[med-svn] [jmodeltest] branch upstream updated (5f03be0 -> 4cee886)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository jmodeltest.

      from  5f03be0   Imported Upstream version 2.1.8+dfsg
       new  d924798   Imported Upstream version 2.1.9+dfsg
       new  4cee886   Imported Upstream version 2.1.10+dfsg

The 2 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 +-
 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 +-
 36 files changed, 1940 insertions(+), 287 deletions(-)
 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

-- 
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