BioJava

Cleanup in 3D alignment display, fixed issues with CE-CP and fatcat flexible

hope this fixes a too many open FTP connections issue

new test for the webstart client

Fixing a display issue with CP results

better way to set algorithm name

resources now in structure core, since this is where they are needed

slwoing down server communication if no results returned

update to new ftp location

Merge with Scooter's check-in and hopefully gives us the beginning point to move forward with this code. We now have the beginnings of Edits along with a nieve implementation which allows us to join sequences together. This code is still alpha and known to be buggy but it needs to go in. We also support ambigious translations.

Moved FastaReaderHelper and FastaWriterHelper into the sequence io package which means some test cases needed to change