JAL-1990 suggested revision to separate references to UI components from datamodel...

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 7df42fd..41390b1 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -152,6 +152,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     this.ap = alp;
   }
 
+  @Override
   public AlignmentPanel[] getAllAlignmentPanels()
   {
     AlignmentPanel[] t, list = new AlignmentPanel[0];
@@ -267,6 +268,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected abstract AAStructureBindingModel getBindingModel();
 
+  protected abstract IProgressIndicator getIProgressIndicator();
+
   /**
    * add a new structure (with associated sequences and chains) to this viewer,
    * retrieving it if necessary first.
@@ -291,6 +294,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         // queue.
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             while (worker != null && worker.isAlive() && _started)
@@ -411,7 +415,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * create the mappings
      */
     apanel.getStructureSelectionManager().setMapping(seq, chains,
-            pdbFilename, AppletFormatAdapter.FILE);
+            pdbFilename, AppletFormatAdapter.FILE, getIProgressIndicator());
 
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features