X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=1b2d19a0d9b55f71c848300dcffb2ee8875e19ba;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=aa1ab2177250cd3df74095613c6772ccdaf7fec2;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index aa1ab21..1b2d19a 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -56,6 +56,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.util.List;
 import java.util.Vector;
 
 public class APopupMenu extends java.awt.PopupMenu implements
@@ -113,10 +114,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
 
-  MenuItem copy = new MenuItem(
-          MessageManager.getString("label.jalview_copy"));
+  MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
 
-  MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
+  MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
 
   MenuItem toUpper = new MenuItem(
           MessageManager.getString("label.to_upper_case"));
@@ -152,6 +152,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
   MenuItem selSeqDetails = new MenuItem(
           MessageManager.getString("label.sequence_details") + "...");
 
+  MenuItem makeReferenceSeq = new MenuItem();
+  
   Sequence seq;
 
   MenuItem revealAll = new MenuItem();
@@ -347,6 +349,17 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
+      if (seq == ap.av.getAlignment().getSeqrep())
+      {
+        makeReferenceSeq.setLabel(MessageManager
+                .getString("action.unmark_as_reference"));// Unmark
+                                                          // representative");
+      }
+      else
+      {
+        makeReferenceSeq.setLabel(MessageManager
+                .getString("action.set_as_reference")); // );
+      }
       repGroup.setLabel(MessageManager.formatMessage(
               "label.represent_group_with", new String[]
               { seq.getName() }));
@@ -515,6 +528,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       editName();
     }
+    else if (source == makeReferenceSeq)
+    {
+      makeReferenceSeq_actionPerformed();
+    }
     else if (source == sequenceDetails)
     {
       showSequenceDetails();
@@ -602,10 +619,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else if (source == toUpper || source == toLower || source == toggleCase)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
-      Vector regions = new Vector();
       if (sg != null)
       {
-        int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+        List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
                 sg.getStartRes(), sg.getEndRes() + 1);
 
         String description;
@@ -698,8 +714,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     // TODO consider using getSequenceSelection instead here
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
-            e.getActionCommand(), 
-            ap.av.showJVSuffix, ap.av, true));
+            e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
 
   }
 
@@ -909,6 +924,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     toLower.addActionListener(this);
     editMenu.add(toggleCase);
     seqMenu.add(sequenceName);
+    seqMenu.add(makeReferenceSeq);
     // seqMenu.add(sequenceDetails);
 
     if (!ap.av.applet.useXtrnalSviewer)
@@ -928,6 +944,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     repGroup.addActionListener(this);
     revealAll.addActionListener(this);
     revealSeq.addActionListener(this);
+    makeReferenceSeq.addActionListener(this);
   }
 
   void refresh()
@@ -1005,7 +1022,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
-      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
 
@@ -1013,7 +1030,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else
     // remove PIDColouring
     {
-      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     refresh();
@@ -1117,6 +1134,28 @@ public class APopupMenu extends java.awt.PopupMenu implements
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
+  public void makeReferenceSeq_actionPerformed()
+  {
+    if (!ap.av.getAlignment().hasSeqrep())
+    {
+      // initialise the display flags so the user sees something happen
+      ap.av.setDisplayReferenceSeq(true);
+      ap.av.setColourByReferenceSeq(true);
+      ap.av.getAlignment().setSeqrep(seq);
+    }
+    else
+    {
+      if (ap.av.getAlignment().getSeqrep() == seq)
+      {
+        ap.av.getAlignment().setSeqrep(null);
+      }
+      else
+      {
+        ap.av.getAlignment().setSeqrep(seq);
+      }
+    }
+    refresh();
+  }
 
   public void showNonconserved_itemStateChanged()
   {