X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=b0d3f7a63b7e9aee059db35d039354f92374876a;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=3e1f1b4a0742202c1166b48348009fc365cda38d;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 3e1f1b4..b0d3f7a 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 2.9.0b1)
- * Copyright (C) 2015 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.
  * 
@@ -26,6 +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 +49,11 @@ 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,
@@ -64,13 +64,12 @@ public class ExtJmol extends JalviewJmolBinding
     notifyFileLoaded(null, null, null, null, 0);
   }
 
+  @Override
   public void updateColours(Object source)
   {
-
-    // TODO Auto-generated method stub
-
   }
 
+  @Override
   public void showUrl(String arg0)
   {
     showUrl(arg0, "jmol");
@@ -79,10 +78,10 @@ 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 +89,7 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+
   @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
@@ -126,6 +126,7 @@ public class ExtJmol extends JalviewJmolBinding
     // ignore
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
@@ -134,8 +135,8 @@ 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++)
     {
@@ -169,8 +170,8 @@ 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);
   }
 
@@ -178,7 +179,6 @@ public class ExtJmol extends JalviewJmolBinding
   protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -193,14 +193,11 @@ public class ExtJmol extends JalviewJmolBinding
   @Override
   public void releaseReferences(Object svl)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public Map<String, Object> getJSpecViewProperty(String arg0)
   {
-    // TODO Auto-generated method stub
     return null;
   }