BioJava

[maven-release-plugin] prepare for next development iteration

[maven-release-plugin] prepare release biojava-3.0-alpha3

WindowedSequence has now gone to a view system. We've also had to alter some base classes since they were delegating onto the backing sequence far too much which meant views were redundant/broken. All tests have been rerun & pass on my box. Translation may now be faster!

code cleanup, removing warnings

some small cleanup for nicer web site display

multiple improvements to visualize protmods on RCSB PDB website

this actually compiles with Java 1.5

updating dependencies

updating dependencies

updating dependencies