Merge pull request #9 from biojava/master

Merge pull request #80 from emckee2006/master
Merge pull request #10 from biojava/master

Catch back up with biojava/master
Merge pull request #11 from biojava/master

Catch back up with biojava/master
Merge pull request #12 from biojava/master

Catch back up with biojava/master
Merge pull request #13 from biojava/master

Catch back up with biojava/master
Merge pull request #14 from biojava/master

Catch back up with biojava/master
Correct SuppressWarning from unchecked to rawtypes so that latest Java 7
will allow it to compile.
Merge pull request #89 from emckee2006/master

Correction to Warning Suppression
Merge pull request #15 from biojava/master

Merge pull request #89 from emckee2006/master
Remove warnings
Merge pull request #90 from emckee2006/master

Remove a few warnings in core