[med-svn] [clustalo] branch upstream updated (650b294 -> bacfc62)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository clustalo.

      from  650b294   Imported Upstream version 1.2.1
       new  bacfc62   Imported Upstream version 1.2.2

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:
 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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