X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f832fd662b129020ac8c58c1236f8eb4bf2b5ff3;hb=55cae9b50608f760cbf6ae2627e1d79d16746186;hp=4039cdd32e88b94f15b5c0e3e6d41d2fbe6b1e6f;hpb=a394f0df3650d5b1e0b76e0319b650fe8ac98e41;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4039cdd..f832fd6 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,24 +20,26 @@
  */
 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.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.AlignFile;
 import jalview.io.FileParse;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
-public class PDBfile extends jalview.io.AlignFile
+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 AlignFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
 
@@ -383,7 +385,7 @@ public class PDBfile extends jalview.io.AlignFile
                 "getSeqsAsArray", new Class[]
                 {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[]
-        { Alignment.class }).invoke(jmf, al);
+        { AlignmentI.class }).invoke(jmf, al);
         for (SequenceI sq : al.getSequences())
         {
           if (sq.getDatasetSequence() != null)
@@ -531,7 +533,7 @@ public class PDBfile extends jalview.io.AlignFile
     }
   }
 
-  public void setColours(jalview.schemes.ColourSchemeI cs)
+  public void setColours(ColourSchemeI cs)
   {
     for (int i = 0; i < chains.size(); i++)
     {