Added a convenience getScop(String) method.
Added getTMScoreAlternate().
Made updateSuperposition() set block rotation matrices and shift
vectors.
Added a demo for using FastaAFPChainConverter for display.
Added an extra CP test, and fixed a test to work with change in
updateSuperposition().
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
Merge branch 'master' of https://github.com/biojava/biojava
Added another CP factory method.
Merge branch 'master' of https://github.com/biojava/biojava