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refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Removed the executable property
Reorganised the project with a src folder for java source files. Added a jars dir with all jars needed for the project. Added .project and .classpath pointing to relative path of jars. The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
Copied the aglappe-jung branch into trunk.
Re-branching for JUNG2 development
MySQLConnection now throwing SQLException on connect Many files changed following this: all calling classes now re-throwing or catching the SQLException
Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)
moved executables (classes with main function) to root directory
Added package tools.
Initial commit of the ClusterConnection class + small test class to test it out.
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