[med-svn] [libbpp-seq] branch master updated (7b9d17b -> e6dacb3)

[Julien Dutheil]

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jdutheil-guest pushed a change to branch master
in repository libbpp-seq.

      from  7b9d17b   Rebuild with gcc-7, Standards-Version: 4.0.1
       new  0dc6a7e   New upstream version 2.3.2
       new  d9b3c89   Update upstream source from tag 'upstream/2.3.2'
       new  2bfb7c7   Version 2.3.2.
       new  a1a1c1c   Removed deprecated patch.
       new  e6dacb3   Version 2.3.2.

The 5 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:
 Doxyfile                                           | 477 +++++--------
 debian/changelog                                   |   6 +
 debian/control                                     |   8 +-
 debian/patches/relax_test_timeout.patch            |  19 -
 .../rm_VectorProbabilisticSiteContainer.patch      | 322 ---------
 debian/patches/series                              |   2 -
 debian/patches/unforce-cxxflags.patch              |   2 +-
 debian/rules                                       |   1 -
 src/Bpp/Seq/Alphabet/AlphabetTools.cpp             |   1 +
 src/Bpp/Seq/Alphabet/AlphabetTools.h               |   5 +-
 src/Bpp/Seq/Alphabet/CodonAlphabet.cpp             | 163 +++--
 src/Bpp/Seq/Alphabet/CodonAlphabet.h               | 577 +++++++++++-----
 src/Bpp/Seq/Alphabet/WordAlphabet.cpp              |  14 +-
 src/Bpp/Seq/Alphabet/WordAlphabet.h                | 738 ++++++++++++---------
 src/Bpp/Seq/CodonSiteTools.cpp                     |  13 +-
 src/Bpp/Seq/CodonSiteTools.h                       |   2 +-
 .../Container/VectorProbabilisticSiteContainer.cpp | 187 ------
 .../Container/VectorProbabilisticSiteContainer.h   | 123 ----
 src/Bpp/Seq/SequenceTools.cpp                      |  22 +-
 src/Bpp/Seq/StringSequenceTools.cpp                |   8 +-
 src/Bpp/Seq/SymbolListTools.cpp                    |   4 +-
 test/CMakeLists.txt                                |   2 +
 test/test_alphabets.cpp                            |   9 +
 23 files changed, 1233 insertions(+), 1472 deletions(-)
 delete mode 100644 debian/patches/relax_test_timeout.patch
 delete mode 100644 debian/patches/rm_VectorProbabilisticSiteContainer.patch
 delete mode 100644 src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
 delete mode 100644 src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h

-- 
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