[med-svn] [pftools] 02/07: Merge tag 'upstream/3'
Andreas Tille
tille at debian.org
Mon Mar 27 11:54:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pftools.
commit 47bbf239fcbd9178738e455de97c4d4c555b0b89
Merge: 8687a60 92d286c
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 24 16:03:13 2017 +0100
Merge tag 'upstream/3'
Upstream version 3
AUTHORS | 5 +
COPYING | 674 +++
ChangeLog | 0
INSTALL | 365 ++
Makefile | 901 +++-
Makefile.am | 3 +
Makefile.in | 789 +++
NEWS | 0
README | 170 +-
aclocal.m4 | 1454 ++++++
compile | 143 +
config.guess | 1545 ++++++
config.log | 2144 ++++++++
config.status | 1247 +++++
config.sub | 1791 +++++++
configure | 7939 ++++++++++++++++++++++++++++++
configure.ac | 221 +
CVPBR322 => data/CVPBR322 | 0
GTPA_HUMAN => data/GTPA_HUMAN | 0
MYSA_HUMAN => data/MYSA_HUMAN | 0
R76849.seq => data/R76849.seq | 0
blosum100.cmp => data/blosum100.cmp | 0
blosum30.cmp => data/blosum30.cmp | 0
blosum45.cmp => data/blosum45.cmp | 0
blosum50.cmp => data/blosum50.cmp | 0
blosum62.cmp => data/blosum62.cmp | 0
blosum65.cmp => data/blosum65.cmp | 0
blosum80.cmp => data/blosum80.cmp | 0
coils.prf => data/coils.prf | 0
ecp.prf => data/ecp.prf | 0
gonnet.cmp => data/gonnet.cmp | 0
pam120.cmp => data/pam120.cmp | 0
pam160.cmp => data/pam160.cmp | 0
pam200.cmp => data/pam200.cmp | 0
pam220.cmp => data/pam220.cmp | 0
pam250.cmp => data/pam250.cmp | 0
pam30.cmp => data/pam30.cmp | 0
pam40.cmp => data/pam40.cmp | 0
pam400.cmp => data/pam400.cmp | 0
pam80.cmp => data/pam80.cmp | 0
pfam_sh3.hmm => data/pfam_sh3.hmm | 0
data/pfam_sh3.prf | 235 +
prosite13.prf => data/prosite13.prf | 0
score.lis => data/score.lis | 0
sh3.gpr => data/sh3.gpr | 0
sh3.msf => data/sh3.msf | 0
sh3.prf => data/sh3.prf | 0
sh3.seq => data/sh3.seq | 0
standard.random => data/standard.random | 0
test.out => data/test.out | 346 +-
test.sh => data/test.sh | 34 +-
depcomp | 630 +++
profile.txt => doc/profile.txt | 0
install-sh | 520 ++
install_pftools.sh | 228 -
io.c | 15 -
jprsm.f | 97 -
man/2ft.1 | 121 +-
man/6ft.1 | 117 +-
man/gtop.1 | 260 +-
man/htop.1 | 383 +-
man/pfmake.1 | 536 +-
man/pfscale.1 | 308 +-
man/pfscan.1 | 409 +-
man/pfsearch.1 | 415 --
man/pfsearchV2.1 | 133 +
man/pfw.1 | 222 +-
man/psa.5 | 197 -
man/psa2msa.1 | 251 +-
man/ptof.1 | 306 +-
man/ptoh.1 | 289 +-
man/xpsa.5 | 396 --
missing | 376 ++
pfscan.1 | 416 --
pfsearch.f | 923 ----
psa.5 | 197 -
src/C/.deps/pfdump-io.Po | 170 +
src/C/.deps/pfsearchV3-pfsearch.Po | 210 +
src/C/Makefile | 554 +++
src/C/Makefile.am | 40 +
src/C/Makefile.in | 554 +++
src/C/a.out | Bin 0 -> 36296 bytes
src/C/generic/heuristic.c | 747 +++
src/C/generic/xali1_old.c | 410 ++
src/C/generic/xalip.c | 790 +++
src/C/include/config.h | 216 +
src/C/include/config.h.in | 215 +
src/C/include/profile.h | 737 +++
src/C/include/sequence.h | 115 +
src/C/include/stamp-h1 | 1 +
src/C/include/system.h | 950 ++++
src/C/pfdunp | Bin 0 -> 36296 bytes
src/C/prg/numa_threads.h | 850 ++++
src/C/prg/pfsearch.c | 1566 ++++++
src/C/prg/testHeuristic.c | 366 ++
