[med-svn] [fsa] 08/10: Merge tag 'upstream/1.15.9+dfsg'
Andreas Tille
tille at debian.org
Mon Dec 21 18:43:35 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fsa.
commit b17c6712d743dcd15e1c4a18b800229dacfeb5e6
Merge: 041894a 5dd84fe
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 21 19:41:15 2015 +0100
Merge tag 'upstream/1.15.9+dfsg'
Upstream version 1.15.9+dfsg
COPYING | 674 ++
LICENSE | 18 +
MW/COPYING | 0
MW/INSTALL | 55 +
MW/Makefile.in | 119 +
MW/README | 15 +
MW/acinclude.m4 | 21 +
MW/aclocal.m4 | 15 +
MW/configure | 5669 ++++++++++++
MW/configure.in | 268 +
MW/doxygen.conf | 1117 +++
MW/install-sh | 251 +
MW/missing | 0
MW/mkinstalldirs | 40 +
MW/src/BlackBox/MWDriver_blackbox.C | 92 +
MW/src/BlackBox/MWDriver_blackbox.h | 77 +
MW/src/BlackBox/MWTask_blackbox.C | 247 +
MW/src/BlackBox/MWTask_blackbox.h | 95 +
MW/src/BlackBox/MWWorkerMain_blackbox.C | 57 +
MW/src/BlackBox/MWWorker_blackbox.C | 138 +
MW/src/BlackBox/MWWorker_blackbox.h | 49 +
MW/src/BlackBox/Makefile.in | 181 +
MW/src/MW.C | 24 +
MW/src/MW.h | 136 +
MW/src/MWControlTasks/MWNWSTask.C | 229 +
MW/src/MWControlTasks/MWNWSTask.h | 110 +
MW/src/MWControlTasks/Makefile.in | 133 +
MW/src/MWDriver.C | 4517 ++++++++++
MW/src/MWDriver.h | 1274 +++
MW/src/MWGroup.C | 99 +
MW/src/MWGroup.h | 49 +
MW/src/MWList.C | 873 ++
MW/src/MWList.h | 1088 +++
MW/src/MWMasterMain.C | 43 +
MW/src/MWStats.C | 539 ++
MW/src/MWStats.h | 153 +
MW/src/MWSystem.h | 15 +
MW/src/MWTask.C | 129 +
MW/src/MWTask.h | 191 +
MW/src/MWTaskContainer.C | 157 +
MW/src/MWTaskContainer.h | 112 +
MW/src/MWUnixSystem.C | 52 +
MW/src/MWWinSystem.C | 47 +
MW/src/MWWorker.C | 541 ++
MW/src/MWWorker.h | 190 +
MW/src/MWWorkerID.C | 659 ++
MW/src/MWWorkerID.h | 395 +
MW/src/MWWorkerMain.C | 42 +
MW/src/MWprintf.C | 106 +
MW/src/MWprintf.h | 82 +
MW/src/Makefile.in | 171 +
MW/src/RMComm/MW-CondorPVM/MWCondorPvmRC.C | 1290 +++
MW/src/RMComm/MW-CondorPVM/MWCondorPvmRC.h | 287 +
MW/src/RMComm/MW-CondorPVM/Makefile.in | 140 +
MW/src/RMComm/MW-File/MWFileError.h | 35 +
MW/src/RMComm/MW-File/MWFileRC.C | 2992 +++++++
MW/src/RMComm/MW-File/MWFileRC.h | 397 +
MW/src/RMComm/MW-File/MWFileRCSymbol.h | 37 +
MW/src/RMComm/MW-File/MWFileSend.h | 58 +
MW/src/RMComm/MW-File/MWFileTypes.h | 42 +
MW/src/RMComm/MW-File/MWFileWorker.h | 68 +
MW/src/RMComm/MW-File/Makefile.in | 143 +
MW/src/RMComm/MW-File/chirp_client.c | 623 ++
MW/src/RMComm/MW-File/chirp_client.h | 202 +
MW/src/RMComm/MW-File/chirp_protocol.h | 50 +
MW/src/RMComm/MW-Independent/MWIndRC.C | 500 ++
MW/src/RMComm/MW-Independent/MWIndRC.h | 230 +
MW/src/RMComm/MW-Independent/Makefile.in | 122 +
MW/src/RMComm/MW-Socket/MWSocketRC.C | 2114 +++++
MW/src/RMComm/MW-Socket/MWSocketRC.h | 434 +
MW/src/RMComm/MW-Socket/Makefile.in | 139 +
MW/src/RMComm/MW-StaticMPI/MWStaticMPIRC.C | 754 ++
MW/src/RMComm/MW-StaticMPI/MWStaticMPIRC.h | 371 +
MW/src/RMComm/MW-StaticMPI/Makefile.in | 120 +
MW/src/RMComm/MWRMComm.C | 457 +
MW/src/RMComm/MWRMComm.h | 493 ++
MW/src/RMComm/Makefile.in | 155 +
Makefile.am | 91 +
Makefile.in | 872 ++
README | 357 +
acinclude.m4 | 114 +
aclocal.m4 | 1210 +++
build-aux/ar-lib | 270 +
build-aux/compile | 347 +
build-aux/config.guess | 1501 ++++
