[med-svn] [psortb] branch master updated (52fbfec -> b0700ac)

[Andreas Tille]

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tille pushed a change to branch master
in repository psortb.

      from  52fbfec   Add biosquid-dev
       new  1cee463   Remove copies of biosquid - possibly  an old version drained from an old version of hmmer2
       new  ff5aa84   New upstream version 3.0.4+dfsg
       new  3ad9701   Merge tag 'upstream/3.0.4+dfsg'
       new  b0700ac   Use libsquid

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:
 algorithm-hmm/src/include/gki.h                  |  51 ---
 algorithm-hmm/src/include/msa.h                  | 286 --------------
 algorithm-hmm/src/include/rk.h                   |  40 --
 algorithm-hmm/src/include/sqfuncs.h              | 293 --------------
 algorithm-hmm/src/include/squid.h                | 473 -----------------------
 algorithm-hmm/src/include/squidconf.h            |  77 ----
 algorithm-hmm/src/include/ssi.h                  | 193 ---------
 algorithm-hmm/src/include/stopwatch.h            |  59 ---
 debian/changelog                                 |   4 +-
 debian/control                                   |   3 +-
 debian/copyright                                 |   8 +
 debian/patches/biosquid_includes.patch           |  15 +
 debian/patches/series                            |   2 +
 debian/patches/use_declaration_of_biosquid.patch |  14 +
 debian/watch                                     |   3 +-
 15 files changed, 46 insertions(+), 1475 deletions(-)
 delete mode 100644 algorithm-hmm/src/include/gki.h
 delete mode 100644 algorithm-hmm/src/include/msa.h
 delete mode 100644 algorithm-hmm/src/include/rk.h
 delete mode 100644 algorithm-hmm/src/include/sqfuncs.h
 delete mode 100644 algorithm-hmm/src/include/squid.h
 delete mode 100644 algorithm-hmm/src/include/squidconf.h
 delete mode 100644 algorithm-hmm/src/include/ssi.h
 delete mode 100644 algorithm-hmm/src/include/stopwatch.h
 create mode 100644 debian/patches/biosquid_includes.patch
 create mode 100644 debian/patches/series
 create mode 100644 debian/patches/use_declaration_of_biosquid.patch

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