[med-svn] [jmodeltest] branch master updated (191e2de -> b3ec1f8)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository jmodeltest.

      from  191e2de   Add Build-Depends
       new  2e86fa3   Patch to use packaged jars
       new  d924798   Imported Upstream version 2.1.9+dfsg
       new  70a968a   Merge tag 'upstream/2.1.9+dfsg'
       new  bcbb15f   New upstream version
       new  f3a901c   Use xz compression
       new  d269782   There are better solutions than stripping UTF-8 strings
       new  3fcbb6e   Use Debian packaged JARs
       new  4cee886   Imported Upstream version 2.1.10+dfsg
       new  0a0e733   Merge tag 'upstream/2.1.10+dfsg'
       new  aa4e9ad   New upstream version
       new  1270aaa   Add missing Build-Depends
       new  f7a520f   Typo
       new  ef4c3d2   cme fix dpkg-control
       new  b3ec1f8   Homepage moved to Github

The 14 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:
 Manifest                                           |   2 +-
 README.md                                          |   6 +-
 build.xml                                          |  18 +-
 debian/changelog                                   |   2 +-
 debian/control                                     |   9 +-
 debian/patches/encoding.patch                      |  37 --
 debian/patches/series                              |   2 +-
 debian/patches/use_debian_packaged_jars.patch      |  26 +
 debian/watch                                       |   2 +-
 manual/changelog.tex                               | 141 ++++
 manual/manual.tex                                  | 162 +----
 .../darwin/jmodeltest/ApplicationOptions.java      |   7 +-
 .../java/es/uvigo/darwin/jmodeltest/ModelTest.java |  52 +-
 .../darwin/jmodeltest/ModelTestConfiguration.java  |  34 +-
 .../jmodeltest/exception/InternalException.java    |   8 +-
 .../jmodeltest/exe/ExternalExecutionManager.java   | 108 ++++
 .../darwin/jmodeltest/exe/MultipleDistributor.java |   3 -
 .../darwin/jmodeltest/exe/PhymlSingleModel.java    |  33 +-
 .../uvigo/darwin/jmodeltest/exe/RunConsense.java   |  20 +-
 .../es/uvigo/darwin/jmodeltest/exe/RunPhyml.java   | 109 +++-
 .../es/uvigo/darwin/jmodeltest/gui/FrameMain.java  |   4 +-
 .../darwin/jmodeltest/gui/Frame_Progress.java      |   2 +-
 .../es/uvigo/darwin/jmodeltest/gui/XManager.java   |   5 +-
 .../es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif | Bin
 .../es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif | Bin
 .../es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif | Bin
 .../uvigo/darwin/jmodeltest/gui/icons/Open16.gif   | Bin
 .../uvigo/darwin/jmodeltest/gui/icons/Open24.gif   | Bin
 .../darwin/jmodeltest/io/AlignmentReader.java      |  24 +-
 .../uvigo/darwin/jmodeltest/io/HtmlReporter.java   |  12 +-
 .../es/uvigo/darwin/jmodeltest/io/RFHistogram.java |   4 +-
 .../es/uvigo/darwin/jmodeltest/tree/Consensus.java | 717 +++++++++++++++++++++
 .../darwin/jmodeltest/tree/TreeDistancesCache.java |   2 +-
 .../darwin/jmodeltest/tree/TreeUtilities.java      | 196 +++++-
 .../WeightedTree.java}                             |  48 +-
 .../darwin/jmodeltest/utilities/FixedBitSet.java   | 268 ++++++++
 .../jmodeltest/utilities/MyFormattedOutput.java    | 181 ++++++
 .../darwin/jmodeltest/utilities/Utilities.java     |  33 +-
 src/main/resources/CHANGELOG                       |  13 +
 src/main/resources/README                          |   2 +-
 src/main/resources/conf/jmodeltest.conf            |   5 +-
 src/main/resources/resources/template/index.html   |   8 +-
 42 files changed, 1974 insertions(+), 331 deletions(-)
 delete mode 100644 debian/patches/encoding.patch
 create mode 100644 debian/patches/use_debian_packaged_jars.patch
 create mode 100644 manual/changelog.tex
 create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/exe/ExternalExecutionManager.java
 rename src/main/{resources => java}/es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif (100%)
 rename src/main/{resources => java}/es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif (100%)
 rename src/main/{resources => java}/es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif (100%)
 rename src/main/{resources => java}/es/uvigo/darwin/jmodeltest/gui/icons/Open16.gif (100%)
 rename src/main/{resources => java}/es/uvigo/darwin/jmodeltest/gui/icons/Open24.gif (100%)
 create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/tree/Consensus.java
 copy src/main/java/es/uvigo/darwin/jmodeltest/{exception/AlignmentParseException.java => tree/WeightedTree.java} (51%)
 mode change 100755 => 100644
 create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/FixedBitSet.java
 create mode 100644 src/main/java/es/uvigo/darwin/jmodeltest/utilities/MyFormattedOutput.java

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jmodeltest.git