[med-svn] [libbpp-phyl-omics] branch upstream updated (f9473fb -> f6eee0f)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository libbpp-phyl-omics.

      from  f9473fb   Imported Upstream version 2.2.0
       new  f6eee0f   New upstream version 2.3.1

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:
 CMakeLists.txt                                     |  175 +-
 ChangeLog                                          |    8 +
 Doxyfile                                           | 2662 ++++++++++++--------
 INSTALL.txt                                        |   19 +-
 bpp-phyl-omics.spec                                |  141 +-
 debian/changelog                                   |   18 -
 debian/compat                                      |    1 -
 debian/control                                     |   25 -
 debian/copyright                                   |   66 -
 debian/libbpp-phyl-omics-dev.install               |    3 -
 debian/libbpp-phyl-omics1.install                  |    1 -
 debian/postinst                                    |   57 -
 debian/postrm                                      |   59 -
 debian/prerm                                       |   41 -
 debian/rules                                       |  122 -
 debian/source/format                               |    1 -
 genIncludes.py                                     |   16 -
 genIncludes.sh                                     |   35 -
 package.cmake.in                                   |   27 +
 .../Io/Maf/AbstractDistanceEstimationMafIterator.h |   19 +-
 .../Io/Maf/CountDistanceEstimationMafIterator.h    |    5 +-
 ...stanceBasedPhylogenyReconstructionMafIterator.h |    2 +-
 ...eeMafIterator.cpp => FilterTreeMafIterator.cpp} |   43 +-
 ...utTreeMafIterator.h => FilterTreeMafIterator.h} |   68 +-
 ...imumLikelihoodDistanceEstimationMafIterator.cpp |    4 +-
 ...aximumLikelihoodDistanceEstimationMafIterator.h |   10 +-
 .../Maf/MaximumLikelihoodModelFitMafStatistics.cpp |   36 +-
 .../Maf/MaximumLikelihoodModelFitMafStatistics.h   |  143 +-
 ...tor.cpp => OutputDistanceMatrixMafIterator.cpp} |   37 +-
 ...terator.h => OutputDistanceMatrixMafIterator.h} |   54 +-
 src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp       |   29 +-
 src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h         |   14 +-
 src/CMakeLists.txt                                 |   77 +-
 33 files changed, 2107 insertions(+), 1911 deletions(-)
 delete mode 100644 debian/changelog
 delete mode 100644 debian/compat
 delete mode 100644 debian/control
 delete mode 100644 debian/copyright
 delete mode 100644 debian/libbpp-phyl-omics-dev.install
 delete mode 100644 debian/libbpp-phyl-omics1.install
 delete mode 100755 debian/postinst
 delete mode 100755 debian/postrm
 delete mode 100755 debian/prerm
 delete mode 100755 debian/rules
 delete mode 100644 debian/source/format
 delete mode 100644 genIncludes.py
 delete mode 100755 genIncludes.sh
 create mode 100644 package.cmake.in
 copy src/Bpp/Seq/Io/Maf/{OutputTreeMafIterator.cpp => FilterTreeMafIterator.cpp} (59%)
 copy src/Bpp/Seq/Io/Maf/{OutputTreeMafIterator.h => FilterTreeMafIterator.h} (56%)
 copy src/Bpp/Seq/Io/Maf/{OutputTreeMafIterator.cpp => OutputDistanceMatrixMafIterator.cpp} (58%)
 copy src/Bpp/Seq/Io/Maf/{OutputTreeMafIterator.h => OutputDistanceMatrixMafIterator.h} (63%)

-- 
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