[cartwheel-svn] Revision 300 [All]

[Commit messages for Cartwheel.]

Revision: 300
Author:   t
Date:     Tue, 05 Feb 2008 09:02:46 -0800

Log message:
merge of trunk into stable.



Changed paths:
M    branches/stable/cartwheel-server/bin/canal.fcgi
M    branches/stable/cartwheel-server/config.rc
M    branches/stable/cartwheel-server/data-model/load-website.sql
A +  branches/stable/cartwheel-server/data-model/website/motifs.sql
M    branches/stable/cartwheel-server/lib/cartwheel/dsl.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/IUPACMotif.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/LeafFolder.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/NamedMotif.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/PWMMotif.py
A +  branches/stable/cartwheel-server/lib/cartwheel/website/RawPWMMotif.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/__init__.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/publish.py
M    branches/stable/cartwheel-server/lib/cartwheel/website/qsession.py
M    branches/stable/cartwheel-server/lib/cucumber/_utils.py
A +  branches/stable/cartwheel-server/lib/htmlfill.py
AM+  branches/stable/cartwheel-server/lib/pygr_draw/
M    branches/stable/cartwheel-server/tests/README.txt
M    branches/stable/cartwheel-server/tests/functional-tests/__init__.py
A +  branches/stable/cartwheel-server/tests/functional-tests/data/empty-file.txt
M    branches/stable/cartwheel-server/tests/functional-tests/test-batchqueue-legacy-tests/test-queue.py
M    branches/stable/cartwheel-server/tests/functional-tests/test-with-user/__init__.py
M    branches/stable/cartwheel-server/tests/functional-tests/test-with-user/test-web/__init__.py
A +  branches/stable/cartwheel-server/tests/functional-tests/test-with-user/test-web/test-folder-motifs.py
A +  branches/stable/cartwheel-server/tests/functional-tests/test-with-user/test-web/test-sequences.py
M    branches/stable/cartwheel-server/tests/functional-tests/testconfig.rc
M    branches/stable/cartwheel-server/website/canal/__init__.py
M    branches/stable/cartwheel-server/website/canal/folder/leaf.py
M    branches/stable/cartwheel-server/website/canal/folder/node.py
M    branches/stable/cartwheel-server/website/canal/login.py
AM+  branches/stable/cartwheel-server/website/canal/motif/
M    branches/stable/cartwheel-server/website/canal/pages.ptl
M    branches/stable/cartwheel-server/website/canal/sequence/__init__.py
M    branches/stable/cartwheel-server/website/canal/sequence/pages.ptl
M    branches/stable/cartwheel-server/website/canal/sequence/upload.ptl
M    branches/stable/cartwheel-server/website/canal/templates.ptl
M    branches/stable/motility/CMakeLists.txt
M    branches/stable/motility/README.txt
M    branches/stable/motility/TODO
M    branches/stable/motility/doc/Makefile
M    branches/stable/motility/doc/index.html
M    branches/stable/motility/doc/index.txt
M    branches/stable/motility/doc/python-interface.txt
A +  branches/stable/motility/doc/python-tutorial.html
A +  branches/stable/motility/doc/python-tutorial.txt
A +  branches/stable/motility/doc/run-doctests.py
M    branches/stable/motility/python/CMakeLists.txt
M    branches/stable/motility/python/_motilitymodule.cc
M    branches/stable/motility/python/motility/__init__.py
A +  branches/stable/motility/python/motility/build.py
M    branches/stable/motility/python/motility/objects.py
M    branches/stable/motility/python/motility/op_en.py
A +  branches/stable/motility/python/parallel-work-in-progress.py
M    branches/stable/motility/python/setup.py
M    branches/stable/motility/src/DnaSequence.cc
M    branches/stable/motility/src/DnaSequence.hh
M    branches/stable/motility/src/EnergyOperator.cc
M    branches/stable/motility/src/EnergyOperator.hh
M    branches/stable/motility/src/IupacMotif.cc
M    branches/stable/motility/src/IupacMotif.hh
M    branches/stable/motility/src/LiteralMotif.cc
M    branches/stable/motility/src/LiteralMotif.hh
M    branches/stable/motility/src/Motif.hh
M    branches/stable/motility/src/MotifMatch.hh
M    branches/stable/motility/src/PwmMotif.cc
M    branches/stable/motility/src/PwmMotif.hh
M    branches/stable/motility/src/_MatrixMotif.cc
M    branches/stable/motility/src/_MatrixMotif.hh
M    branches/stable/motility/src/_MatrixRow.hh
M    branches/stable/motility/src/motility.cc
M    branches/stable/motility/src/motility.hh
M    branches/stable/motility/tests/CMakeLists.txt
M    branches/stable/motility/tests/__init__.py
A +  branches/stable/motility/tests/profile-iupac.cc
A +  branches/stable/motility/tests/test-doctests.py
M    branches/stable/motility/tests/test-find-iupac.cc
M    branches/stable/motility/tests/test-find-literal.cc
M    branches/stable/motility/tests/test-find-op.cc
M    branches/stable/motility/tests/test-find-pwm.cc
M    branches/stable/motility/tests/test-python-interface.py
M    branches/stable/paircomp/python/paircomp/objects.py
M    branches/stable/paircomp/python/setup.py