build-aux/config.sub | 1705 ++++
build-aux/depcomp | 630 ++
build-aux/install-sh | 520 ++
build-aux/missing | 376 +
build-aux/test-driver | 127 +
config.h.in | 167 +
configure | 8958 +++++++++++++++++++
configure.ac | 303 +
debian/changelog | 10 -
debian/compat | 1 -
debian/control | 50 -
debian/copyright | 53 -
debian/docs | 3 -
debian/examples | 1 -
debian/patches/no-display.patch | 17 -
debian/patches/removed-pdf-only-docs.patch | 22 -
debian/patches/series | 2 -
debian/rules | 50 -
debian/source/format | 1 -
debian/upstream/metadata | 12 -
debian/watch | 2 -
display/Makefile.am | 78 +
display/Makefile.in | 503 ++
display/classnoinst.stamp | 1 +
display/mad/AlignDAG.java | 641 ++
display/mad/Alignment.java | 328 +
display/mad/AlignmentPanel.java | 337 +
display/mad/Alignments.java | 364 +
display/mad/BatchDocument.java | 87 +
display/mad/JpegImagesToMovie.java | 530 ++
display/mad/MAD.java | 67 +
display/mad/MadApplet.java | 37 +
display/mad/MadPanel.java | 792 ++
display/mad/Node.java | 618 ++
display/mad/ProbabilityMatrices.java | 169 +
display/mad/PropertyChangeHandler.java | 37 +
display/mad/PropertyChangeIDs.java | 11 +
display/mad/SaveAsFastaAction.java | 59 +
display/mad/SaveAsMovAction.java | 31 +
display/mad/SaveAsTiffAction.java | 53 +
display/mad/SparseMatrix.java | 257 +
display/mad/legend.jpg | Bin 0 -> 2289 bytes
display/mad/manifest.mf | 4 +
display/mad/manifest.mf.in | 4 +
examples/Makefile.am | 23 +
examples/Makefile.in | 431 +
examples/README | 36 +
examples/RV12.BBS12030.fasta | 36 +
examples/RV12.BBS12030.fasta.gui | 2599 ++++++
examples/RV12.BBS12030.fasta.probs | 12627 +++++++++++++++++++++++++++
examples/RV12.BBS12030.mfa | 13 +
examples/RV12.BBS12030.reference.mfa | 36 +
examples/RV12.BBS12030.reference.stock | 8 +
examples/RV12.BBS12030.stock | 10 +
examples/U5.aln1.fasta | 20 +
examples/U5.aln1.fasta.gui | 1048 +++
examples/U5.aln1.fasta.probs | 5984 +++++++++++++
examples/U5.aln1.mfa | 11 +
examples/U5.aln1.reference.mfa | 20 +
examples/U5.aln1.reference.stock | 13 +
examples/U5.aln1.stock | 9 +
examples/tRNA.aln1.fasta | 15 +
examples/tRNA.aln1.fasta.gui | 636 ++
examples/tRNA.aln1.fasta.probs | 3731 ++++++++
examples/tRNA.aln1.mfa | 11 +
examples/tRNA.aln1.reference.mfa | 15 +
examples/tRNA.aln1.reference.stock | 13 +
examples/tRNA.aln1.stock | 9 +
html/FAQ.html | 532 ++
html/Makefile.am | 3 +
html/Makefile.in | 411 +
html/pretty.css | 12 +
perl/FSA/Model.pm | 493 ++
perl/FSA/SparseMatrices.pm | 490 ++
perl/GFF.pm | 271 +
perl/GFF/Database.pm | 201 +
perl/Makefile.am | 14 +
perl/Makefile.in | 422 +
perl/Stockholm.pm | 1788 ++++
perl/Stockholm/Database.pm | 284 +
perl/accuracy.pl | 97 +
perl/cmpalign.pl | 277 +
perl/dartlog.pl | 168 +
perl/fasta2stockholm.pl | 59 +
perl/prettify.pl | 36 +
perl/seqdotplot.pl | 173 +
perl/stockholm2fasta.pl | 63 +
src/annealing/Makefile.am | 35 +
src/annealing/Makefile.in | 569 ++
src/annealing/SparseMatrix.h | 530 ++
src/annealing/alignment_DAG.cc | 1666 ++++
src/annealing/alignment_DAG.h | 742 ++
src/annealing/dotplot.cc | 53 +
src/annealing/dotplot.h | 62 +
src/annealing/tree_weights.cc | 100 +
src/annealing/tree_weights.h | 96 +
src/fsa/Makefile.am | 37 +
