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 7fc88bc..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();
@@ -965,7 +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);
@@ -1209,10 +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();
     }
@@ -1301,35 +1298,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void hideSequences(boolean representGroup)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null || sg.getSize() < 1)
-    {
-      ap.av.hideSequence(new SequenceI[] { seq });
-      return;
-    }
-
-    ap.av.setSelectionGroup(null);
-
-    if (representGroup)
-    {
-      ap.av.hideRepSequences(seq, sg);
-
-      return;
-    }
-
-    int gsize = sg.getSize();
-    SequenceI[] hseqs;
-
-    hseqs = new SequenceI[gsize];
-
-    int index = 0;
-    for (int i = 0; i < gsize; i++)
-    {
-      hseqs[index++] = sg.getSequenceAt(i);
-    }
-
-    ap.av.hideSequence(hseqs);
-    ap.av.sendSelection();
+    ap.av.hideSequences(seq, representGroup);
   }
 
   /**
@@ -1353,7 +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);