JAL-3390 pull-up refactoring towards functional changes...

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index f822358..69f4c6b 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -41,13 +41,20 @@ public class AppJmolBinding extends JalviewJmolBinding
   private AppJmol appJmolWindow;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
     super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
   @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return appJmolWindow.progressBar;
+  }
+
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -102,21 +109,6 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    // ignore events from panels not used to colour this view
-    if (!appJmolWindow.isUsedforcolourby(ap))
-    {
-      return;
-    }
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap);
-    }
-  }
-
-  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
@@ -198,8 +190,9 @@ public class AppJmolBinding extends JalviewJmolBinding
   public jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null)
+            ? appJmolWindow.getAlignmentPanel()
+            : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
       return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;