[med-svn] [pftools] branch upstream updated (f670c22 -> 9a90cdc)
Andreas Tille
tille at debian.org
Mon Mar 27 11:54:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository pftools.
from f670c22 New upstream version 2.3.5.d
new 92d286c New upstream version 3
new 9a90cdc New upstream version 3+dfsg
The 2 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:
AUTHORS | 5 +
COPYING | 674 +++++++++++++
ChangeLog | 0
Makefile | 112 ---
Makefile.am | 3 +
NEWS | 0
README | 170 +---
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 +-
profile.txt => doc/profile.txt | 0
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 --------
pfscan.1 | 416 --------
pfsearch.f | 923 ------------------
psa.5 | 197 ----
src/C/Makefile.am | 40 +
src/C/generic/heuristic.c | 747 ++++++++++++++
src/C/generic/xali1_old.c | 410 ++++++++
src/C/generic/xalip.c | 790 +++++++++++++++
src/C/include/profile.h | 737 ++++++++++++++
src/C/include/sequence.h | 115 +++
src/C/include/system.h | 950 ++++++++++++++++++
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.am | 19 +
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 -------
152 files changed, 16624 insertions(+), 6428 deletions(-)
create mode 100644 AUTHORS
create mode 100644 COPYING
create mode 100644 ChangeLog
delete mode 100644 Makefile
create mode 100644 Makefile.am
create mode 100644 NEWS
create mode 100644 configure.ac
rename CVPBR322 => data/CVPBR322 (100%)
rename GTPA_HUMAN => data/GTPA_HUMAN (100%)
rename MYSA_HUMAN => data/MYSA_HUMAN (100%)
rename R76849.seq => data/R76849.seq (100%)
rename blosum100.cmp => data/blosum100.cmp (100%)
rename blosum30.cmp => data/blosum30.cmp (100%)
rename blosum45.cmp => data/blosum45.cmp (100%)
rename blosum50.cmp => data/blosum50.cmp (100%)
rename blosum62.cmp => data/blosum62.cmp (100%)
rename blosum65.cmp => data/blosum65.cmp (100%)
rename blosum80.cmp => data/blosum80.cmp (100%)
rename coils.prf => data/coils.prf (100%)
rename ecp.prf => data/ecp.prf (100%)
rename gonnet.cmp => data/gonnet.cmp (100%)
rename pam120.cmp => data/pam120.cmp (100%)
rename pam160.cmp => data/pam160.cmp (100%)
rename pam200.cmp => data/pam200.cmp (100%)
rename pam220.cmp => data/pam220.cmp (100%)
rename pam250.cmp => data/pam250.cmp (100%)
rename pam30.cmp => data/pam30.cmp (100%)
rename pam40.cmp => data/pam40.cmp (100%)
rename pam400.cmp => data/pam400.cmp (100%)
rename pam80.cmp => data/pam80.cmp (100%)
rename pfam_sh3.hmm => data/pfam_sh3.hmm (100%)
create mode 100644 data/pfam_sh3.prf
rename prosite13.prf => data/prosite13.prf (100%)
rename score.lis => data/score.lis (100%)
rename sh3.gpr => data/sh3.gpr (100%)
rename sh3.msf => data/sh3.msf (100%)
rename sh3.prf => data/sh3.prf (100%)
rename sh3.seq => data/sh3.seq (100%)
rename standard.random => data/standard.random (100%)
rename test.out => data/test.out (71%)
rename test.sh => data/test.sh (69%)
rename profile.txt => doc/profile.txt (100%)
delete mode 100755 install_pftools.sh
delete mode 100644 io.c
delete mode 100644 jprsm.f
delete mode 100644 man/pfsearch.1
create mode 100644 man/pfsearchV2.1
delete mode 100644 man/psa.5
delete mode 100644 man/xpsa.5
delete mode 100644 pfscan.1
delete mode 100644 pfsearch.f
delete mode 100644 psa.5
create mode 100644 src/C/Makefile.am
create mode 100644 src/C/generic/heuristic.c
create mode 100644 src/C/generic/xali1_old.c
create mode 100644 src/C/generic/xalip.c
create mode 100644 src/C/include/profile.h
create mode 100644 src/C/include/sequence.h
create mode 100644 src/C/include/system.h
create mode 100644 src/C/prg/numa_threads.h
