X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=14e67048a86bd6cd460c0b0fabda3bbd9b8e008b;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=53115d2af6573770c398800b43e19cfe7073dce5;hpb=1d282590b622a5c8bbf8a294e76f8f12bdee50e8;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 53115d2..14e6704 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -441,14 +441,15 @@ public class AppletJmol extends Frame
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";color gold;wireframe 100");
+    eval.append(";wireframe 100");//;color gold
 
     Color col = new Color(viewer.getAtomArgb(atomIndex));
 
-    resetLastRes.append(";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];wireframe 0");
+    resetLastRes.append(";wireframe 0;"//color["
+                       // + col.getRed() + ","
+                       // + col.getGreen() + ","
+                       // + col.getBlue() + "]"
+                       );
 
     viewer.evalStringQuiet(eval.toString());
 
@@ -471,6 +472,7 @@ public class AppletJmol extends Frame
   }
 
   FeatureRenderer fr;
+  String lastCommand;
   public void colourBySequence(AlignmentPanel ap)
   {
     if(!colourBySequence)
@@ -482,7 +484,7 @@ public class AppletJmol extends Frame
     if (mapping.length < 1)
       return;
 
-    SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
 
     boolean showFeatures = false;
     if (ap.av.showSequenceFeatures)
@@ -549,7 +551,10 @@ public class AppletJmol extends Frame
       }
     }
 
-    viewer.evalStringQuiet(command.toString());
+    if (lastCommand == null || !lastCommand.equals(command.toString()))
+      viewer.evalStringQuiet(command.toString());
+
+    lastCommand = command.toString();
   }
 
   StringBuffer condenseCommand(String command, int pos)