X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=a64072e489e769c2e89137d0ce57232bb4bd2201;hb=c66902a9536b10a5477b58aaf7c2d75772890a5d;hp=7fa300e523df1bf0c0329dd9d142960edefc381a;hpb=e775f1627590b62ccad7cc5104667d347079497b;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 7fa300e..a64072e 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -20,28 +20,27 @@
  */
 package jalview.gui;
 
-import java.awt.Container;
-import java.util.BitSet;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.structure.StructureSelectionManager;
 
+import java.awt.Container;
+import java.util.BitSet;
+
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 import org.openscience.jmol.app.jmolpanel.AppConsole;
 
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
 {
-
-  /**
-   * 
-   */
   private AppJmol appJmolWindow;
 
+  private FeatureRenderer fr = null;
+
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
           String protocol)
@@ -50,10 +49,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     appJmolWindow = appJmol;
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
+  public FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
@@ -74,7 +71,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(
+  public SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -130,7 +127,9 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     AlignmentPanel ap = (AlignmentPanel) source, topap;
     // ignore events from panels not used to colour this view
     if (!appJmolWindow.isUsedforcolourby(ap))
+    {
       return;
+    }
     if (!isLoadingFromArchive())
     {
       colourBySequence(ap.av.getShowSequenceFeatures(), ap);
@@ -153,7 +152,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-
     jmolpopup = new JmolPopup();
     jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
@@ -185,9 +183,9 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
   {
-    for (int pe = 0; pe < pdbentry.length; pe++)
+    for (int pe = 0; pe < getPdbCount(); pe++)
     {
-      if (pdbentry[pe].getFile().equals(pdbFile))
+      if (getPdbEntry(pe).getFile().equals(pdbFile))
       {
         addSequence(pe, seq);
       }
@@ -205,20 +203,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected void releaseUIResources()
   {
     appJmolWindow = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
+    closeConsole();
   }
 
   @Override
@@ -227,8 +212,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     if (svl instanceof SeqPanel)
     {
       appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
     }
-    ;
   }
 }