X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=2037ca08160160c1ec35549b6ce0987e0340b0a1;hb=7fadc8dc33be5781fac68507b08a9e387ddb5761;hp=948c8e55f66f92fe254d42a206c9c6849c13ab7d;hpb=048a384fa19ac37fbe2b63bbba139d5fa17107c5;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 948c8e5..2037ca0 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -43,7 +43,6 @@ import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -70,8 +69,6 @@ import java.util.Vector;
 public class APopupMenu extends java.awt.PopupMenu implements
         ActionListener, ItemListener
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   Menu groupMenu = new Menu();
 
   MenuItem editGroupName = new MenuItem();
@@ -895,9 +892,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void addPDB()
   {
-    if (seq.getAllPDBEntries() != null)
+    Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+    if (pdbs != null&& !pdbs.isEmpty())
     {
-      PDBEntry entry = seq.getAllPDBEntries().firstElement();
+      PDBEntry entry = pdbs.firstElement();
 
       if (ap.av.applet.jmolAvailable)
       {
@@ -966,7 +964,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
             "label.represent_group_with", new Object[] { "" }));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
-    menu1.setLabel(MessageManager.getString("label.group") + ":");
+    menu1.setLabel(MessageManager.getString("label.group:"));
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
@@ -1210,10 +1208,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (conservationMenuItem.getState())
     {
 
-      sg.cs.setConservation(Conservation.calculateConservation("Group",
-              ResidueProperties.propHash, 3, sg.getSequences(ap.av
-                      .getHiddenRepSequences()), 0, ap.av.getAlignment()
-                      .getWidth(), false, ap.av.getConsPercGaps(), false));
+      sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
+              sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+                      .getAlignment().getWidth(), false, ap.av
+                      .getConsPercGaps(), false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
@@ -1326,7 +1324,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+    final List<String> all = Arrays.asList(new String[] { MessageManager
+            .getString("label.all") });
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);