From caaee4e56aa9e2d6206a1cd19883cd7e58234062 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 18 Apr 2014 10:50:15 +0100
Subject: [PATCH] JAL-1477 first implementation of 'View all representative
 structures' option.

---
 resources/lang/Messages.properties |    1 +
 src/jalview/gui/PopupMenu.java     |   24 ++++++++++++++++++++----
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index ce534e1..329eb8d 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -617,6 +617,7 @@ label.2d_rna_sequence_name = 2D RNA - {0}
 label.edit_name_and_description_current_group = Edit name and description of current group.
 label.view_structure_for = View structure for {0}
 label.view_all_structures = View all {0} structures.
+label.view_all_representative_structures = View all {0} representative structures.
 label.associate_structure_with_sequence = Associate Structure with Sequence
 label.from_file = from file
 label.enter_pdb_id = Enter PDB Id
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0e39f34..66cafc5 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -472,7 +472,7 @@ 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 +480,7 @@ 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 +494,16 @@ 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)})));
         }
         else
         {
-          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
+          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));          
         }
         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
         gpdbview.addActionListener(new ActionListener()
@@ -513,6 +515,20 @@ 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
-- 
1.7.10.2