[cartwheel-svn] Revision 210 [All]

Commit messages for Cartwheel. cartwheel-svn at lists.idyll.org
Fri Mar 30 14:30:59 PDT 2007


Revision: 210
Author:   t
Date:     Fri, 30 Mar 2007 14:30:59 -0700

Log message:
updated to latest trunk, - nway.



Changed paths:
MM   branches/stable/
A +  branches/stable/.svnignore
A +  branches/stable/CMakeLists.txt
MM   branches/stable/FRII/
D    branches/stable/FRII/.cvsignore
A +  branches/stable/FRII/.svnignore
A +  branches/stable/FRII/CMakeLists.txt
D    branches/stable/FRII/Makefile
MM   branches/stable/FRII/app/
D    branches/stable/FRII/app/.cvsignore
A +  branches/stable/FRII/app/.svnignore
A +  branches/stable/FRII/app/CMakeLists.txt
M    branches/stable/FRII/app/FRII.cc
D    branches/stable/FRII/app/Makefile
A +  branches/stable/FRII/app/fltk-app-test.cc
A +  branches/stable/FRII/app/make-nway.cc
MM   branches/stable/FRII/cartwheel-interface/
D    branches/stable/FRII/cartwheel-interface/.cvsignore
A +  branches/stable/FRII/cartwheel-interface/.svnignore
M    branches/stable/FRII/cartwheel-interface/AlignedFeaturesCloseupView.hh
M    branches/stable/FRII/cartwheel-interface/AlignmentCloseupView.hh
A +  branches/stable/FRII/cartwheel-interface/CMakeLists.txt
M    branches/stable/FRII/cartwheel-interface/FeatureInfoDisplayWindow.hh
M    branches/stable/FRII/cartwheel-interface/LoadFileWindow.hh
M    branches/stable/FRII/cartwheel-interface/LoginWindow.hh
D    branches/stable/FRII/cartwheel-interface/Makefile
A +  branches/stable/FRII/cartwheel-interface/NwayView.cc
A +  branches/stable/FRII/cartwheel-interface/NwayView.hh
M    branches/stable/FRII/cartwheel-interface/PairView.cc
M    branches/stable/FRII/cartwheel-interface/ParsedSeqcompPairwiseAnalysis.cc
M    branches/stable/FRII/cartwheel-interface/ParsedSimplePairwiseAnalysis.cc
M    branches/stable/FRII/cartwheel-interface/PreferencesWindow.hh
M    branches/stable/FRII/cartwheel-interface/SearchPlug.hh
M    branches/stable/FRII/cartwheel-interface/SingleView.cc
M    branches/stable/FRII/cartwheel-interface/TripleView.cc
M    branches/stable/FRII/cartwheel-interface/load_sister.cc
MM   branches/stable/FRII/dist-files/
D    branches/stable/FRII/dist-files/.cvsignore
A +  branches/stable/FRII/dist-files/.svnignore
A +  branches/stable/FRII/dist-files/FRII.app/Contents/Frameworks/
M    branches/stable/FRII/dist-files/make-macosx.sh
D    branches/stable/FRII/doc/.cvsignore
A +  branches/stable/FRII/doc/.svnignore
MM   branches/stable/FRII/ext/
A +  branches/stable/FRII/ext/.svnignore
A +  branches/stable/FRII/ext/CMakeLists.txt
D    branches/stable/FRII/ext/Makefile
MM   branches/stable/FRII/gui/
D    branches/stable/FRII/gui/.cvsignore
A +  branches/stable/FRII/gui/.svnignore
A +  branches/stable/FRII/gui/CMakeLists.txt
D    branches/stable/FRII/gui/Makefile
M    branches/stable/FRII/gui/SeqcompMappingContainer.cc
M    branches/stable/FRII/gui/SeqcompMappingContainer.hh
A +  branches/stable/FindXercesC.cmake
M    branches/stable/README.txt
D    branches/stable/cartwheel-clients/batchqueue.java/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue.java/.svnignore
D    branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/.svnignore
D    branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/stub/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/stub/.svnignore
D    branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/xmlrpc/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue.java/edu/caltech/cartwheel/batchqueueAPI/xmlrpc/.svnignore
MM   branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/
D    branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/.svnignore
MM   branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/xmlrpc/
D    branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/xmlrpc/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/xmlrpc/.svnignore
M    branches/stable/cartwheel-clients/batchqueue/batchqueueAPI/xmlrpc/__init__.py
MM   branches/stable/cartwheel-clients/batchqueue/test/
D    branches/stable/cartwheel-clients/batchqueue/test/.cvsignore
A +  branches/stable/cartwheel-clients/batchqueue/test/.svnignore
M    branches/stable/cartwheel-clients/batchqueue/test/testAPI.py
MM   branches/stable/cartwheel-clients/canal.c++/
