refactoring DB search code to be independent of UI

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9998 7c6358e6-4a41-0410-a743-a5b2a554c398
new utility classes for checking and downloading PDB files

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@9999 7c6358e6-4a41-0410-a743-a5b2a554c398
now accepting new parameters searchFile and nrCPU

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10000 7c6358e6-4a41-0410-a743-a5b2a554c398
now accepting new parameters searchFile and nrCPU

git-svn-id: file:///home/svn-repositories/biojava/biojava-live/trunk@10001 7c6358e6-4a41-0410-a743-a5b2a554c398