/CauchyDistributionImpl.java | 288 ++
.../math/distribution/ChiSquaredDistribution.java | 56 +
.../distribution/ChiSquaredDistributionImpl.java | 289 ++
.../math/distribution/ContinuousDistribution.java | 54 +
.../math/distribution/DiscreteDistribution.java | 35 +
.../commons/math/distribution/Distribution.java | 55 +
.../math/distribution/ExponentialDistribution.java | 56 +
.../distribution/ExponentialDistributionImpl.java | 259 ++
.../commons/math/distribution/FDistribution.java | 64 +
.../math/distribution/FDistributionImpl.java | 302 ++
.../math/distribution/GammaDistribution.java | 72 +
.../math/distribution/GammaDistributionImpl.java | 315 ++
.../commons/math/distribution/HasDensity.java | 45 +
.../distribution/HypergeometricDistribution.java | 82 +
.../HypergeometricDistributionImpl.java | 363 ++
.../math/distribution/IntegerDistribution.java | 85 +
.../math/distribution/NormalDistribution.java | 73 +
.../math/distribution/NormalDistributionImpl.java | 327 ++
.../math/distribution/PascalDistribution.java | 73 +
.../math/distribution/PascalDistributionImpl.java | 233 +
.../math/distribution/PoissonDistribution.java | 64 +
.../math/distribution/PoissonDistributionImpl.java | 286 ++
.../math/distribution/SaddlePointExpansion.java | 204 +
.../commons/math/distribution/TDistribution.java | 48 +
.../math/distribution/TDistributionImpl.java | 237 +
.../math/distribution/WeibullDistribution.java | 70 +
.../math/distribution/WeibullDistributionImpl.java | 280 ++
.../math/distribution/ZipfDistribution.java | 71 +
.../math/distribution/ZipfDistributionImpl.java | 221 +
src/org/apache/commons/math/special/Beta.java | 198 +
src/org/apache/commons/math/special/Erf.java | 57 +
src/org/apache/commons/math/special/Gamma.java | 345 ++
.../commons/math/util/ContinuedFraction.java | 213 +
src/org/apache/commons/math/util/MathUtils.java | 1864 ++++++++
.../commons/math/util/OpenIntToDoubleHashMap.java | 680 +++
src/org/json/CDL.java | 279 ++
src/org/json/Cookie.java | 169 +
src/org/json/CookieList.java | 90 +
src/org/json/HTTP.java | 163 +
src/org/json/HTTPTokener.java | 77 +
src/org/json/JSONArray.java | 987 ++++
src/org/json/JSONException.java | 41 +
src/org/json/JSONML.java | 467 ++
src/org/json/JSONObject.java | 1665 +++++++
src/org/json/JSONString.java | 18 +
src/org/json/JSONStringer.java | 78 +
src/org/json/JSONTokener.java | 446 ++
src/org/json/JSONWriter.java | 327 ++
src/org/json/Kim.java | 373 ++
src/org/json/Property.java | 74 +
src/org/json/README | 68 +
src/org/json/XML.java | 508 +++
src/org/json/XMLTokener.java | 365 ++
src/org/json/zip/BitInputStream.java | 169 +
src/org/json/zip/BitOutputStream.java | 154 +
src/org/json/zip/BitReader.java | 41 +
src/org/json/zip/BitWriter.java | 51 +
src/org/json/zip/Compressor.java | 575 +++
src/org/json/zip/Decompressor.java | 325 ++
src/org/json/zip/Huff.java | 406 ++
src/org/json/zip/JSONzip.java | 281 ++
src/org/json/zip/Keep.java | 84 +
src/org/json/zip/MapKeep.java | 160 +
src/org/json/zip/None.java | 15 +
src/org/json/zip/PostMortem.java | 47 +
src/org/json/zip/README | 2 +
src/org/json/zip/TrieKeep.java | 396 ++
src/test/beast/BEASTTestCase.java | 140 +
src/test/beast/app/BeautiSubTemplateTest.java | 257 ++
src/test/beast/app/BeautiTest.java | 152 +
src/test/beast/app/beauti/BeautiBase.java | 358 ++
.../app/beauti/BeautiDivergenceDatingTest.java | 601 +++
.../beast/app/beauti/BeautiRateTutorialTest.java | 388 ++
src/test/beast/app/beauti/BeautiSimpleTest.java | 129 +
src/test/beast/app/beauti/BeautiStarBeastTest.java | 181 +
