X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=89228d51cdf51e6a024792ec4c373ba5462df984;hb=75db7abd6c89a9465861dc7604faca4893c52101;hp=c1035bd4255f95ca0d6dd9984623c86e5c0fdece;hpb=f59ae49cdd2bb8f6721424ea6ce167e8245e7d15;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index c1035bd..89228d5 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -26,6 +26,8 @@ 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;
@@ -48,12 +50,11 @@ 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(Viewer viewer, AlignmentPanel alignPanel,
@@ -64,6 +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)
   {
 
@@ -71,6 +80,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
   public void showUrl(String arg0)
   {
     showUrl(arg0, "jmol");
@@ -79,10 +89,10 @@ public class ExtJmol extends JalviewJmolBinding
   @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
     {
@@ -90,6 +100,7 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+
   @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
@@ -126,6 +137,7 @@ public class ExtJmol extends JalviewJmolBinding
     // ignore
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
@@ -134,12 +146,12 @@ public class ExtJmol extends JalviewJmolBinding
   @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<PDBEntry> pdbids = sq[s].getPDBId();
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
       if (pdbids != null)
       {
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
@@ -169,8 +181,8 @@ 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);
   }