[med-svn] [jmodeltest] 03/05: Merge tag 'upstream/2.1.8+dfsg'
Andreas Tille
tille at debian.org
Wed Oct 28 21:24:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository jmodeltest.
commit e584853f03cdb9fd4cdf534d87d1a469ed567ff8
Merge: 8da2dc9 5f03be0
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 28 21:53:12 2015 +0100
Merge tag 'upstream/2.1.8+dfsg'
Upstream version 2.1.8+dfsg
.hgignore | 2 +
INSTALL | 28 +-
Manifest | 5 +
README.md | 55 +
build.xml | 77 +
lib/BrowserLauncher2-all-1_3.jar | Bin 186442 -> 0 bytes
lib/readseq.jar | Bin 763870 -> 0 bytes
manual/biblio.bib | 370 ++++
manual/images/bic.pdf | Bin 0 -> 9472 bytes
manual/images/consensus.pdf | Bin 0 -> 8653 bytes
manual/images/dLRT.png | Bin 0 -> 134234 bytes
manual/images/hLRT.png | Bin 0 -> 97522 bytes
manual/images/html-log.pdf | Bin 0 -> 152908 bytes
manual/images/lkl-settings.pdf | Bin 0 -> 13118 bytes
manual/images/main-window.pdf | Bin 0 -> 17523 bytes
manual/images/results.pdf | Bin 0 -> 27952 bytes
manual/manual.tex | 360 ++++
manual/natbib.bst | 1288 ++++++++++++++
manual/natbib.sty | 803 +++++++++
manual/sec-arguments.tex | 178 ++
manual/sec-config.tex | 145 ++
manual/sec-quickstart.tex | 315 ++++
manual/sec-theory.tex | 199 +++
.../darwin/jmodeltest/ApplicationOptions.java | 764 ++++++++
.../jmodeltest/InvalidArgumentException.java | 108 ++
.../java/es/uvigo/darwin/jmodeltest/ModelTest.java | 1841 ++++++++++++++++++++
.../darwin/jmodeltest/ModelTestConfiguration.java | 188 ++
.../uvigo/darwin/jmodeltest/ModelTestService.java | 171 ++
.../darwin/jmodeltest/WeakStateException.java | 37 +
.../exception/AlignmentParseException.java | 46 +
.../jmodeltest/exception/CheckedException.java | 42 +
.../jmodeltest/exception/InputFileException.java | 24 +
.../jmodeltest/exception/InternalException.java | 44 +
.../uvigo/darwin/jmodeltest/exe/Distributor.java | 231 +++
.../darwin/jmodeltest/exe/GuidedSearchManager.java | 274 +++
.../darwin/jmodeltest/exe/MultipleDistributor.java | 316 ++++
.../darwin/jmodeltest/exe/PhymlParallelModel.java | 118 ++
.../darwin/jmodeltest/exe/PhymlSingleModel.java | 542 ++++++
.../darwin/jmodeltest/exe/ProcessManager.java | 64 +
.../uvigo/darwin/jmodeltest/exe/RunConsense.java | 320 ++++
.../es/uvigo/darwin/jmodeltest/exe/RunPhyml.java | 387 ++++
.../darwin/jmodeltest/exe/RunPhymlClustering.java | 137 ++
.../darwin/jmodeltest/exe/RunPhymlHybrid.java | 301 ++++
.../uvigo/darwin/jmodeltest/exe/RunPhymlMPJ.java | 205 +++
.../darwin/jmodeltest/exe/RunPhymlThread.java | 190 ++
.../uvigo/darwin/jmodeltest/exe/StreamGobbler.java | 103 ++
.../es/uvigo/darwin/jmodeltest/gui/FrameMain.java | 1225 +++++++++++++
.../darwin/jmodeltest/gui/FramePreferences.java | 341 ++++
.../uvigo/darwin/jmodeltest/gui/FrameResults.java | 352 ++++
.../es/uvigo/darwin/jmodeltest/gui/Frame_AIC.java | 366 ++++
.../es/uvigo/darwin/jmodeltest/gui/Frame_BIC.java | 325 ++++
.../darwin/jmodeltest/gui/Frame_CalcLike.java | 943 ++++++++++
.../darwin/jmodeltest/gui/Frame_Consense.java | 348 ++++
.../es/uvigo/darwin/jmodeltest/gui/Frame_DT.java | 313 ++++
.../darwin/jmodeltest/gui/Frame_LRTcalculator.java | 363 ++++
.../darwin/jmodeltest/gui/Frame_Progress.java | 663 +++++++
.../es/uvigo/darwin/jmodeltest/gui/Frame_hLRT.java | 519 ++++++
.../darwin/jmodeltest/gui/JModelTestFrame.java | 34 +
.../es/uvigo/darwin/jmodeltest/gui/XManager.java | 258 +++
.../darwin/jmodeltest/io/AlignmentReader.java | 139 ++
.../darwin/jmodeltest/io/DocumentOutputStream.java | 107 ++
.../uvigo/darwin/jmodeltest/io/HtmlReporter.java | 664 +++++++
.../darwin/jmodeltest/io/NullPrintStream.java | 31 +
.../es/uvigo/darwin/jmodeltest/io/RFHistogram.java | 99 ++
.../darwin/jmodeltest/io/TextInputStream.java | 1 +
