X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=e5a17330f4c3061a92426a0a6583da5c4f6ee32e;hb=e1a435a213f105bac3ea0258c6fe26f11df2a392;hp=762b08e47885f801fa5f8429de93cd7914bdcfb5;hpb=9811278f9e18ee6cb88470dbae98da046734a0af;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 762b08e..e5a1733 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -135,15 +135,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * prepare the view for a given set of models/chains. chainList contains
    * strings of the form 'pdbfilename:Chaincode'
-   * 
-   * @param chainList
-   *          list of chains to make visible
    */
-  public void centerViewer(Vector<String> chainList)
+  public void centerViewer()
   {
     StringBuilder cmd = new StringBuilder(128);
     int mlength, p;
-    for (String lbl : chainList)
+    for (String lbl : chainsToShow)
     {
       mlength = 0;
       do
@@ -159,7 +156,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       cmd.setLength(cmd.length() - 4);
     }
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
+    String command = "select *;restrict " + cmd + ";cartoon;center " + cmd;
+    evalStateCommand(command);
   }
 
   public void closeViewer()
@@ -1419,8 +1417,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public void showStructures(AlignViewportI av)
+  public void showStructures(AlignViewportI av, boolean refocus)
   {
     // TODO show Jmol structure optionally restricted to visible alignment
+    // and/or selected chains
   }
 }