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.
Fixed String vs Character comparisons.
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
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.
Merge branch 'dev-3.1.0' after cherry-picking

All commits should be already included, so this should be an empty commit.
Bumping version to 4.0.0

This reflects the removal of deprecated code from this
branch.
working on releasing our code to Maven Central via OSS Sonatype
Merge branch 'master' of github.com:biojava/biojava

Conflicts:
	pom.xml