[med-svn] [libbpp-phyl-omics] branch master updated (7b2aaaf -> e17dfcf)

[Andreas Tille]

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

      from  7b2aaaf   Add misssing Build-Depends: d-shlibs
       new  421eb51   New upstream version, d/watch: point to github
       new  f6eee0f   New upstream version 2.3.1
       new  48584f5   Updated version 2.3.1 from 'upstream/2.3.1'
       new  794f9e6   debhelper 10
       new  e17dfcf   Adapt package names to soversion change, Hardening

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Summary of changes:
 CMakeLists.txt                                     |  175 +-
 ChangeLog                                          |    8 +
 Doxyfile                                           | 2662 ++++++++++++--------
 INSTALL.txt                                        |   19 +-
 bpp-phyl-omics.spec                                |  141 +-
 debian/changelog                                   |   10 +
 debian/compat                                      |    2 +-
 debian/control                                     |   16 +-
 debian/rules                                       |   12 +-
 debian/watch                                       |    5 +-
 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 +-
 27 files changed, 2131 insertions(+), 1538 deletions(-)
 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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