Merge pull request #3 from biojava/master

Catch back up with biojava/master
uncommenting version 1.75B and .175C until #69 gets resolved
adding new survival module
adding new survival module
renaming submodule
Merge pull request #4 from biojava/master

Catch back up with biojava/master
Test Committ
Check in of Cox Regression code for survival analysis ported from the R survival package
Merge pull request #5 from biojava/master

Catch back up with biojava/master
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.
Fix a NullPointer in createAFPChain

Ignore errors when trying to set the structure names
Fix ScopFactory bug

The current version was being returned sometimes,
even when an older version was requested.
updating example to latest API
Merge pull request #6 from biojava/master

Catch back up with biojava/master
some cleanup
Merge pull request #73 from andreasprlic/master

some cleanup
Merge branch 'master' of https://github.com/biojava/biojava
Checking for empty SCOP files

SCOP files can occationally be empty (eg if the server was down
at time of access). Future calls will now attempt to redownload them.