[med-svn] [jmodeltest] 03/14: Merge tag 'upstream/2.1.9+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository jmodeltest.

commit 70a968ac809ef81e1dcf3a816722078ec41b4f6c
Merge: 2e86fa3 d924798
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 15 17:38:54 2016 +0100

    Merge tag 'upstream/2.1.9+dfsg'
    
    Upstream version 2.1.9+dfsg

 build.xml                                          |  18 ++--
 manual/manual.tex                                  |   9 ++
 .../darwin/jmodeltest/ApplicationOptions.java      |   7 +-
 .../java/es/uvigo/darwin/jmodeltest/ModelTest.java |  48 ++++------
 .../darwin/jmodeltest/ModelTestConfiguration.java  |   6 +-
 .../jmodeltest/exception/InternalException.java    |   2 +-
 .../darwin/jmodeltest/exe/PhymlSingleModel.java    |  33 ++++---
 .../es/uvigo/darwin/jmodeltest/exe/RunPhyml.java   | 106 +++++++++++++++++++--
 .../es/uvigo/darwin/jmodeltest/gui/FrameMain.java  |   4 +-
 .../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
 .../uvigo/darwin/jmodeltest/io/HtmlReporter.java   |   1 +
 .../darwin/jmodeltest/tree/TreeDistancesCache.java |   2 +-
 .../darwin/jmodeltest/utilities/Utilities.java     |  33 +++++--
 src/main/resources/CHANGELOG                       |   7 ++
 src/main/resources/README                          |   2 +-
 src/main/resources/conf/jmodeltest.conf            |   5 +-
 21 files changed, 205 insertions(+), 83 deletions(-)

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