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 0e39f34..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
@@ -472,7 +477,7 @@ public class PopupMenu extends JPopupMenu
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),reppdb=new Hashtable<String,PDBEntry>();
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
@@ -480,6 +485,7 @@ public class PopupMenu extends JPopupMenu
                 .getPDBId();
         if (pes != null)
         {
+          reppdb.put(pes.get(0).getId(),pes.get(0));
           for (PDBEntry pe : pes)
           {
             pdbe.put(pe.getId(), pe);
@@ -493,15 +499,16 @@ public class PopupMenu extends JPopupMenu
       if (pdbe.size() > 0)
       {
         final PDBEntry[] pe = pdbe.values().toArray(
-                new PDBEntry[pdbe.size()]);
-        final JMenuItem gpdbview;
+                new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
+                        new PDBEntry[reppdb.size()]);
+        final JMenuItem gpdbview,rpdbview;
         if (pdbe.size() == 1)
         {
           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
         }
         else
         {
-          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
+          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));          \r
         }
         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
         gpdbview.addActionListener(new ActionListener()
@@ -513,6 +520,20 @@ public class PopupMenu extends JPopupMenu
             new AppJmol(ap, pe, ap.av.collateForPDB(pe));
           }
         });
+        if (reppdb.size()>1 && reppdb.size()<pdbe.size())
+        {
+          structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
+          rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+          rpdbview.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+            }
+          });
+        }
       }
     }
     else
@@ -1090,7 +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
@@ -1109,6 +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);
@@ -1303,6 +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());