X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=75e0c5e3d091cf5f12a824a59545429fc147424b;hb=24680a271861e9309a2241c8884874656ac111b1;hp=3a376b89b96e74dd5657e5e827511270e36933e0;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 3a376b8..75e0c5e 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,19 +21,20 @@
 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;
-import java.util.BitSet;
+import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
+import org.jmol.java.BS;
+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)
@@ -71,12 +70,12 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     if (console != null)
@@ -85,6 +84,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     if (console != null && strStatus != null)
@@ -114,6 +114,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
@@ -122,9 +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))
     {
@@ -132,10 +134,11 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      colourBySequence(ap);
     }
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
@@ -144,39 +147,43 @@ public class AppJmolBinding extends JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
+  public void newJmolPopup(String menuName)
   {
-    jmolpopup = new JmolPopup();
-    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
-  public void selectionChanged(BitSet arg0)
+  @Override
+  public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
 
   }
 
+  @Override
   public void refreshPdbEntries()
   {
     // TODO Auto-generated method stub
 
   }
 
+  @Override
   public void showConsole(boolean b)
   {
     appJmolWindow.showConsole(b);
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
+    viewer.setJmolCallbackListener(this);
     return new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
@@ -195,4 +202,17 @@ public class AppJmolBinding extends JalviewJmolBinding
       appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
     }
   }
+
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
 }