.../darwin/jmodeltest/io/TextOutputStream.java | 612 +++++++
.../es/uvigo/darwin/jmodeltest/model/Model.java | 625 +++++++
.../darwin/jmodeltest/model/ModelComparator.java | 46 +
.../darwin/jmodeltest/model/ModelConstants.java | 297 ++++
.../observer/ConsoleProgressObserver.java | 209 +++
.../darwin/jmodeltest/observer/ProgressInfo.java | 97 ++
.../es/uvigo/darwin/jmodeltest/selection/AIC.java | 276 +++
.../es/uvigo/darwin/jmodeltest/selection/AICc.java | 295 ++++
.../es/uvigo/darwin/jmodeltest/selection/BIC.java | 277 +++
.../es/uvigo/darwin/jmodeltest/selection/DT.java | 272 +++
.../es/uvigo/darwin/jmodeltest/selection/HLRT.java | 643 +++++++
.../jmodeltest/selection/InformationCriterion.java | 660 +++++++
.../darwin/jmodeltest/statistics/Statistics.java | 1 +
.../darwin/jmodeltest/threads/SwingWorker.java | 1 +
.../darwin/jmodeltest/tree/TreeDistancesCache.java | 146 ++
.../tree/TreeEuclideanDistancesCache.java | 44 +
.../jmodeltest/tree/TreeRFDistancesCache.java | 44 +
.../uvigo/darwin/jmodeltest/tree/TreeSummary.java | 405 +++++
.../darwin/jmodeltest/tree/TreeUtilities.java | 170 ++
.../jmodeltest/utilities/InitialFocusSetter.java | 42 +
.../darwin/jmodeltest/utilities/ModelDef.java | 60 +
.../jmodeltest/utilities/MyTableCellRenderer.java | 87 +
.../darwin/jmodeltest/utilities/MyTableModel.java | 292 ++++
.../jmodeltest/utilities/PrintUtilities.java | 101 ++
.../darwin/jmodeltest/utilities/Simulation.java | 491 ++++++
.../darwin/jmodeltest/utilities/TableMap.java | 91 +
.../darwin/jmodeltest/utilities/TableSorter.java | 326 ++++
.../darwin/jmodeltest/utilities/Utilities.java | 489 ++++++
CHANGELOG => src/main/resources/CHANGELOG | 6 +
src/main/resources/COPYING | 621 +++++++
INSTALL => src/main/resources/INSTALL | 0
README => src/main/resources/README | 2 +-
src/main/resources/THIRDPARTYLICENSES | 576 ++++++
{conf => src/main/resources/conf}/jmodeltest.conf | 0
.../uvigo/darwin/jmodeltest/gui/icons/JMT24.gif | Bin
.../uvigo/darwin/jmodeltest/gui/icons/JMT48.gif | Bin
.../uvigo/darwin/jmodeltest/gui/icons/JMT96.gif | Bin
.../uvigo/darwin/jmodeltest/gui/icons/Open16.gif | Bin
.../uvigo/darwin/jmodeltest/gui/icons/Open24.gif | Bin
.../main/resources/example-data}/18S_insects2.nex | 0
.../main/resources/example-data}/Birds.nex | 0
.../main/resources/example-data}/HIV_vpu.ref2.fas | 0
.../main/resources/example-data}/HIVpol.groupM.nex | 0
.../main/resources/example-data}/Hex_EF1a.nex | 0
.../main/resources/example-data}/aP6.fas | 0
.../main/resources/example-data}/aP6.phy | 0
.../main/resources/example-data}/channa.nex | 0
.../main/resources/example-data}/data.phy | 0
.../main/resources/example-data}/example.nex | 0
.../resources/example-data}/gusanos16S.mafft.fas | 0
.../resources/example-data}/gusanosCOI.mafft.fas | 0
.../main/resources/example-data}/primate-mtDNA.nex | 0
.../main/resources/example-data}/rodents.nex | 0
src/main/resources/exe/phyml/README | 10 +
.../resources/extra}/filecluster8.conf.template | 0
{extra => src/main/resources/extra}/machines | 0
src/main/resources/extra/mpj.tar.gz | Bin 0 -> 3293593 bytes
.../main/resources/resources}/template/index.html | 0
.../resources}/template/resources/homeIcon.gif | Bin
.../resources}/template/resources/logo0.png | Bin
.../resources}/template/resources/style.css | 0
.../resources}/template/resources/topIcon.gif | Bin
.../main/resources/runjmodeltest-cluster.sh | 0
.../main/resources/runjmodeltest-gui.bat | 0
.../main/resources/runjmodeltest-gui.sh | 0
{trees => src/main/resources/trees}/aP6.tree | 0
{trees => src/main/resources/trees}/aP6b.tree | 0
132 files changed, 25663 insertions(+), 20 deletions(-)
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