src/fsa/Makefile.in | 583 ++
src/fsa/algebras.cc | 52 +
src/fsa/algebras.h | 554 ++
src/fsa/aminoacid_indel2dp.cc | 2445 ++++++
src/fsa/aminoacid_indel2dp.h | 315 +
src/fsa/aminoaciddp.cc | 2205 +++++
src/fsa/aminoaciddp.h | 315 +
src/fsa/anchors.cc | 1536 ++++
src/fsa/anchors.h | 818 ++
src/fsa/constraints.cc | 101 +
src/fsa/constraints.h | 195 +
src/fsa/dptables.h | 438 +
src/fsa/fsa.cc | 1887 ++++
src/fsa/fsa.h | 406 +
src/fsa/model.cc | 392 +
src/fsa/model.h | 915 ++
src/fsa/mybanding.h | 111 +
src/fsa/nucleotide_indel2dp.cc | 2253 +++++
src/fsa/nucleotide_indel2dp.h | 315 +
src/fsa/nucleotidedp.cc | 2013 +++++
src/fsa/nucleotidedp.h | 315 +
src/fsa/sequence_pair_selector.cc | 360 +
src/fsa/sequence_pair_selector.h | 122 +
src/main/Makefile.am | 55 +
src/main/Makefile.in | 806 ++
src/main/gapcleaner.cc | 116 +
src/main/isect_mercator_alignment_gff.cc | 244 +
src/main/main.cc | 59 +
src/main/map_coords.cc | 205 +
src/main/map_gff_coords.cc | 204 +
src/main/percentid.cc | 108 +
src/main/prot2codon.cc | 133 +
src/main/slice_fasta.cc | 170 +
src/main/slice_fasta_gff.cc | 173 +
src/main/slice_mercator_alignment.cc | 227 +
src/main/translate.cc | 107 +
src/manager/Makefile.am | 49 +
src/manager/Makefile.in | 585 ++
src/manager/db_adapter.cc | 263 +
src/manager/db_adapter.h | 108 +
src/manager/db_misc.cc | 36 +
src/manager/db_misc.h | 162 +
src/manager/db_postgres.cc | 1011 +++
src/manager/db_postgres.h | 301 +
src/manager/manager.cc | 772 ++
src/manager/manager.h | 217 +
src/manager/mw_adapter.cc | 31 +
src/manager/mw_adapter.h | 54 +
src/manager/mw_master.cc | 530 ++
src/manager/mw_master.h | 93 +
src/manager/mw_task.cc | 62 +
src/manager/mw_task.h | 63 +
src/manager/mw_worker.cc | 232 +
src/manager/mw_worker.h | 63 +
src/manager/transfer_data.cc | 634 ++
src/math/Makefile.am | 10 +
src/math/Makefile.in | 549 ++
src/math/mathematics.cc | 36 +
src/math/mathematics.h | 195 +
src/math/mst.cc | 101 +
src/math/mst.h | 166 +
src/seq/Makefile.am | 22 +
src/seq/Makefile.in | 567 ++
src/seq/alignment.cc | 1154 +++
src/seq/alignment.h | 729 ++
src/seq/alphabet.cc | 193 +
src/seq/alphabet.h | 320 +
src/seq/gff.cc | 364 +
src/seq/gff.h | 531 ++
src/seq/interval.h | 130 +
src/seq/mercator.cc | 856 ++
src/seq/mercator.h | 465 +
src/seq/sequence.cc | 587 ++
src/seq/sequence.h | 506 ++
src/seq/similarity_matrix.cc | 204 +
src/seq/similarity_matrix.h | 198 +
src/util/Makefile.am | 24 +
src/util/Makefile.in | 570 ++
src/util/array2d.h | 421 +
src/util/dexception.cc | 120 +
src/util/dexception.h | 58 +
src/util/hash_fcn.h | 200 +
src/util/logfile.cc | 337 +
src/util/logfile.h | 277 +
src/util/logtags.h | 13 +
src/util/macros.h | 84 +
src/util/memcheck.cc | 51 +
src/util/memcheck.h | 17 +
src/util/misc.cc | 90 +
src/util/misc.h | 390 +
src/util/opts_list.cc | 433 +
src/util/opts_list.h | 160 +
src/util/regexp.cc | 1758 ++++
src/util/regexp.h | 49 +
src/util/sstring.cc | 159 +
src/util/sstring.h | 131 +
tests/Makefile.am | 3 +
tests/Makefile.in | 1198 +++
version.m4 | 1 +
281 files changed, 134147 insertions(+), 224 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fsa.git
More information about the debian-med-commit
mailing list