src/C/prg/testHeuristicMatchDeletion.c | 67 +
src/C/prg/testXali1.c | 681 +++
src/C/prg/testheader.c | 35 +
src/C/prg/threads.h | 375 ++
src/C/sse2/heuristic_sse2.c | 395 ++
src/C/sse2/sse2_inline_fcts.h | 113 +
src/C/sse2/xali1_sse2.c | 245 +
src/C/sse2/xalip_sse2.c | 785 +++
src/C/sse2/xalit_sse2.c | 628 +++
src/C/sse41/heuristic_sse41.c | 427 ++
src/C/sse41/xali1_sse41.c | 280 ++
src/C/sse41/xalip_sse41.c | 808 +++
src/C/sse41/xalit_sse41.c | 567 +++
src/C/utils/Normalization.c | 176 +
src/C/utils/ReadSequence.c | 324 ++
src/C/utils/io.c | 1201 +++++
src/C/utils/output.c | 242 +
2ft.f => src/Fortran/2ft.f | 4 +-
6ft.f => src/Fortran/6ft.f | 4 +-
CFAve.f => src/Fortran/CFAve.f | 2 +-
CPAve.f => src/Fortran/CPAve.f | 2 +-
src/Fortran/Makefile | 546 ++
src/Fortran/Makefile.am | 19 +
src/Fortran/Makefile.in | 546 ++
NtoR.f => src/Fortran/NtoR.f | 2 +-
RtoN.f => src/Fortran/RtoN.f | 2 +-
Xblnk.f => src/Fortran/Xblnk.f | 2 +-
abini.f => src/Fortran/abini.f | 2 +-
ardim.f => src/Fortran/ardim.f | 2 +-
avdat.f => src/Fortran/avdat.f | 2 +-
codat.f => src/Fortran/codat.f | 2 +-
cvini.f => src/Fortran/cvini.f | 2 +-
dfdat.f => src/Fortran/dfdat.f | 2 +-
dfnul.f => src/Fortran/dfnul.f | 2 +-
djdat.f => src/Fortran/djdat.f | 2 +-
gsdat.f => src/Fortran/gsdat.f | 2 +-
gtop.f => src/Fortran/gtop.f | 4 +-
hmdat.f => src/Fortran/hmdat.f | 2 +-
htop.f => src/Fortran/htop.f | 4 +-
src/Fortran/io.c | 15 +
lblnk.f => src/Fortran/lblnk.f | 2 +-
nodat.f => src/Fortran/nodat.f | 2 +-
pfdat.f => src/Fortran/pfdat.f | 2 +-
pfind.f => src/Fortran/pfind.f | 2 +-
pfmake.f => src/Fortran/pfmake.f | 11 +-
pfscale.f => src/Fortran/pfscale.f | 4 +-
pfscan.f => src/Fortran/pfscan.f | 4 +-
pfsearch.f.cpy => src/Fortran/pfsearch.f | 2 +-
src/Fortran/pfsearchV2.f | 550 +++
pfw.f => src/Fortran/pfw.f | 4 +-
pmali.f => src/Fortran/pmali.f | 2 +-
prali.f => src/Fortran/prali.f | 2 +-
prsp.f => src/Fortran/prsp.f | 2 +-
prxp.f => src/Fortran/prxp.f | 2 +-
psa2msa.f => src/Fortran/psa2msa.f | 4 +-
psdat.f => src/Fortran/psdat.f | 2 +-
ptof.f => src/Fortran/ptof.f | 4 +-
ptoh.f => src/Fortran/ptoh.f | 4 +-
pxdat.f => src/Fortran/pxdat.f | 2 +-
recmd.f => src/Fortran/recmd.f | 2 +-
regpr.f => src/Fortran/regpr.f | 2 +-
remsa.f => src/Fortran/remsa.f | 2 +-
remsf.f => src/Fortran/remsf.f | 2 +-
reprf.f => src/Fortran/reprf.f | 2 +-
reseq.f => src/Fortran/reseq.f | 2 +-
rfseq.f => src/Fortran/rfseq.f | 4 +-
rhmmer.f => src/Fortran/rhmmer.f | 2 +-
rhmmer2.f => src/Fortran/rhmmer2.f | 2 +-
rhnul.f => src/Fortran/rhnul.f | 2 +-
schmm.f => src/Fortran/schmm.f | 2 +-
sterr.f => src/Fortran/sterr.f | 2 +-
wprsm.f => src/Fortran/wprsm.f | 2 +-
wrhmr.f => src/Fortran/wrhmr.f | 2 +-
wrprf.f => src/Fortran/wrprf.f | 2 +-
wrsam.f => src/Fortran/wrsam.f | 2 +-
xali1.f => src/Fortran/xali1.f | 2 +-
xalip.f => src/Fortran/xalip.f | 2 +-
xalit.f => src/Fortran/xalit.f | 2 +-
xprsm.f => src/Fortran/xprsm.f | 16 +-
xpsa.5 | 370 --
175 files changed, 39368 insertions(+), 6428 deletions(-)
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