[med-svn] [clustalo] branch master updated (1589fe5 -> d6d65c5)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository clustalo.

      from  1589fe5   Moved packaging from SVN to Git
       new  bacfc62   Imported Upstream version 1.2.2
       new  9fe5d64   Merge tag 'upstream/1.2.2'
       new  39eeda6   New upstream version
       new  d6d65c5   hardening=+all

The 4 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                        |   2 +-
 INSTALL                         |  64 ++++
 configure                       |  20 +-
 configure.ac                    |   6 +-
 debian/changelog                |   4 +-
 debian/rules                    |   2 +
 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 +++++-
 35 files changed, 1165 insertions(+), 401 deletions(-)

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