Merge branch 'develop' into features/JAL-1723_sequenceReport

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 948c8e5..1544265 100644 (file)
--- 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();
@@ -853,7 +850,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
 
-    StringBuffer contents = new StringBuffer();
+    StringBuilder contents = new StringBuilder(128);
     for (SequenceI seq : sequences)
     {
       contents.append(MessageManager.formatMessage(
@@ -864,7 +861,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
               seq,
               true,
               true,
-              false,
               (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
                       .getMinMax() : null);
       contents.append("</p>");
@@ -966,7 +962,7 @@ 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 +1206,10 @@ 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 +1322,8 @@ 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);