still trying to prevent null painting

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 29cc070..14e6704 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -169,9 +169,7 @@ public class AppletJmol extends Frame
           viewer.openFile(pdbentry.getFile());
     }
 
-    this.setBounds(400, 400, 400, 400);
-
-    this.setVisible(true);
+    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
   }
 
   public void loadInline(String string)
@@ -443,14 +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());
 
@@ -473,6 +472,7 @@ public class AppletJmol extends Frame
   }
 
   FeatureRenderer fr;
+  String lastCommand;
   public void colourBySequence(AlignmentPanel ap)
   {
     if(!colourBySequence)
@@ -484,7 +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)
@@ -551,7 +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)