import java.awt.Graphics;
import java.awt.Graphics2D;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
import java.awt.Graphics;
import java.awt.Graphics2D;
// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+ ap.alignFrame);