Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 66cafc5..71fb2bd 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -19,7 +19,6 @@
 package jalview.gui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
@@ -89,6 +88,8 @@ public class PopupMenu extends JPopupMenu
   JMenuItem sequenceDetails = new JMenuItem();
 
   JMenuItem sequenceSelDetails = new JMenuItem();
+  
+  JMenuItem makeReferenceSeq = new JMenuItem();
 
   SequenceI sequence;
   JMenuItem createGroupMenuItem = new JMenuItem();
@@ -224,6 +225,12 @@ public class PopupMenu extends JPopupMenu
     if (seq != null)
     {
       sequenceMenu.setText(sequence.getName());
+      if (seq == ap.av.getAlignment().getSeqrep())
+      {
+        makeReferenceSeq.setText("Unmark representative");
+      } else {
+        makeReferenceSeq.setText("Mark as representative");
+      }
 
       if (seq.getDatasetSequence().getPDBId() != null
               && seq.getDatasetSequence().getPDBId().size() > 0)
@@ -268,7 +275,6 @@ public class PopupMenu extends JPopupMenu
         }
         // structureMenu.remove(colStructureMenu);
       }
-
       if (ap.av.getAlignment().isNucleotide() == true)
       {
         AlignmentAnnotation[] aa = ap.av.getAlignment()
@@ -321,7 +327,6 @@ public class PopupMenu extends JPopupMenu
             }
           }
         }
-
       }
 
       menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
@@ -1106,7 +1111,17 @@ public class PopupMenu extends JPopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
-
+    makeReferenceSeq.setText("Mark as representative");
+    makeReferenceSeq.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        makeReferenceSeq_actionPerformed(actionEvent);
+        
+      }
+    });
     /*
      * annotationMenuItem.setText("By Annotation");
      * annotationMenuItem.addActionListener(new ActionListener() { public void
@@ -1125,6 +1140,7 @@ public class PopupMenu extends JPopupMenu
     groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
     sequenceMenu.add(sequenceDetails);
+    sequenceMenu.add(makeReferenceSeq);
     colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -1319,6 +1335,29 @@ public class PopupMenu extends JPopupMenu
             });
   }
 
+  protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
+  {
+    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(sequence);
+    }
+    else
+    {
+      if (ap.av.getAlignment().getSeqrep() == sequence)
+      {
+        ap.av.getAlignment().setSeqrep(null);
+      }
+      else
+      {
+        ap.av.getAlignment().setSeqrep(sequence);
+      }
+    }
+    refresh();
+  }
+
   protected void sequenceSelectionDetails_actionPerformed()
   {
     createSequenceDetailsReport(ap.av.getSequenceSelection());