import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.IProgressIndicator;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
-import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
-import com.sun.xml.internal.ws.client.ClientTransportException;
-
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Score;