X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f7eba09157c592a1ed5c548a67fb7cca3c2e0b26;hb=63bb86fb2312c426063e8cd79de4685c05c4bc35;hp=c1018a325efa6ac49abfdcc061f16aff6814482a;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index c1018a3..f7eba09 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -24,6 +24,8 @@ import jalview.analysis.AlignSeq;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
@@ -94,11 +96,13 @@ public class PDBfile extends jalview.io.AlignFile
     doParse();
   }
 
+  @Override
   public String print()
   {
     return null;
   }
 
+  @Override
   public void parse() throws IOException
   {
     // TODO set the filename sensibly - try using data source name.
@@ -285,8 +289,8 @@ public class PDBfile extends jalview.io.AlignFile
    */
   protected SequenceI postProcessChain(PDBChain chain)
   {
-    SequenceI dataset = chain.sequence;
-    dataset.setName(id + "|" + dataset.getName());
+    SequenceI pdbSequence = chain.sequence;
+    pdbSequence.setName(id + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(id);
     entry.setType(PDBEntry.Type.PDB);
@@ -305,9 +309,19 @@ public class PDBfile extends jalview.io.AlignFile
       // TODO: decide if we should dump the datasource to disk
       entry.setFile(getDataName());
     }
-    dataset.addPDBId(entry);
+
+    DBRefEntry sourceDBRef = new DBRefEntry();
+    sourceDBRef.setAccessionId(id);
+    sourceDBRef.setSource(DBRefSource.PDB);
+    sourceDBRef.setStartRes(pdbSequence.getStart());
+    sourceDBRef.setEndRes(pdbSequence.getEnd());
+
     // PDBChain objects maintain reference to dataset
-    SequenceI chainseq = dataset.deriveSequence();
+    SequenceI chainseq = pdbSequence.deriveSequence();
+    chainseq.setSourceDBRef(sourceDBRef);
+    chainseq.addPDBId(entry);
+    chainseq.addDBRef(sourceDBRef);
+
     seqs.addElement(chainseq);
 
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@ -372,7 +386,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     try
     {
-      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+      Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
         final Constructor constructor = cl