X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;fp=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=e88946742aa2b8fbdfc0c47d73ce4cb0f4585ad8;hb=c5a7bc3f03aef928f1b06e5e9ab53d06970aeb12;hp=b48070c5c40d9af5b011e85edd2af98827e6827a;hpb=578c59366e6a562567a37ad03f66f3cd38272306;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b48070c..e889467 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -60,6 +60,7 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class AppletJmol extends EmbmenuFrame implements
@@ -129,7 +130,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  ArrayList _aps = new ArrayList();
+  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+                                                               // added to
 
   String fileLoadingError;
 
@@ -279,7 +281,7 @@ public class AppletJmol extends EmbmenuFrame implements
       dispose();
       return;
     }
-    jmb.newJmolPopup(true, "Jmol", true);
+    // jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -369,7 +371,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector chains)
+  void setChainMenuItems(Vector<String> chains)
   {
     chainMenu.removeAll();
 
@@ -379,10 +381,9 @@ public class AppletJmol extends EmbmenuFrame implements
     chainMenu.add(menuItem);
 
     CheckboxMenuItem menuItemCB;
-    for (int c = 0; c < chains.size(); c++)
+    for (String ch : chains)
     {
-      menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
-              true);
+      menuItemCB = new CheckboxMenuItem(ch, true);
       menuItemCB.addItemListener(this);
       chainMenu.add(menuItemCB);
     }
@@ -392,9 +393,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector toshow = new Vector();
-    String lbl;
-    int mlength, p, mnum;
+    Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -546,7 +545,7 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      jmb.colourBySequence(ap);
     }
     else if (!allChainsSelected)
     {
@@ -575,8 +574,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    AlignmentPanel panel = (AlignmentPanel) source;
+    jmb.colourBySequence(panel);
   }
 
   public void updateTitleAndMenus()
@@ -587,7 +586,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -695,9 +694,9 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     for (int i = 0; i < _aps.size(); i++)
     {
-      if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+      if (_aps.get(i).av.getAlignment() == alignment)
       {
-        return ((AlignmentPanel) _aps.get(i));
+        return (_aps.get(i));
       }
     }
     return ap;