[med-svn] [clustalo] 02/04: Merge tag 'upstream/1.2.2'

[Andreas Tille]

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tille pushed a commit to branch master
in repository clustalo.

commit 9fe5d64754c9015ec9b5e04410f06e7762994745
Merge: 1589fe5 bacfc62
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 4 11:14:49 2016 +0200

    Merge tag 'upstream/1.2.2'
    
    Upstream version 1.2.2

 Doxyfile                        |   2 +-
 INSTALL                         |  64 ++++
 configure                       |  20 +-
 configure.ac                    |   6 +-
 src/clustal-omega-config.h      |  10 +-
 src/clustal-omega.c             |  78 ++++-
 src/clustal-omega.h             |   2 +
 src/clustal/hhalign_wrapper.c   | 171 ++++++++--
 src/clustal/ktuple_pair.c       |   8 +-
 src/clustal/mbed.c              |  11 +-
 src/clustal/pair_dist.c         |  38 ++-
 src/clustal/pair_dist.h         |   6 +-
 src/clustal/seq.c               | 106 ++++++-
 src/clustal/seq.h               |   8 +-
 src/clustal/symmatrix.c         |  48 ++-
 src/hhalign/hash-C.h            |   6 +-
 src/hhalign/hhalign.cpp         |  12 +-
 src/hhalign/hhalign.h           |   4 +-
 src/hhalign/hhalignment-C.h     | 687 ++++++++++++++++++++++++----------------
 src/hhalign/hhfullalignment-C.h |   3 +-
 src/hhalign/hhfunc-C.h          |   7 +-
 src/hhalign/hhhalfalignment-C.h |   3 +-
 src/hhalign/hhhit-C.h           |   7 +-
 src/hhalign/hhhitlist-C.h       |   8 +-
 src/hhalign/hhhmm-C.h           |   3 +-
 src/hhalign/util-C.h            |   3 +-
 src/mymain.c                    |  22 +-
 src/squid/a2m.c                 |   9 +-
 src/squid/msa.c                 |  78 ++++-
 src/squid/msa.h                 |   7 +-
 src/squid/sqio.c                |  21 +-
 src/squid/squid.h               |   3 +
 src/squid/stockholm.c           |  99 +++++-
 33 files changed, 1160 insertions(+), 400 deletions(-)

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