Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 13dcd05..75cb494 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -19,7 +19,6 @@
 package jalview.appletgui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
@@ -117,6 +116,8 @@ 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();
@@ -308,6 +309,12 @@ 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()}));
     }
     else
@@ -474,6 +481,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       editName();
     }
+    else if (source == makeReferenceSeq)
+    {
+      makeReferenceSeq_actionPerformed();
+    }
     else if (source == sequenceDetails)
     {
       showSequenceDetails();
@@ -851,6 +862,7 @@ 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)
@@ -870,6 +882,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     repGroup.addActionListener(this);
     revealAll.addActionListener(this);
     revealSeq.addActionListener(this);
+    makeReferenceSeq.addActionListener(this);
   }
 
   void refresh()
@@ -1059,6 +1072,28 @@ 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()
   {