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
Get rid of a few debugging println calls
Merge pull request #30 from ulyssecarion/non-verbose

Get rid of a few debugging println calls
Merge pull request #29 from ulyssecarion/master

Add an isWater method for Groups
catching NPE
Merge branch 'master' of github.com:biojava/biojava
making sure cache can't be null
adding cleaner logging and new option to disable domain based alignments
Added another CP factory method.
Merge branch 'master' of https://github.com/biojava/biojava
Added support for SCOP com files. ScopDatabase now has a getComments()
method.
Created tests for ScopInstallation and BerkeleyScopInstallation.
Return an empty list when sunId is not listed, rather than null.
Added Log4J to POM.