*/
package MCview;
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.io.FileParse;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
public class PDBfile extends jalview.io.AlignFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
final Object[] args = new Object[]
{ new FileParse(getDataName(), type) };
Object jmf = constructor.newInstance(args);
- Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
"getSeqsAsArray", new Class[]
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]