X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=3a376b89b96e74dd5657e5e827511270e36933e0;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a64072e489e769c2e89137d0ce57232bb4bd2201;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index a64072e..3a376b8 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -53,13 +53,13 @@ public class AppJmolBinding extends JalviewJmolBinding
   public FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
             : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
-        fr = ap.cloneFeatureRenderer();
+        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
       }
       else
       {
@@ -132,7 +132,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
   }
 
@@ -173,25 +173,6 @@ public class AppJmolBinding extends JalviewJmolBinding
     appJmolWindow.showConsole(b);
   }
 
-  /**
-   * add the given sequences to the mapping scope for the given pdb file handle
-   * 
-   * @param pdbFile
-   *          - pdbFile identifier
-   * @param seq
-   *          - set of sequences it can be mapped to
-   */
-  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
-  {
-    for (int pe = 0; pe < getPdbCount(); pe++)
-    {
-      if (getPdbEntry(pe).getFile().equals(pdbFile))
-      {
-        addSequence(pe, seq);
-      }
-    }
-  }
-
   @Override
   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
           Container consolePanel, String buttonsToShow)