new flag to update remediated files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10095 7c6358e6-4a41-0410-a743-a5b2a554c398
new flag to update remediated files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10096 7c6358e6-4a41-0410-a743-a5b2a554c398
updated toString method

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10097 7c6358e6-4a41-0410-a743-a5b2a554c398
Reverting debugging statements introduced in r10020

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10098 7c6358e6-4a41-0410-a743-a5b2a554c398
fixing broken print functionality

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10099 7c6358e6-4a41-0410-a743-a5b2a554c398
Minor bug fixes in AlignmentTools (rmsd calculation) 

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10100 7c6358e6-4a41-0410-a743-a5b2a554c398
now threads sleep longer

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10101 7c6358e6-4a41-0410-a743-a5b2a554c398
propagaingt server config to the remote domain lookup services

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10102 7c6358e6-4a41-0410-a743-a5b2a554c398
making sure this ends with the correct URL

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10103 7c6358e6-4a41-0410-a743-a5b2a554c398
making atomcache more extensible.  Now can be extended by DB-based implementation, rather than file system based.

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10104 7c6358e6-4a41-0410-a743-a5b2a554c398