+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.io.NewickFile;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+