Improve error messages in AlignmentGui

Show an error if the selected output directory is unwritable.
Use message dialogs for errors rather than stdout.
adding IntelliJ config to gitignore
 adding new constructor
Merge branch 'master' of github.com:biojava/biojava
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