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
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.
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
 adding new constructor
Improve error messages in AlignmentGui

Show an error if the selected output directory is unwritable.
Use message dialogs for errors rather than stdout.
Put date formatting/parsing into critical sections.