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.
Modifying CE-CP to duplicate the shorter structure.

This reduces the chance for a large insertion at the duplication
boundary, which could incur a gap penalty large enough to block CP
detection.
Fixing compile problem.

Can be reverted  after merging into BioJava 4.0.0 branch,
where the exception has been removed.
Fixing superposition bug in CeCPMain.invertAlignment
Adding CECPParameters class

Stores parameters for CeCPMain:
- __DuplicationHint__ controls which protein gets duplicated
- __minCPLength__ controls minimum block length

Tests run with DUPLICATE_RIGHT to simulate existing behavior,
but the default is DUPLICATE_SHORTER for performance and
(hopefully) quality.
Adding Enums to ParameterGUI
Added nice names to DuplicationHints

The toString method is displayed now, while the name() method
identifies the enum internally.