mc_view references were MCview

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 49219b9..7fda3c4 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -134,7 +134,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+  List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
                                                                // added to
 
   String fileLoadingError;
@@ -213,7 +213,7 @@ public class AppletJmol extends EmbmenuFrame implements
     {
       reader = StructureSelectionManager
               .getStructureSelectionManager(ap.av.applet)
-              .setMapping(seq, chains, pdbentry.getFile(), protocol);
+              .setMapping(seq, chains, pdbentry.getFile(), protocol, null);
       // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
       // FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
@@ -335,7 +335,7 @@ public class AppletJmol extends EmbmenuFrame implements
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
             fp.mark();
-            // reader = new MCview.PDBfile(fp);
+            // reader = new mc_view.PDBfile(fp);
             // could set ID, etc.
             // if (!reader.isValid())
             // {
@@ -394,7 +394,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector<String> toshow = new Vector<String>();
+    Vector<String> toshow = new Vector<>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)