src/test/beast/app/beauti/CloneTest.java | 158 +
src/test/beast/app/beauti/FixedMeanRateTest.java | 98 +
src/test/beast/app/beauti/LinkUnlinkTest.java | 546 +++
.../beast/app/beauti/SimpleClockModelTest.java | 111 +
src/test/beast/app/beauti/SimpleTreePriorTest.java | 64 +
src/test/beast/beast2vs1/ClockModelTest.java | 111 +
src/test/beast/beast2vs1/StarBEASTTest.java | 134 +
.../beast/beast2vs1/SubstitutionModelTest.java | 117 +
src/test/beast/beast2vs1/TaxonOrderTest.java | 71 +
src/test/beast/beast2vs1/TestFramework.java | 86 +
src/test/beast/beast2vs1/TipTimeTest.java | 114 +
src/test/beast/beast2vs1/TreePriorTest.java | 201 +
src/test/beast/beast2vs1/TreeTest.java | 73 +
.../beast/beast2vs1/trace/DiscreteStatistics.java | 394 ++
src/test/beast/beast2vs1/trace/Expectation.java | 95 +
src/test/beast/beast2vs1/trace/LogAnalyser.java | 357 ++
src/test/beast/beast2vs1/trace/LogFileTraces.java | 218 +
.../beast/beast2vs1/trace/NumberFormatter.java | 164 +
src/test/beast/beast2vs1/trace/TraceException.java | 43 +
.../beast/beast2vs1/trace/TraceStatistics.java | 209 +
src/test/beast/beast2vs1/trace/TraceType.java | 33 +
src/test/beast/beast2vs1/trace/TrimLineReader.java | 78 +
src/test/beast/core/BEASTInterfaceTest.java | 123 +
src/test/beast/core/StateNodeInitialiserTest.java | 50 +
.../core/parameter/BooleanParameterListTest.java | 161 +
.../core/parameter/IntegerParameterListTest.java | 129 +
src/test/beast/core/parameter/ParameterTest.java | 33 +
.../core/parameter/RealParameterListTest.java | 129 +
.../evolution/alignment/FilteredAlignmentTest.java | 284 ++
.../alignment/UncertainAlignmentTest.java | 119 +
.../alignment/UnorderedAlignmentsTest.java | 107 +
.../evolution/likelihood/TreeLikelihoodTest.java | 690 +++
.../evolution/operator/ExchangeOperatorTest.java | 130 +
.../operator/IntRandomWalkOperatorTest.java | 79 +
.../operator/UniformIntegerOperatorTest.java | 94 +
.../speciation/BirthDeathGernhard08ModelTest.java | 65 +
src/test/beast/evolution/substmodel/GTRTest.java | 188 +
src/test/beast/evolution/substmodel/HKYTest.java | 137 +
src/test/beast/evolution/tree/RandomTreeTest.java | 158 +
.../beast/evolution/tree/TreeAnnotatorTest.java | 158 +
.../tree/coalescent/BayesianSkylineTest.java | 42 +
.../evolution/tree/coalescent/CoalescentTest.java | 62 +
.../evolution/tree/newick/NewickTreeTest.java | 39 +
src/test/beast/integration/DocumentationTest.java | 119 +
.../beast/integration/ExampleJSONParsingTest.java | 127 +
.../beast/integration/ExampleXmlParsingTest.java | 137 +
src/test/beast/integration/InputTypeTest.java | 50 +
src/test/beast/integration/ResumeTest.java | 60 +
src/test/beast/integration/XMLElementNameTest.java | 122 +
src/test/beast/integration/XMLProducerTest.java | 82 +
src/test/beast/math/distributions/GammaTest.java | 28 +
.../LogNormalDistributionModelTest.java | 86 +
.../beast/math/distributions/MRCAPriorTest.java | 123 +
.../MeanOfParametricDistributionTest.java | 133 +
src/test/beast/util/ClusterTreeTest.java | 77 +
src/test/beast/util/JSONTest.java | 29 +
src/test/beast/util/NexusParserTest.java | 162 +
src/test/beast/util/TreeParserTest.java | 111 +
templates/ClockModels.xml | 293 ++
templates/ParametricDistributions.xml | 134 +
templates/Standard.xml | 356 ++
templates/StarBeast.xml | 437 ++
templates/SubstModels.xml | 384 ++
templates/TreePriors.xml | 414 ++
test.xml | 50 +
949 files changed, 169101 insertions(+), 1955 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git
More information about the debian-med-commit
mailing list