Start of fix to issue #70. Updated BerkeleyScopInstallation to work with new version 2.0.x. Also advanced default version of BerkeleyScopInstallation to 2.0.3.
Continuation of fix to issue #70. Just added 2.0.x version names to ScopFactory.
Continued fix of issue #70. Corrected new version numbers: "2.03", not "2.0.3". Also, have VERSION1_75C point to "2.03", etc.
Merge branch 'master' of https://github.com/biojava/biojava
Merge branch 'master' of https://github.com/biojava/biojava
Merge branch 'master' of https://github.com/biojava/biojava
Merge branch 'master' of https://github.com/biojava/biojava
Added getFailedLines() to Astral.
Fixed a bug in ScopFactory: as per the comment, forceLocalData should be
true by default. Also made DEFAULT_VERSION public.
Fixed a serious caching bug in the recent modifications to
BerkeleyScopInstallation.
Working on issue #81. Created CathFactory, which behaves like
ScopFactory. Added setCathVersion() setter to CathInstallation. Made
related changes in AtomCache.
To make more consistent with ScopFactory, renamed getCath and setCath to
getCathDatabase and setCathDatabase, respectively.
Working on issue #81. Created StructureFactory as a utility to handle
retrieval of arbitrary structural identifiers.
Merge branch 'master' of https://github.com/biojava/biojava

Fixed conflict in Astral.
Merge branch 'master' of https://github.com/dmyersturnbull/biojava.git
Merge branch 'master' of https://github.com/biojava/biojava
Compounds not included in the scoring matrix will default to the alternative case of the compound if it exists in the scoring matrix instead of the min matrix value
Added multiple test cases for various alignment bugs including #81
Added multiple test cases for various alignment bugs including #78
Merge branch 'master' of https://github.com/d-cameron/biojava