X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBViewer.java;h=2471f32185fd6cf1e8c192bf875a1768a360c2d5;hb=6af5ebe6f1879c7b705a42dab3bd51857e4e30b2;hp=b610122919aa3c76b88d3be5076b1efa41c7cd36;hpb=269257481bdc261d6f99cb43dac33c10c3b4e9e1;p=jalview.git

diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index b610122..2471f32 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -33,6 +33,7 @@ public class AppletPDBViewer
 
   public AppletPDBViewer(PDBEntry pdbentry,
                          SequenceI[] seq,
+                         String [] chains,
                          AlignmentPanel ap,
                          String protocol)
   {
@@ -45,13 +46,11 @@ public class AppletPDBViewer
       ex.printStackTrace();
     }
 
-    pdbcanvas = new AppletPDBCanvas(pdbentry, seq, ap, protocol);
+    pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
 
 
     add(pdbcanvas, BorderLayout.CENTER);
 
-    System.out.println(seq[0].getName()+" ASFA");
-
     StringBuffer title = new StringBuffer(seq[0].getName()
                                           + ":"
                                           + pdbcanvas.pdbentry.getFile());
@@ -89,9 +88,7 @@ public class AppletPDBViewer
     else if (evt.getSource() == seqButton)
     {
       pdbcanvas.bysequence = true;
-      pdbcanvas.colourBySequence(pdbcanvas.ap.getSequenceRenderer(),
-                                 pdbcanvas.ap.av.getShowSequenceFeatures() ?
-                                 pdbcanvas.ap.getFeatureRenderer() : null);
+      pdbcanvas.colourBySequence();
 
     }
     else if (evt.getSource() == zappo)