Merge pull request #18 from biojava/master

Catch back up with biojava/master
Put date formatting/parsing into critical sections.
Fixed String vs Character comparisons.
Merge pull request #116 from Elinow/master

Put date formatting/parsing into critical sections.
Be more flexible with parsing short HEADER records.

This allows parsing of pre-submission PDB files which don't
contain a proper HEADER with PDB ID and deposition date
Fix parsing of SCOP 1.71 (#115)

- Accept some poorly-formatted comment definitions
- Use the first chain found for '_' domains (#115)
- Add tests for 1.71
Fixed bug in latest HEADER parsing change

Does 5928eff8 correctly.
Merge pull request #118 from sbliven/master

Minor fixes for parsing old or non-standard files
Fixed bug: empty strings or very short SG strings should return null
Merge pull request #19 from biojava/master

Catch back up with biojava/master
Fix integration tests (#128), which I broke in 3c7315eb

- We now allow '_' as a synonym for chain 'A' (needed in old files), so
  the test specifically disallowing this was failing.
- I changed it to check for an actual missing chain
- BerkeleyScop has slightly different comments than MRC scop, and the
  test cases are inflexible.
Trim spaces off structure names.
Bug #117: Adding support for ~ in AtomClass
fixing typo in javadoc
fixing typo in javadoc
less verbose test
allows to reproduce #109
fix for #109
cleaning up docu #110
adding IntelliJ config to gitignore