*/
package jalview.gui;
+import jalview.analysis.AnnotationSorter;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
}
}
+ /**
+ * Repaint the alignment including the annotations and overview panels (if
+ * shown).
+ */
public void paintAlignment(boolean updateOverview)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment()
+ .getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
if (updateOverview)