A +  branches/stable/cartwheel-clients/canal.c++/.svnignore
M    branches/stable/cartwheel-clients/canal.c++/BUILD.txt
A +  branches/stable/cartwheel-clients/canal.c++/CMakeLists.txt
A +  branches/stable/cartwheel-clients/canal.c++/Doxyfile
MM   branches/stable/cartwheel-clients/canal.c++/src/
D    branches/stable/cartwheel-clients/canal.c++/src/.cvsignore
A +  branches/stable/cartwheel-clients/canal.c++/src/.svnignore
A +  branches/stable/cartwheel-clients/canal.c++/src/CMakeLists.txt
D    branches/stable/cartwheel-clients/canal.c++/src/Makefile
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpc.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcClient.cpp
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcClient.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcDispatch.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcException.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcSocket.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcSource.cpp
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcSource.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcUtil.cpp
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcUtil.h
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcValue.cpp
M    branches/stable/cartwheel-clients/canal.c++/src/XmlRpcValue.h
M    branches/stable/cartwheel-clients/canal.c++/src/test-xmlrpc.cc
M    branches/stable/cartwheel-clients/canal.c++/src/xmlrpcAPI.hh
D    branches/stable/cartwheel-clients/canal.java/.cvsignore
A +  branches/stable/cartwheel-clients/canal.java/.svnignore
D    branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/.cvsignore
A +  branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/.svnignore
D    branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/stub/.cvsignore
A +  branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/stub/.svnignore
D    branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/xmlrpc/.cvsignore
A +  branches/stable/cartwheel-clients/canal.java/edu/caltech/cartwheel/canalAPI/xmlrpc/.svnignore
D    branches/stable/cartwheel-clients/canal/canalAPI/.cvsignore
A +  branches/stable/cartwheel-clients/canal/canalAPI/.svnignore
M    branches/stable/cartwheel-clients/canal/canalAPI/stub.py
M    branches/stable/cartwheel-clients/canal/canalAPI/xmlrpc.py
A +  branches/stable/cartwheel-clients/canal/canalAPI/xmlrpc_inprocess_utils.py
M    branches/stable/cartwheel-clients/canal/examples/create-pairwise-analysis.py
MM   branches/stable/cartwheel-clients/canal/test/
D    branches/stable/cartwheel-clients/canal/test/.cvsignore
A +  branches/stable/cartwheel-clients/canal/test/.svnignore
M    branches/stable/cartwheel-clients/canal/test/test-pyro.py
M    branches/stable/cartwheel-clients/canal/test/test-xmlrpc.py
M    branches/stable/cartwheel-clients/canal/test/testAPI.py
M    branches/stable/cartwheel-server/TODO
A +  branches/stable/cartwheel-server/data-model/load-test.sql
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/BatchqueueRequest.py
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/BatchqueueResult.py
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/BlastzRequest.py
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/CommandLineResult.py
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/LaganRequest.py
M    branches/stable/cartwheel-server/lib/cartwheel/batchqueue/LaganVistaRequest.py
M    branches/stable/cartwheel-server/lib/cartwheel/dsl.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/Lab.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/NwayAnalysisGroup.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/NwayAnalysisSeqcompLinkage.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/NwayAnalysisSequenceLinkage.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/__init__.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/db_queue.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/publish.py
M    branches/stable/cartwheel-server/lib/cucumber/Catalog.py
M    branches/stable/cartwheel-server/lib/cucumber/DeepCatalog.py
M    branches/stable/cartwheel-server/lib/cucumber/ForwardCatalog.py
M    branches/stable/cartwheel-server/lib/cucumber/Manager.py
