Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 57e2674..f9b3f8e 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -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();
@@ -673,7 +690,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
               features, true, ap))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
-        ap.av.showSequenceFeatures(true);
+        ap.av.setShowSequenceFeatures(true);;
         ap.highlightSearchResults(null);
       }
     }
@@ -732,7 +749,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
                       true,
                       true,
                       false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
                               : null);
       contents.append("</p>");
     }
@@ -909,6 +926,7 @@ 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 +946,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     repGroup.addActionListener(this);
     revealAll.addActionListener(this);
     revealSeq.addActionListener(this);
+    makeReferenceSeq.addActionListener(this);
   }
 
   void refresh()
@@ -1117,6 +1136,28 @@ 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()
   {