X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b860a36a416452c9fbad13661f93327dd8af876f;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=3aed7ec21fd8216a7b3abf71e7f208af61024fef;hpb=b879c4a2d32d3489e63ac06917e81637e6bb4068;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 3aed7ec..b860a36 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -20,6 +20,25 @@
  */
 package jalview.appletgui;
 
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -57,25 +76,6 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-import java.util.Vector;
-
 public class APopupMenu extends java.awt.PopupMenu
         implements ActionListener, ItemListener
 {
@@ -835,8 +835,8 @@ public class APopupMenu extends java.awt.PopupMenu
         if (start <= end)
         {
           seqs.add(sg.getSequenceAt(i));
-          features.add(new SequenceFeature(null, null, start, end,
-                  "Jalview"));
+          features.add(
+                  new SequenceFeature(null, null, start, end, "Jalview"));
         }
       }
 
@@ -900,7 +900,7 @@ public class APopupMenu extends java.awt.PopupMenu
       contents.append(MessageManager
               .formatMessage("label.annotation_for_displayid", new Object[]
               { seq.getDisplayId(true) }));
-      new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+      new SequenceAnnotationReport(false).createSequenceAnnotationReport(
               contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
       contents.append("</p>");
     }
@@ -945,8 +945,8 @@ public class APopupMenu extends java.awt.PopupMenu
       }
       else
       {
-        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
-                DataSourceType.URL);
+        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+                ap, DataSourceType.URL);
       }
 
     }
@@ -1056,7 +1056,7 @@ public class APopupMenu extends java.awt.PopupMenu
     BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
     BLOSUM62Colour.addItemListener(this);
     PIDColour.setLabel(
-            MessageManager.getString("label.colourScheme_%_identity"));
+            MessageManager.getString("label.colourScheme_%identity"));
     PIDColour.setName(JalviewColourScheme.PID.toString());
     PIDColour.addItemListener(this);
     zappoColour
@@ -1072,20 +1072,20 @@ public class APopupMenu extends java.awt.PopupMenu
     hydrophobicityColour
             .setName(JalviewColourScheme.Hydrophobic.toString());
     hydrophobicityColour.addItemListener(this);
-    helixColour.setLabel(MessageManager
-            .getString("label.colourScheme_helix_propensity"));
+    helixColour.setLabel(
+            MessageManager.getString("label.colourScheme_helixpropensity"));
     helixColour.setName(JalviewColourScheme.Helix.toString());
     helixColour.addItemListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.colourScheme_strand_propensity"));
+            .getString("label.colourScheme_strandpropensity"));
     strandColour.setName(JalviewColourScheme.Strand.toString());
     strandColour.addItemListener(this);
     turnColour.setLabel(
-            MessageManager.getString("label.colourScheme_turn_propensity"));
+            MessageManager.getString("label.colourScheme_turnpropensity"));
     turnColour.setName(JalviewColourScheme.Turn.toString());
     turnColour.addItemListener(this);
     buriedColour.setLabel(
-            MessageManager.getString("label.colourScheme_buried_index"));
+            MessageManager.getString("label.colourScheme_buriedindex"));
     buriedColour.setName(JalviewColourScheme.Buried.toString());
     buriedColour.addItemListener(this);
     nucleotideColour.setLabel(