M    branches/stable/cartwheel-server/lib/cucumber/_utils.py
M    branches/stable/cartwheel-server/lib/programs/__init__.py
M    branches/stable/cartwheel-server/lib/test_utils.py
D    branches/stable/cartwheel-server/test/
A +  branches/stable/cartwheel-server/tests/
MM   branches/stable/cartwheel-server/tests/functional-tests/
MM   branches/stable/cartwheel-server/tests/functional-tests/0-test-empty/
MM   branches/stable/cartwheel-server/tests/functional-tests/test-batchqueue-legacy-tests/
MM   branches/stable/cartwheel-server/tests/functional-tests/test-client-api/
MM   branches/stable/cartwheel-server/tests/functional-tests/test-data-model/
MM   branches/stable/cartwheel-server/tests/functional-tests/test-with-user/
MM   branches/stable/cartwheel-server/tests/functional-tests/test-with-user/test-web/
M    branches/stable/cartwheel-server/tests/functional-tests/test-with-user/test-web/__init__.py
D    branches/stable/cartwheel-server/tests2/
M    branches/stable/cartwheel-server/website/canal/group/maps.py
AM+  branches/stable/cartwheel-server/website/canal/group/nway/
M    branches/stable/cartwheel-server/website/canal/group/pages.ptl
M    branches/stable/cartwheel-server/website/canal/group/pair/__init__.py
M    branches/stable/cartwheel-server/website/canal/group/pair/pages.ptl
M    branches/stable/cartwheel-server/website/canal/services/canal_svc/__init__.py
M    branches/stable/cartwheel-server/website/canal/services/canal_svc/api.py
D    branches/stable/ctb/developer/.cvsignore
A +  branches/stable/ctb/developer/.svnignore
D    branches/stable/ctb/overview/.cvsignore
A +  branches/stable/ctb/overview/.svnignore
MM   branches/stable/motility/
A +  branches/stable/motility/.svnignore
M    branches/stable/motility/BUILD.txt
A +  branches/stable/motility/CMakeLists.txt
D    branches/stable/motility/Makefile
D    branches/stable/motility/doc/.cvsignore
A +  branches/stable/motility/doc/.svnignore
MM   branches/stable/motility/python/
D    branches/stable/motility/python/.cvsignore
A +  branches/stable/motility/python/.svnignore
A +  branches/stable/motility/python/CMakeLists.txt
D    branches/stable/motility/python/Makefile
M    branches/stable/motility/python/_motilitymodule.cc
MM   branches/stable/motility/python/motility/
D    branches/stable/motility/python/motility/.cvsignore
A +  branches/stable/motility/python/motility/.svnignore
MM   branches/stable/motility/src/
D    branches/stable/motility/src/.cvsignore
A +  branches/stable/motility/src/.svnignore
A +  branches/stable/motility/src/CMakeLists.txt
D    branches/stable/motility/src/Makefile
M    branches/stable/motility/src/_MatrixMotif.cc
D    branches/stable/motility/swig/.cvsignore
A +  branches/stable/motility/swig/.svnignore
D    branches/stable/motility/swig/perl/.cvsignore
A +  branches/stable/motility/swig/perl/.svnignore
D    branches/stable/motility/swig/python/.cvsignore
A +  branches/stable/motility/swig/python/.svnignore
MM   branches/stable/motility/tests/
D    branches/stable/motility/tests/.cvsignore
A +  branches/stable/motility/tests/.svnignore
A +  branches/stable/motility/tests/CMakeLists.txt
D    branches/stable/motility/tests/Makefile
A +  branches/stable/motility/tests/__init__.py
D    branches/stable/motility/tests/_testdir.py
D    branches/stable/motility/tests/py-test-count.py
A +  branches/stable/motility/tests/test-count.py
M    branches/stable/motility/tests/test-find-iupac.cc
M    branches/stable/motility/tests/test-python-interface.py
A +  branches/stable/motility/tests/test-run-c++-programs.py
MM   branches/stable/paircomp/
A +  branches/stable/paircomp/.svnignore
A +  branches/stable/paircomp/CMakeLists.txt
A +  branches/stable/paircomp/Doxyfile
D    branches/stable/paircomp/Makefile
MM   branches/stable/paircomp/bin/
D    branches/stable/paircomp/bin/.cvsignore
M    branches/stable/paircomp/bin/.svnignore
A +  branches/stable/paircomp/bin/CMakeLists.txt
D    branches/stable/paircomp/bin/Makefile
D    branches/stable/paircomp/doc/.cvsignore
A +  branches/stable/paircomp/doc/.svnignore
D    branches/stable/paircomp/doc/theory/.cvsignore
A +  branches/stable/paircomp/doc/theory/.svnignore
D    branches/stable/paircomp/doc/theory/R/.cvsignore
A +  branches/stable/paircomp/doc/theory/R/.svnignore
