[Biojava-l] couple of new structure alignment & protein domain features

[Andreas Prlic]

Hi,

I just committed a couple of new features related to protein structure
alignments and working with protein domains:

- better support for SCOP domains:
- rather than using a local SCOP installation the default is now to
fetch SCOP domain data via remote web service calls (much more memory
friendly)
- the user interface for structure alignments now has a new
auto-suggest panel that makes it easier to enter SCOP domain IDs
- structures that don't have SCOP domains assigned, can get
automatically split into domains with ProteinDomainParser (also can be
fetched from remote)
- database searches now display % sequence ID in the alignment as a new column.

Andreas