[med-svn] [jmodeltest] branch upstream updated (9a1f0a3 -> 5f03be0)
Andreas Tille
tille at debian.org
Wed Oct 28 21:24:31 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository jmodeltest.
from 9a1f0a3 Imported Upstream version 2.1.7-20150220+dfsg
new 5f03be0 Imported Upstream version 2.1.8+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 +
COPYING => src/main/resources/COPYING | 0
INSTALL => src/main/resources/INSTALL | 0
README => src/main/resources/README | 2 +-
.../main/resources/THIRDPARTYLICENSES | 0
{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, 24466 insertions(+), 20 deletions(-)
create mode 100644 .hgignore
create mode 100644 Manifest
create mode 100644 README.md
create mode 100644 build.xml
delete mode 100644 lib/BrowserLauncher2-all-1_3.jar
delete mode 100644 lib/readseq.jar
create mode 100644 manual/biblio.bib
create mode 100644 manual/images/bic.pdf
create mode 100644 manual/images/consensus.pdf
create mode 100644 manual/images/dLRT.png
create mode 100644 manual/images/hLRT.png
create mode 100644 manual/images/html-log.pdf
create mode 100644 manual/images/lkl-settings.pdf
create mode 100644 manual/images/main-window.pdf
create mode 100644 manual/images/results.pdf
create mode 100644 manual/manual.tex
create mode 100755 manual/natbib.bst
create mode 100755 manual/natbib.sty
create mode 100644 manual/sec-arguments.tex
create mode 100644 manual/sec-config.tex
create mode 100644 manual/sec-quickstart.tex
create mode 100644 manual/sec-theory.tex
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/InvalidArgumentException.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/ModelTestConfiguration.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/WeakStateException.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/exception/AlignmentParseException.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/exception/CheckedException.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exception/InputFileException.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/exception/InternalException.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/Distributor.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/GuidedSearchManager.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/MultipleDistributor.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlParallelModel.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/ProcessManager.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunConsense.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlClustering.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlHybrid.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlMPJ.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhymlThread.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/StreamGobbler.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/FramePreferences.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameResults.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_AIC.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_BIC.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_CalcLike.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_Consense.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_DT.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_LRTcalculator.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_Progress.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/Frame_hLRT.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/JModelTestFrame.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/gui/XManager.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/io/AlignmentReader.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/io/DocumentOutputStream.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/io/NullPrintStream.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/io/RFHistogram.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/io/TextInputStream.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/io/TextOutputStream.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/model/Model.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/model/ModelComparator.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/model/ModelConstants.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/observer/ConsoleProgressObserver.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/observer/ProgressInfo.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/AIC.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/AICc.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/BIC.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/DT.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/HLRT.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/selection/InformationCriterion.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/statistics/Statistics.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/threads/SwingWorker.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeDistancesCache.java
create mode 100755 src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeEuclideanDistancesCache.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeRFDistancesCache.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeSummary.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeUtilities.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/InitialFocusSetter.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/ModelDef.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/MyTableCellRenderer.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/MyTableModel.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/PrintUtilities.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/Simulation.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableMap.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/TableSorter.java
create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java
rename CHANGELOG => src/main/resources/CHANGELOG (97%)
copy COPYING => src/main/resources/COPYING (100%)
copy INSTALL => src/main/resources/INSTALL (100%)
rename README => src/main/resources/README (99%)
copy THIRDPARTYLICENSES => src/main/resources/THIRDPARTYLICENSES (100%)
rename {conf => src/main/resources/conf}/jmodeltest.conf (100%)
rename {es => src/main/resources/es}/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif (100%)
rename {es => src/main/resources/es}/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif (100%)
rename {es => src/main/resources/es}/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif (100%)
rename {es => src/main/resources/es}/uvigo/darwin/jmodeltest/gui/icons/Open16.gif (100%)
rename {es => src/main/resources/es}/uvigo/darwin/jmodeltest/gui/icons/Open24.gif (100%)
rename {example-data => src/main/resources/example-data}/18S_insects2.nex (100%)
rename {example-data => src/main/resources/example-data}/Birds.nex (100%)
rename {example-data => src/main/resources/example-data}/HIV_vpu.ref2.fas (100%)
rename {example-data => src/main/resources/example-data}/HIVpol.groupM.nex (100%)
mode change 100644 => 100755
rename {example-data => src/main/resources/example-data}/Hex_EF1a.nex (100%)
rename {example-data => src/main/resources/example-data}/aP6.fas (100%)
rename {example-data => src/main/resources/example-data}/aP6.phy (100%)
rename {example-data => src/main/resources/example-data}/channa.nex (100%)
rename {example-data => src/main/resources/example-data}/data.phy (100%)
rename {example-data => src/main/resources/example-data}/example.nex (100%)
rename {example-data => src/main/resources/example-data}/gusanos16S.mafft.fas (100%)
rename {example-data => src/main/resources/example-data}/gusanosCOI.mafft.fas (100%)
rename {example-data => src/main/resources/example-data}/primate-mtDNA.nex (100%)
rename {example-data => src/main/resources/example-data}/rodents.nex (100%)
create mode 100644 src/main/resources/exe/phyml/README
rename {extra => src/main/resources/extra}/filecluster8.conf.template (100%)
rename {extra => src/main/resources/extra}/machines (100%)
create mode 100644 src/main/resources/extra/mpj.tar.gz
rename {resources => src/main/resources/resources}/template/index.html (100%)
rename {resources => src/main/resources/resources}/template/resources/homeIcon.gif (100%)
rename {resources => src/main/resources/resources}/template/resources/logo0.png (100%)
rename {resources => src/main/resources/resources}/template/resources/style.css (100%)
rename {resources => src/main/resources/resources}/template/resources/topIcon.gif (100%)
rename runjmodeltest-cluster.sh => src/main/resources/runjmodeltest-cluster.sh (100%)
rename runjmodeltest-gui.bat => src/main/resources/runjmodeltest-gui.bat (100%)
rename runjmodeltest-gui.sh => src/main/resources/runjmodeltest-gui.sh (100%)
rename {trees => src/main/resources/trees}/aP6.tree (100%)
rename {trees => src/main/resources/trees}/aP6b.tree (100%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jmodeltest.git
More information about the debian-med-commit
mailing list