X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=d3177228ff0cf05ca2b3e7c83231718856fbdf8c;hb=2d62933ef95beb94c1ec2444bcced4a3a7ec42c0;hp=c0a1e0dc4a2279c03cfb8e55084014c1658b4f58;hpb=6cbfab156ee784944a03caaa0a7374b71325a871;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index c0a1e0d..d317722 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,9 +20,9 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
@@ -134,15 +134,12 @@ 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
@@ -158,7 +155,8 @@ 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()
@@ -511,16 +509,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   /**
    * @param files
-   * @param sr
    * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+          String[] files, AlignmentViewPanel viewPanel)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, viewPanel);
+            this, viewPanel);
   }
 
   /**
@@ -1416,4 +1413,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     showConsole(false);
   }
+
+  @Override
+  public void showStructures(AlignViewportI av, boolean refocus)
+  {
+    // TODO show Jmol structure optionally restricted to visible alignment
+    // and/or selected chains
+  }
 }