[ssm] 02/04: Merge tag 'upstream/1.4'

[Frédéric-Emmanuel Picca]

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picca pushed a commit to branch master
in repository ssm.

commit 255b63feb0670b11c5ad0c694019bb2fc8d6b2ec
Merge: 8c5474b 420b928
Author: Picca Frédéric-Emmanuel <picca at debian.org>
Date:   Wed Dec 31 12:19:20 2014 +0100

    Merge tag 'upstream/1.4'
    
    Upstream version 1.4

 INSTALL                                    |  15 +-
 Makefile.am                                |  21 +-
 Makefile.in                                | 311 ++++++++++-----
 aclocal.m4                                 | 276 +++++++------
 build-aux/ar-lib                           |   2 +-
 build-aux/config.guess                     | 182 +++++----
 build-aux/config.sub                       |  88 ++--
 build-aux/depcomp                          | 454 ++++++++++++---------
 build-aux/missing                          | 405 +++++++------------
 configure                                  |  98 +++--
 configure.ac                               |  24 +-
 ssm.pc.in                                  |  12 +
 ssm_align.cpp => ssm/ssm_align.cpp         | 195 +++++----
 ssm/ssm_align.h                            | 217 ++++++++++
 ssm_csia.cpp => ssm/ssm_csia.cpp           | 219 +++++-----
 ssm/ssm_csia.h                             | 184 +++++++++
 ssm/ssm_defs.h                             | 125 ++++++
 ssm_graph.cpp => ssm/ssm_graph.cpp         | 378 ++++++++++--------
 ssm_graph.h => ssm/ssm_graph.h             | 162 ++++----
 ssm_malign.cpp => ssm/ssm_malign.cpp       | 622 ++++++++++++++++-------------
 ssm/ssm_malign.h                           | 345 ++++++++++++++++
 ssm_superpose.cpp => ssm/ssm_superpose.cpp | 607 +++++++++++++++-------------
 ssm/ssm_superpose.h                        | 295 ++++++++++++++
 ssm_vxedge.cpp => ssm/ssm_vxedge.cpp       | 368 +++++++++--------
 ssm/ssm_vxedge.h                           | 241 +++++++++++
 ssm_align.h                                | 193 ---------
 ssm_csia.h                                 | 162 --------
 ssm_defs.h                                 |  89 -----
 ssm_malign.h                               | 313 ---------------
 ssm_superpose.h                            | 268 -------------
 ssm_vxedge.h                               | 219 ----------
 sup_defs.h                                 |  60 ++-
 sup_multiple.cpp                           | 103 +++--
 sup_multiple.h                             |  67 +++-
 sup_pairwise.cpp                           |  70 +++-
 sup_pairwise.h                             |  67 +++-
 superpose.cpp                              | 130 +++---
 37 files changed, 4163 insertions(+), 3424 deletions(-)

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