MM   branches/stable/paircomp/lib/
A +  branches/stable/paircomp/lib/.svnignore
A +  branches/stable/paircomp/lib/CMakeLists.txt
M    branches/stable/paircomp/lib/Comparison.hh
M    branches/stable/paircomp/lib/ImmutableComparison.cc
M    branches/stable/paircomp/lib/ImmutableComparison.hh
D    branches/stable/paircomp/lib/Makefile
M    branches/stable/paircomp/lib/Makefile.deps
M    branches/stable/paircomp/lib/Match.hh
M    branches/stable/paircomp/lib/MutableComparison.cc
M    branches/stable/paircomp/lib/MutableComparison.hh
A +  branches/stable/paircomp/lib/NwayComparison.cc
A +  branches/stable/paircomp/lib/NwayComparison.hh
M    branches/stable/paircomp/lib/algorithms.cc
M    branches/stable/paircomp/lib/algorithms.hh
M    branches/stable/paircomp/lib/algorithms2.cc
M    branches/stable/paircomp/lib/algorithms2.hh
MM   branches/stable/paircomp/lib/c++-tests/
D    branches/stable/paircomp/lib/c++-tests/.cvsignore
A +  branches/stable/paircomp/lib/c++-tests/.svnignore
A +  branches/stable/paircomp/lib/c++-tests/CMakeLists.txt
D    branches/stable/paircomp/lib/c++-tests/Makefile
M    branches/stable/paircomp/lib/paircomp.hh
MM   branches/stable/paircomp/python/
D    branches/stable/paircomp/python/.cvsignore
A +  branches/stable/paircomp/python/.svnignore
A +  branches/stable/paircomp/python/CMakeLists.txt
M    branches/stable/paircomp/python/c++-ext/_paircomp_parser.cc
MM   branches/stable/paircomp/python/paircomp/
A +  branches/stable/paircomp/python/paircomp/.svnignore
M    branches/stable/paircomp/python/paircomp/__init__.py
A +  branches/stable/paircomp/python/paircomp/nway.py
M    branches/stable/paircomp/python/setup.py
A +  branches/stable/paircomp/tests/
A +  branches/stable/paircomp/tests/README.txt
A +  branches/stable/paircomp/tests/br.txt
A +  branches/stable/paircomp/tests/el.txt
A +  branches/stable/paircomp/tests/fasta.py
A +  branches/stable/paircomp/tests/orig-el-br.txt
A +  branches/stable/paircomp/tests/re.txt
A +  branches/stable/paircomp/tests/regression-data/
A +  branches/stable/paircomp/tests/regression-data/delta-lv.txt
A +  branches/stable/paircomp/tests/regression-data/delta-sp.txt
A +  branches/stable/paircomp/tests/regression-data/delta-v0.8.cmp
A +  branches/stable/paircomp/tests/regression-data/delta-v0.9.cmp
A +  branches/stable/paircomp/tests/regression-data/gcm-lv.txt
A +  branches/stable/paircomp/tests/regression-data/gcm-sp.txt
A +  branches/stable/paircomp/tests/regression-data/gcm-v0.8.cmp
A +  branches/stable/paircomp/tests/regression-data/gcm-v0.9.cmp
A +  branches/stable/paircomp/tests/regression-data/make.sh
A +  branches/stable/paircomp/tests/regression-data/otx-lv.txt
A +  branches/stable/paircomp/tests/regression-data/otx-sp.txt
A +  branches/stable/paircomp/tests/regression-data/otx-v0.8.cmp
A +  branches/stable/paircomp/tests/regression-data/otx-v0.9.cmp
A +  branches/stable/paircomp/tests/t1.fa
A +  branches/stable/paircomp/tests/t2.fa
A +  branches/stable/paircomp/tests/t3.fa
A +  branches/stable/paircomp/tests/test-1bp-matches.py
A +  branches/stable/paircomp/tests/test-compare-mussa.py
A +  branches/stable/paircomp/tests/test-errors.py
A +  branches/stable/paircomp/tests/test-memory-free.py
A +  branches/stable/paircomp/tests/test-python-interface.py
A +  branches/stable/paircomp/tests/test-regress.py
A +  branches/stable/paircomp/tests/test-transitive-2.py
A +  branches/stable/paircomp/tests/test-transitive.py
A +  branches/stable/paircomp/tests/test-very-slow-3way.py
MM   branches/stable/xml/sister.c++/
A +  branches/stable/xml/sister.c++/.svnignore
A +  branches/stable/xml/sister.c++/CMakeLists.txt
A +  branches/stable/xml/sister.c++/Doxyfile
MM   branches/stable/xml/sister.c++/src/
D    branches/stable/xml/sister.c++/src/.cvsignore
A +  branches/stable/xml/sister.c++/src/.svnignore
A +  branches/stable/xml/sister.c++/src/CMakeLists.txt
D    branches/stable/xml/sister.c++/src/Makefile
M    branches/stable/xml/sister.c++/src/iff.hh
M    branches/stable/xml/sister.c++/src/sister.cc
M    branches/stable/xml/sister.c++/src/sister.hh
D    branches/stable/xml/sister/sister/.cvsignore
A +  branches/stable/xml/sister/sister/.svnignore




More information about the cartwheel-svn mailing list