Handle Windows-style path separators.


git-svn-id: https://svn.salilab.org/imp/trunk@16398 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Update avro library name.


git-svn-id: https://svn.salilab.org/imp/trunk@16400 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix doxygen markup.


git-svn-id: https://svn.salilab.org/imp/trunk@16401 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Make sure that tested Python applications on Windows can find C++ applications
in the PATH.


git-svn-id: https://svn.salilab.org/imp/trunk@16402 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Ignore generated files.


git-svn-id: https://svn.salilab.org/imp/trunk@16403 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Use correct preprocessor macro.


git-svn-id: https://svn.salilab.org/imp/trunk@16404 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix spelling.


git-svn-id: https://svn.salilab.org/imp/trunk@16405 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Ensure that valid hierarchies are produced.


git-svn-id: https://svn.salilab.org/imp/trunk@16406 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix spelling.


git-svn-id: https://svn.salilab.org/imp/trunk@16407 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Initial addition of support for log4cxx

This provides a way of getting reasonable context information while logging when running with more than one thread. It changes our log output a lot and isn't installed everywhere, so it is not clear that we want to have it as the only log system though.

git-svn-id: https://svn.salilab.org/imp/trunk@16408 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
give thread tasks names and use them to create log contexts

git-svn-id: https://svn.salilab.org/imp/trunk@16409 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
suppress warnings

git-svn-id: https://svn.salilab.org/imp/trunk@16410 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
restore lost constructor

git-svn-id: https://svn.salilab.org/imp/trunk@16411 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make sure to name UnaryFunction in score_functor

git-svn-id: https://svn.salilab.org/imp/trunk@16412 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
write out build scripts to make them easier to debug

git-svn-id: https://svn.salilab.org/imp/trunk@16413 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
disable extern support in RMF as there seem to be link problems with gcc 4.6

git-svn-id: https://svn.salilab.org/imp/trunk@16414 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add extra braces as come compilers get confused

git-svn-id: https://svn.salilab.org/imp/trunk@16415 e91f8c7b-0e32-4433-a9ac-4502d39a4eab