JAL-2487 remove redundant refreshGUI to minimise threading issues

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 9a570fc..ffce90c 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -20,9 +20,7 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -174,13 +172,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       if (getSsm() != null)
       {
         getSsm().addStructureViewerListener(this);
-        // ssm.addSelectionListener(this);
-        FeatureRenderer fr = getFeatureRenderer(null);
-        if (fr != null)
-        {
-          fr.featuresAdded();
-        }
-        refreshGUI();
       }
       return true;
     } catch (Exception q)
@@ -699,17 +690,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param viewport
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, viewport);
+            getSequence(), sr, viewPanel);
   }
 
   /**
@@ -1110,15 +1099,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     // TODO refactor as required to pull up to an interface
     AlignmentI alignment = avp.getAlignment();
-    FeatureRenderer fr = getFeatureRenderer(avp);
-
-    /*
-     * fr is null if feature display is turned off
-     */
-    if (fr == null)
-    {
-      return 0;
-    }
 
     String[] files = getPdbFile();
     if (files == null)
@@ -1128,7 +1108,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     StructureMappingcommandSet commandSet = ChimeraCommands
             .getSetAttributeCommandsForFeatures(getSsm(), files,
-                    getSequence(), fr, alignment);
+                    getSequence(), avp);
     String[] commands = commandSet.commands;
     if (commands.length > 10)
     {