X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=cadbc77ffcddf40f694e498eb76f31f6c4e5a82c;hb=a79f9e113c51c032070c670e45ce3eb464691166;hp=543d6802240037f8e121a081a19c059524b9ae86;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
old mode 100755
new mode 100644
index 543d680..cadbc77
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -132,7 +132,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     this.pdbentry = pdbentry;
     this.sequence = seq;
 
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = StructureSelectionManager.getStructureSelectionManager(ap.av.applet);
 
     try
     {
@@ -177,8 +177,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // the start and end points.
       // Align the sequence to the pdb
       // TODO: DNa/Pep switch
-      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
-              .elementAt(i)).sequence, ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+      AlignSeq as = new AlignSeq(sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).sequence,
+              ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+                      : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -1102,7 +1104,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   // /StructureListener
   public String[] getPdbFile()
   {
-    return new String[] { pdbentry.getFile() };
+    return new String[]
+    { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1189,4 +1192,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }