[med-svn] [libbpp-phyl-omics] 03/05: Updated version 2.3.1 from 'upstream/2.3.1'

[Andreas Tille]

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

commit 48584f5ec8d865c56037a42e60394653a3f286cf
Merge: 421eb51 f6eee0f
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 13 23:36:08 2017 +0200

    Updated version 2.3.1 from 'upstream/2.3.1'
    
    with Debian dir 6a3a250acfacce6c5e3669a467b8b930c8f105a7

 CMakeLists.txt                                     |  175 +-
 ChangeLog                                          |    8 +
 Doxyfile                                           | 2662 ++++++++++++--------
 INSTALL.txt                                        |   19 +-
 bpp-phyl-omics.spec                                |  141 +-
 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 +-
 22 files changed, 2107 insertions(+), 1517 deletions(-)

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