X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=89228d51cdf51e6a024792ec4c373ba5462df984;hb=ce7259404dbb5bbeeb296d32b6a2543b30a7c924;hp=5ffbaa4c4381c25a53a3898a5003b75e9973593b;hpb=c3b8fbc19c04c2daec702a2bffdfab5d10555143;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 5ffbaa4..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;
@@ -48,9 +50,8 @@ public class ExtJmol extends JalviewJmolBinding
 
   private AlignmentPanel ap;
 
-  protected ExtJmol(jalview.appletgui.AlignFrame alframe,
-          PDBEntry[] pdbentry, SequenceI[][] seq,
-          String protocol)
+  protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+          SequenceI[][] seq, DataSourceType protocol)
   {
     super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
             protocol);
@@ -65,6 +66,13 @@ public class ExtJmol extends JalviewJmolBinding
   }
 
   @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    // no progress indicators on applet (could access javascript for this)
+    return null;
+  }
+
+  @Override
   public void updateColours(Object source)
   {
 
@@ -81,10 +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
     {
@@ -92,6 +100,7 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+
   @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
@@ -137,8 +146,8 @@ 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++)
     {
@@ -172,8 +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);
   }