import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.analysis.SeqsetUtils;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
import jalview.workers.AlignCalcWorker;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.dm.JabaWsParamSet;
getCalcId(),
new AAConSettings(true, service, this.preset,
(arguments != null) ? JabaParamStore
getCalcId(),
new AAConSettings(true, service, this.preset,
(arguments != null) ? JabaParamStore
.debug("Updating result annotation from Job " + rslt
+ " at " + service.getUri());
updateResultAnnotation(true);
.debug("Updating result annotation from Job " + rslt
+ " at " + service.getUri());
updateResultAnnotation(true);
sq.getSequenceAsString(start, end + 1))));
}
if (seq.getSequence().length() > ln)
sq.getSequenceAsString(start, end + 1))));
}
if (seq.getSequence().length() > ln)