Major code refactoring for better integration of new concepts
Large anonymous classes refactored into method calls
Changed fundamental interfaces and further cleaned up the MainWindow class
Updated visualization of local comparison results
Updated window with local comparison plot
Merge branch 'feature-local-as-matrix' into develop
Updated JNLP entry with a new JAR dependency
Cleaned torsion angles selection dialog
Code refactoring
Automatic code clean-up and sorting of methods
Added export capability for sequence alignment
Export capability for structure alignment
Export capability for global comparison
Export capability for local comparison results
Automatic clean up and sort of members
Merge branch 'feature-exportables' into develop
Merge branch 'develop' of github.com:tzok/mcq4structures into develop

Conflicts:
	src/pl/poznan/put/cs/bioserver/gui/MainWindow.java