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
adding a http user agent, so Uniprot gets better feedback who is scripting them
adding a http user agent, so Uniprot gets better feedback who is scripting them
making sure all rows have the same length
adding a new readme file for the structure modules
fixing broken link to image
fixing broken link to image
fixing broken link to image
fixing broken link to image
Adding mirrors to SCOP.

Mirrors are considered sequentially if there are download errors.