Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / appletgui / ExtJmol.java

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 929a871..b369318 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -26,6 +26,7 @@ import jalview.api.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 
 import java.awt.Container;
 import java.util.ArrayList;
@@ -48,12 +49,12 @@ 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 +65,7 @@ public class ExtJmol extends JalviewJmolBinding
     notifyFileLoaded(null, null, null, null, 0);
   }
 
+  @Override
   public void updateColours(Object source)
   {
 
@@ -71,6 +73,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
   public void showUrl(String arg0)
   {
     showUrl(arg0, "jmol");
@@ -79,10 +82,10 @@ 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
     {
@@ -126,6 +129,7 @@ public class ExtJmol extends JalviewJmolBinding
     // ignore
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);