Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 1283019..75e0c5e 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,10 +21,12 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Container;
@@ -32,7 +34,6 @@ import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 public class AppJmolBinding extends JalviewJmolBinding
@@ -42,19 +43,17 @@ public class AppJmolBinding extends JalviewJmolBinding
   private FeatureRenderer fr = null;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow
+            .getAlignmentPanel() : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
@@ -71,8 +70,7 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
@@ -116,6 +114,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
@@ -124,9 +123,10 @@ public class AppJmolBinding extends JalviewJmolBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source, topap;
+    AlignmentPanel ap = (AlignmentPanel) source;
     // ignore events from panels not used to colour this view
     if (!appJmolWindow.isUsedforcolourby(ap))
     {
@@ -134,7 +134,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      colourBySequence(ap);
     }
   }
 
@@ -147,6 +147,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
@@ -154,8 +155,8 @@ public class AppJmolBinding extends JalviewJmolBinding
 
   public void newJmolPopup(String menuName)
   {
-    jmolpopup = new JmolAwtPopup();
-    jmolpopup.jpiInitialize((viewer), menuName);
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
   @Override
@@ -208,4 +209,10 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
 }