adding a warning message
don't look at calculation time when comparing AFPChain objects.
Merge pull request #17 from andreasprlic/master

adding a warning message
Merge pull request #18 from andreasprlic/master

fixing issue #12
Merge pull request #19 from andreasprlic/master

 this is now a multiton and supports several different versions of scop
Merge branch 'master' of github.com:biojava/biojava