create mode 100644 src/C/prg/pfsearch.c
create mode 100644 src/C/prg/testHeuristic.c
create mode 100644 src/C/prg/testHeuristicMatchDeletion.c
create mode 100644 src/C/prg/testXali1.c
create mode 100644 src/C/prg/testheader.c
create mode 100644 src/C/prg/threads.h
create mode 100644 src/C/sse2/heuristic_sse2.c
create mode 100644 src/C/sse2/sse2_inline_fcts.h
create mode 100644 src/C/sse2/xali1_sse2.c
create mode 100644 src/C/sse2/xalip_sse2.c
create mode 100644 src/C/sse2/xalit_sse2.c
create mode 100644 src/C/sse41/heuristic_sse41.c
create mode 100644 src/C/sse41/xali1_sse41.c
create mode 100644 src/C/sse41/xalip_sse41.c
create mode 100644 src/C/sse41/xalit_sse41.c
create mode 100644 src/C/utils/Normalization.c
create mode 100644 src/C/utils/ReadSequence.c
create mode 100644 src/C/utils/io.c
create mode 100644 src/C/utils/output.c
rename 2ft.f => src/Fortran/2ft.f (99%)
rename 6ft.f => src/Fortran/6ft.f (99%)
rename CFAve.f => src/Fortran/CFAve.f (92%)
rename CPAve.f => src/Fortran/CPAve.f (92%)
create mode 100644 src/Fortran/Makefile.am
rename NtoR.f => src/Fortran/NtoR.f (94%)
rename RtoN.f => src/Fortran/RtoN.f (94%)
rename Xblnk.f => src/Fortran/Xblnk.f (92%)
rename abini.f => src/Fortran/abini.f (96%)
rename ardim.f => src/Fortran/ardim.f (96%)
rename avdat.f => src/Fortran/avdat.f (87%)
rename codat.f => src/Fortran/codat.f (91%)
rename cvini.f => src/Fortran/cvini.f (93%)
rename dfdat.f => src/Fortran/dfdat.f (89%)
rename dfnul.f => src/Fortran/dfnul.f (95%)
rename djdat.f => src/Fortran/djdat.f (90%)
rename gsdat.f => src/Fortran/gsdat.f (91%)
rename gtop.f => src/Fortran/gtop.f (98%)
rename hmdat.f => src/Fortran/hmdat.f (87%)
rename htop.f => src/Fortran/htop.f (99%)
create mode 100644 src/Fortran/io.c
rename lblnk.f => src/Fortran/lblnk.f (90%)
rename nodat.f => src/Fortran/nodat.f (92%)
rename pfdat.f => src/Fortran/pfdat.f (97%)
rename pfind.f => src/Fortran/pfind.f (97%)
rename pfmake.f => src/Fortran/pfmake.f (99%)
rename pfscale.f => src/Fortran/pfscale.f (99%)
rename pfscan.f => src/Fortran/pfscan.f (99%)
rename pfsearch.f.cpy => src/Fortran/pfsearch.f (99%)
create mode 100644 src/Fortran/pfsearchV2.f
rename pfw.f => src/Fortran/pfw.f (99%)
rename pmali.f => src/Fortran/pmali.f (98%)
rename prali.f => src/Fortran/prali.f (98%)
rename prsp.f => src/Fortran/prsp.f (97%)
rename prxp.f => src/Fortran/prxp.f (96%)
rename psa2msa.f => src/Fortran/psa2msa.f (99%)
rename psdat.f => src/Fortran/psdat.f (91%)
rename ptof.f => src/Fortran/ptof.f (99%)
rename ptoh.f => src/Fortran/ptoh.f (99%)
rename pxdat.f => src/Fortran/pxdat.f (95%)
rename recmd.f => src/Fortran/recmd.f (92%)
rename regpr.f => src/Fortran/regpr.f (99%)
rename remsa.f => src/Fortran/remsa.f (98%)
rename remsf.f => src/Fortran/remsf.f (98%)
rename reprf.f => src/Fortran/reprf.f (99%)
rename reseq.f => src/Fortran/reseq.f (98%)
rename rfseq.f => src/Fortran/rfseq.f (96%)
rename rhmmer.f => src/Fortran/rhmmer.f (98%)
rename rhmmer2.f => src/Fortran/rhmmer2.f (99%)
rename rhnul.f => src/Fortran/rhnul.f (97%)
rename schmm.f => src/Fortran/schmm.f (99%)
rename sterr.f => src/Fortran/sterr.f (89%)
rename wprsm.f => src/Fortran/wprsm.f (99%)
rename wrhmr.f => src/Fortran/wrhmr.f (98%)
rename wrprf.f => src/Fortran/wrprf.f (99%)
rename wrsam.f => src/Fortran/wrsam.f (98%)
rename xali1.f => src/Fortran/xali1.f (99%)
rename xalip.f => src/Fortran/xalip.f (99%)
rename xalit.f => src/Fortran/xalit.f (99%)
rename xprsm.f => src/Fortran/xprsm.f (96%)
delete mode 100644 xpsa.5
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