[med-svn] [libbpp-raa] branch upstream updated (b6dfbc4 -> 56807c2)

[Andreas Tille]

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

      from  b6dfbc4   Imported Upstream version 2.2.0
       new  56807c2   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                 |  194 +-
 ChangeLog                      |    4 +
 Doxyfile                       | 2662 +++++++++++--------
 INSTALL.txt                    |   19 +-
 bpp-raa.spec                   |  132 +-
 debian/changelog               |   42 -
 debian/compat                  |    1 -
 debian/control                 |   29 -
 debian/copyright               |   66 -
 debian/libbpp-raa-dev.install  |    3 -
 debian/libbpp-raa1.install     |    1 -
 debian/postinst                |   57 -
 debian/postrm                  |   59 -
 debian/prerm                   |   41 -
 debian/rules                   |  121 -
 debian/source/format           |    1 -
 header.html                    |   27 +
 package.cmake.in               |   26 +
 src/Bpp/Raa.all                |    6 -
 src/Bpp/Raa/RAA.cpp            |  958 ++++---
 src/Bpp/Raa/RAA.h              |  861 +++---
 src/Bpp/Raa/RAA_acnuc.c        | 5766 ++++++++++++++++++++++------------------
 src/Bpp/Raa/RAA_acnuc.h        |  421 +--
 src/Bpp/Raa/RaaList.cpp        |  103 +-
 src/Bpp/Raa/RaaList.h          |  270 +-
 src/Bpp/Raa/RaaSeqAttributes.h |  121 +-
 src/Bpp/Raa/RaaSpeciesTree.cpp |  131 +-
 src/Bpp/Raa/RaaSpeciesTree.h   |  237 +-
 src/Bpp/Raa/md5.c              |  409 +--
 src/Bpp/Raa/misc_acnuc.c       |   62 +-
 src/Bpp/Raa/parser.c           |  166 +-
 src/Bpp/Raa/parser.h           |   19 +-
 src/Bpp/Raa/zsockr.c           |  212 +-
 src/CMakeLists.txt             |   93 +-
 34 files changed, 7101 insertions(+), 6219 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-raa-dev.install
 delete mode 100644 debian/libbpp-raa1.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
 create mode 100644 header.html
 create mode 100644 package.cmake.in
 delete mode 100644 src/Bpp/Raa.all

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