Added methods for cyclic permutations.
Fixed negative permutations.
Committing unfinished changes for working with CP FASTAs.
Merge branch 'master' of https://github.com/biojava/biojava
Fixed a couple issues: 1. Can't use
ProteinSequence.getSequenceAsString() to set aligned and unaligned
userCollection. 2. In CP code, don't use cloneCAArray because it doesn't
set the parent Structure.
Fixed a bug in CP code caused by a misused variable. There's still
another bug somewhere.
cpFastaToAfpChain needs to use ungapped CP shift, not gapped.
Add additional methods to AlignmentTools

Improve methods for creating and modifying AFPChains with
new alignments.

Some additional testing required.
Merge branch 'master' of https://github.com/sbliven/biojava-sbliven
Merge branch 'replaceOptAln' of https://github.com/sbliven/biojava-sbliven
Fixed a couple bugs and disabled call to Spencer's new method in
createAfpChain.
Switched back to global alignment.
Fixed multiple bugs, including superposition bug.
Fixed tests, though they're not (even close to) finished.
Wrote a simple test for AlignmentTools.updateSuperposition.
Fixed AlignmentTools.updateSuperposition. The previous code was
incorrectly using the square root of the RMSD, and was also getting 0
for the RMSD in some cases.
Simplified FastaAFPChainConverter using new
AlignmentTools.updateSuperposition.
There's no longer any need to use AFPChainScorer.
Simplified further and set AFPChain block values.
Fixed original test case.