X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=b0d3f7a63b7e9aee059db35d039354f92374876a;hb=35f590cdfe3352c8f6a0592a1f1bf64925f21b98;hp=189fe88e446ae75c1e6b8b0f3439725675f7458f;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 189fe88..b0d3f7a 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -49,9 +49,8 @@ public class ExtJmol extends JalviewJmolBinding
 
   private AlignmentPanel ap;
 
-  protected ExtJmol(AlignFrame alframe,
-          PDBEntry[] pdbentry, SequenceI[][] seq,
-          DataSourceType protocol)
+  protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,
+          SequenceI[][] seq, DataSourceType protocol)
   {
     super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
             protocol);
@@ -68,9 +67,6 @@ public class ExtJmol extends JalviewJmolBinding
   @Override
   public void updateColours(Object source)
   {
-
-    // TODO Auto-generated method stub
-
   }
 
   @Override
@@ -82,10 +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
     {
@@ -93,6 +89,7 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+
   @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
@@ -138,8 +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++)
     {
@@ -173,8 +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);
   }
 
@@ -182,7 +179,6 @@ public class ExtJmol extends JalviewJmolBinding
   protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -197,14 +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;
   }