[ssm] 03/05: Merge tag 'upstream/1.3'

[Frédéric-Emmanuel Picca]

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picca pushed a commit to branch master
in repository ssm.

commit 7f657427152da88787220734931dd9725ba9d130
Merge: 457a00c 806ec2e
Author: Picca Frédéric-Emmanuel <picca at debian.org>
Date:   Sat Aug 31 08:42:42 2013 +0200

    Merge tag 'upstream/1.3'
    
    Upstream version 1.3

 Makefile.am                     |   13 +-
 Makefile.in                     |  245 +++-
 aclocal.m4                      |  446 ++++---
 build-aux/ar-lib                |  270 ++++
 build-aux/config.guess          |  261 ++--
 build-aux/config.sub            |  213 ++-
 build-aux/depcomp               |  189 ++-
 build-aux/install-sh            |   35 +-
 build-aux/missing               |  148 +--
 configure                       | 2793 +++++++++++++++++++++------------------
 configure.ac                    |    7 +-
 m4/libtool.m4                   |  265 +++-
 m4/ltoptions.m4                 |   19 +-
 ss_csia.h                       |  162 ---
 ss_graph.h                      |  266 ----
 ss_vxedge.h                     |  232 ----
 ssm_align.cpp                   |  393 +++---
 ssm_align.h                     |  325 +++--
 ss_csia.cpp => ssm_csia.cpp     |  264 ++--
 ssm_csia.h                      |  162 +++
 ssm_defs.h                      |   89 ++
 ss_graph.cpp => ssm_graph.cpp   |  949 ++++++-------
 ssm_graph.h                     |  238 ++++
 ssm_malign.cpp                  | 2525 +++++++++++++++++++++++++++++++++++
 ssm_malign.h                    |  313 +++++
 ssm_superpose.cpp               |  259 ++--
 ssm_superpose.h                 |  497 ++++---
 ss_vxedge.cpp => ssm_vxedge.cpp |  474 +++----
 ssm_vxedge.h                    |  219 +++
 sup_defs.h                      |   31 +
 sup_multiple.cpp                |  258 ++++
 sup_multiple.h                  |   34 +
 sup_pairwise.cpp                |  273 ++++
 sup_pairwise.h                  |   33 +
 superpose.cpp                   |  464 +++----
 35 files changed, 8946 insertions(+), 4418 deletions(-)

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