[med-svn] [ffp] 03/04: Update upstream source from tag 'upstream/3.19'

[Andreas Tille]

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

tille pushed a commit to branch master
in repository ffp.

commit 71b2274ddbec1ab0ccf146b72468c6bcb9cc11b8
Merge: 55a7aaf 9aeea64
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 6 22:44:37 2017 +0100

    Update upstream source from tag 'upstream/3.19'
    
    Update to upstream version '3.19'
    with Debian dir 437c0e27023d5c0c466cdc08f2b2d79f75e9d590

 AUTHORS                        |    2 +
 COPYING                        |    6 +
 INSTALL                        |  134 +
 Makefile.am                    |    7 +
 Makefile.in                    |  699 ++++
 NEWS                           |  279 ++
 README                         |  619 ++++
 aclocal.m4                     |  951 ++++++
 config.h.in                    |  141 +
 config/config.guess            | 1463 +++++++++
 config/config.sub              | 1579 +++++++++
 config/depcomp                 |  630 ++++
 config/install-sh              |  520 +++
 config/missing                 |  376 +++
 configure                      | 7079 ++++++++++++++++++++++++++++++++++++++++
 configure.ac                   |   94 +
 doc/Makefile.am                |   49 +
 doc/Makefile.in                |  420 +++
 doc/tutorial.in                | 1415 ++++++++
 examples/Figure_1a_consensus   |   10 +
 examples/Figure_1a_tree        |   14 +
 examples/Figure_1b_consensus   |    9 +
 examples/Figure_1b_tree        |   15 +
 examples/Makefile.am           |    3 +
 examples/Makefile.in           |  378 +++
 examples/README                |   96 +
 man/Makefile.am                |  137 +
 man/Makefile.in                |  539 +++
 man/ffpaa.1.in                 |  168 +
 man/ffpboot.1.in               |  101 +
 man/ffpcol.1.in                |  143 +
 man/ffpcomplex.1.in            |  129 +
 man/ffpdf.1.in                 |  139 +
 man/ffpfilt.1.in               |  132 +
 man/ffpjsd.1.in                |  222 ++
 man/ffpmerge.1.in              |   77 +
 man/ffpre.1.in                 |  113 +
 man/ffpreprof.1.in             |   82 +
 man/ffprwn.1.in                |   73 +
 man/ffpry.1.in                 |  204 ++
 man/ffpsubnam.1.in             |   42 +
 man/ffptree.1.in               |  176 +
 man/ffptxt.1.in                |   88 +
 man/ffpvocab.1.in              |   53 +
 man/ffpvprof.1.in              |   93 +
 scripts/Makefile.am            |   60 +
 scripts/Makefile.in            |  440 +++
 scripts/ffpdf.in               |  244 ++
 scripts/ffpgui.in              |  824 +++++
 scripts/ffpreprof.in           |  224 ++
 scripts/ffpsubnam.in           |  167 +
 scripts/ffpvprof.in            |  238 ++
 src/Makefile.am                |   31 +
 src/Makefile.in                |  604 ++++
 src/cdfmacros.h                |   28 +
 src/codon.h                    |   22 +
 src/ffpaa.c                    |  349 ++
 src/ffpboot.c                  |  288 ++
 src/ffpcol.c                   |  285 ++
 src/ffpcomplex.c               |  368 +++
 src/ffpfilt.c                  |  347 ++
 src/ffpjsd.c                   | 1518 +++++++++
 src/ffpmerge.c                 |  266 ++
 src/ffpre.c                    |  267 ++
 src/ffprwn.c                   |  260 ++
 src/ffpry.c                    |  378 +++
 src/ffpry.h                    |   24 +
 src/ffptree.c                  | 1212 +++++++
 src/ffptxt.c                   |  234 ++
 src/ffpvocab.c                 |  189 ++
 src/hash.c                     |  910 ++++++
 src/hash.h                     |  236 ++
 src/hashroll.c                 | 2049 ++++++++++++
 src/hashroll.h                 |  260 ++
 src/mask.c                     |   53 +
 src/mask.h                     |   23 +
 src/parse_features.c           |   82 +
 src/parse_features.h           |   24 +
 src/sighandle.c                |   98 +
 src/sighandle.h                |   23 +
 src/utils.c                    |  533 +++
 src/utils.h                    |  240 ++
 src/vstring.h                  |   27 +
 tests/Makefile.am              |   84 +
 tests/Makefile.in              |  505 +++
 tests/ecoli                    |   50 +
 tests/ecoli.2                  |   30 +
 tests/ecolitest.sh             |  227 ++
 tests/faalist.txt              |    7 +
 tests/ffpaa_test_basic.sh      |   22 +
 tests/ffpaa_test_d.sh          |   20 +
 tests/ffpaa_test_f.sh          |   20 +
 tests/ffpaa_test_m.sh          |   15 +
 tests/ffpaa_test_stdin.sh      |   15 +
 tests/ffpaa_test_w.sh          |   12 +
 tests/ffpboot_test_stdin.sh    |   16 +
 tests/ffpcol_test_stdin.sh     |   15 +
 tests/ffpcomplex_test_stdin.sh |   16 +
 tests/ffpjsd_test.sh           |    9 +
 tests/ffpmerge_test.sh         |   14 +
 tests/ffpre_test.sh            |   18 +
 tests/ffpreprof_test_basic.sh  |    9 +
 tests/ffprwn_test.sh           |   18 +
 tests/ffprwn_test_stdin.sh     |   15 +
 tests/ffprwn_test_stdin2.sh    |   15 +
 tests/ffpry_test_basic.sh      |   14 +
 tests/ffpry_test_d.sh          |   13 +
 tests/ffpry_test_f.sh          |   11 +
 tests/ffpry_test_fidelity.sh   |    9 +
 tests/ffpry_test_fidelity2.sh  |    9 +
 tests/ffpry_test_l.sh          |   14 +
 tests/ffpry_test_m.sh          |   14 +
 tests/ffpry_test_r.sh          |   13 +
 tests/ffpry_test_stdin.sh      |   20 +
 tests/ffpry_test_w.sh          |   11 +
 tests/ffptxt_test.sh           |   18 +
 tests/ffpvocab_test.sh         |   26 +
 tests/ffpvprof_test_basic.sh   |   26 +
 tests/fnalist.txt              |    4 +
 tests/test1.faa                |    3 +
 tests/test1.fna                |    3 +
 tests/test2.faa                |    3 +
 tests/test2.fna                |    4 +
 tests/test3.faa                |    3 +
 tests/test3.fna                |    2 +
 tests/test4.faa                |    4 +
 tests/test4.fna                |    2 +
 tests/test5.fna                |    2 +
 128 files changed, 34504 insertions(+)

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