reload, just close this frame and open a new one

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f4a213f..26d44b1 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -90,7 +90,7 @@ public class PDBfile extends jalview.io.AlignFile {
             }
             else
             {
-              tmpchain = new PDBChain(tmpatom.chain);
+              tmpchain = new PDBChain(id,tmpatom.chain);
               chains.addElement(tmpchain);
               tmpchain.atoms.addElement(tmpatom);
             }
@@ -107,23 +107,15 @@ public class PDBfile extends jalview.io.AlignFile {
         }
         for (int i = 0; i < chains.size(); i++)
         {
-          SequenceI seq = ( (PDBChain) chains.elementAt(i)).
+          SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
               sequence;
-          seq.setName(id + "|" + seq.getName());
-          Sequence dataset = new Sequence(seq.
-                                          getName(),
-                                          seq.getSequence().toString(),
-                                          seq.getStart(), seq.getEnd());
-          dataset.setSequenceFeatures(seq.getSequenceFeatures());
+          dataset.setName(id + "|" + dataset.getName());
           PDBEntry entry = new PDBEntry();
           entry.setId(id);
           if (inFile != null)
             entry.setFile(inFile.getAbsolutePath());
-
-          seq.setDatasetSequence(dataset);
           dataset.addPDBId(entry);
-
-          getSeqs().addElement(seq);
+          getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
         }
       }catch(OutOfMemoryError er)
       {