X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=89228d51cdf51e6a024792ec4c373ba5462df984;hb=75db7abd6c89a9465861dc7604faca4893c52101;hp=cb99f87127d59695c5f01b48757261635e2211b8;hpb=c0aaf84826ff25d510846bd1099e10809c4df711;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index cb99f87..89228d5 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.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.
  * 
@@ -26,15 +26,18 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
 
 import java.awt.Container;
 import java.util.ArrayList;
-import java.util.BitSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
+import org.jmol.java.BS;
+import org.jmol.viewer.Viewer;
 
 /**
  * bind an alignment view to an external Jmol instance.
@@ -47,15 +50,14 @@ public class ExtJmol extends JalviewJmolBinding
 
   private AlignmentPanel ap;
 
-  protected ExtJmol(jalview.appletgui.AlignFrame alframe,
-          PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
-          String protocol)
+  protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+          SequenceI[][] seq, DataSourceType protocol)
   {
     super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
-            chains, protocol);
+            protocol);
   }
 
-  public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
+  public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
           SequenceI[][] seqs)
   {
     super(alignPanel.getStructureSelectionManager(), seqs, viewer);
@@ -63,6 +65,14 @@ public class ExtJmol extends JalviewJmolBinding
     notifyFileLoaded(null, null, null, null, 0);
   }
 
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    // no progress indicators on applet (could access javascript for this)
+    return null;
+  }
+
+  @Override
   public void updateColours(Object source)
   {
 
@@ -70,17 +80,19 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
   public void showUrl(String arg0)
   {
     showUrl(arg0, "jmol");
   }
 
+  @Override
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
+    AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+    if (alignPanel.av.isShowSequenceFeatures())
     {
-      return ap.getFeatureRenderer();
+      return alignPanel.getFeatureRenderer();
     }
     else
     {
@@ -88,54 +100,63 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     // ignore
   }
 
+  @Override
   public void showUrl(String url, String target)
   {
     ap.alignFrame.showURL(url, target);
   }
 
+  @Override
   public void refreshGUI()
   {
     // ignore
   }
 
-  public void selectionChanged(BitSet arg0)
+  @Override
+  public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
   }
 
+  @Override
   public void refreshPdbEntries()
   {
-    List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
-    List<String> fileids = new ArrayList<String>();
+    List<PDBEntry> pdbe = new ArrayList<>();
+    List<String> fileids = new ArrayList<>();
     SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
     for (int s = 0; s < sq.length; s++)
     {
-      Vector pdbids = sq[s].getPDBId();
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
       if (pdbids != null)
       {
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
         {
-          PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
+          PDBEntry pentry = pdbids.elementAt(pe);
           if (!fileids.contains(pentry.getId()))
           {
             pdbe.add(pentry);
@@ -160,13 +181,13 @@ public class ExtJmol extends JalviewJmolBinding
   {
     // This never gets called because we haven't overriden the associated Jmol's
     // console
-    System.err
-            .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+    System.err.println(
+            "WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
                     + show);
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
     // TODO Auto-generated method stub
@@ -188,4 +209,11 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }