ResidueNumber.printFull() is missing an underscore after chainId.
Made ResidueRange more robust, and gave it some methods for iterating,
finding, and checking containment.
Added a method getSubstructureMatchingProteinSequence and a test case
for it. Added @Test annotations to tests in StructureSequenceMatcherTest
(why weren't they there?).
Do Smith-Waterman local alignment rather than global alignment (comment
says local, too). Also, skip null residues in
getSubstructureMatchingProteinSequence.
Adding header comment.
Committing unfinished FastaAFPChainConverter and test.
Added XMLUnit to POM.
Simplified FastaAFPChainConverter substantially, and fixed it.
Finished test for FastaAFPChainConverter.
There's no reason to require the structures have different names or even
have non-null names.
Throw an exception if a structure or sequence is null (just safer).
Set TM-score.
Added tmScore to expected AFPChain.
Removing hard-coded PDB_DIR settings.

Add them to your default VM arguments instead, a la
    -DPDB_DIR=/tmp/pdb
    -DPDB_CACHE_DIR=/tmp/pdb
Calculate and set RMSD. Do SVD rather than rely on AFPChainScorer.
Merge branch 'master' of https://github.com/biojava/biojava
Fixing broken build.
Assume lower-case letters are unaligned.
Set matrix and shift vector in AFPChain as well as AFP.
Adding flexible StructureTools.getStructure(String) method.