From 7e107cbd8d3112584c63396d33a69157f7d1c68d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 23 Apr 2007 11:49:36 +0000
Subject: [PATCH] Test out new arrangement

---
 src/jalview/gui/PopupMenu.java |   59 ++++++++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 45bf5ed..ef87c2f 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -82,6 +82,9 @@ public class PopupMenu
   JMenuItem sequenceFeature = new JMenuItem();
   JMenuItem textColour = new JMenuItem();
   JMenu jMenu1 = new JMenu();
+  JMenu structureMenu = new JMenu();
+  JMenu viewStructureMenu = new JMenu();
+  JMenu colStructureMenu = new JMenu();
 
   /**
    * Creates a new PopupMenu object.
@@ -155,12 +158,11 @@ public class PopupMenu
           final PDBEntry pdb = (PDBEntry) e.nextElement();
 
           menuItem = new JMenuItem();
-          menuItem.setText("View PDB entry: " + pdb.getId());
+          menuItem.setText(pdb.getId());
           menuItem.addActionListener(new java.awt.event.ActionListener()
           {
             public void actionPerformed(ActionEvent e)
             {
-
               Vector seqs = new Vector();
               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
               {
@@ -178,7 +180,6 @@ public class PopupMenu
 
                       continue;
                   }
-
                 }
               }
 
@@ -188,7 +189,18 @@ public class PopupMenu
               new AppJMol(pdb, seqs2, ap);
             }
           });
-          sequenceMenu.add(menuItem);
+          viewStructureMenu.add(menuItem);
+
+          menuItem = new JMenuItem();
+          menuItem.setText(pdb.getId());
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              colourByStructure(pdb.getId());
+            }
+          });
+          colStructureMenu.add(menuItem);
         }
       }
 
@@ -334,7 +346,7 @@ public class PopupMenu
     if (seq == null)
     {
       sequenceMenu.setVisible(false);
-      pdbMenu.setVisible(false);
+      structureMenu.setVisible(false);
     }
 
     if (links != null && links.size() > 0)
@@ -551,15 +563,19 @@ public class PopupMenu
       }
     });
     jMenu1.setText("Group");
+    structureMenu.setText("Structure");
+    viewStructureMenu.setText("View Structure");
+    colStructureMenu.setText("Colour By Structure");
+
     add(groupMenu);
 
     add(sequenceMenu);
+    this.add(structureMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
     groupMenu.add(sequenceFeature);
     groupMenu.add(jMenu1);
     sequenceMenu.add(sequenceName);
-    sequenceMenu.add(pdbMenu);
     colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -613,6 +629,9 @@ public class PopupMenu
     jMenu1.add(showText);
     jMenu1.add(showColourText);
     jMenu1.add(outline);
+    structureMenu.add(pdbMenu);
+    structureMenu.add(viewStructureMenu);
+    structureMenu.add(colStructureMenu);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -1319,8 +1338,13 @@ public class PopupMenu
 
   public void discoverPDB_actionPerformed()
   {
-    new jalview.io.DBRefFetcher(
-        ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+    SequenceI[] sequences =
+         ap.av.selectionGroup == null ?
+           new Sequence[]{sequence}
+         : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
+
+    new jalview.io.DBRefFetcher(sequences,
+        ap.alignFrame).fetchDBRefs(false);
   }
 
   public void sequenceFeature_actionPerformed()
@@ -1360,4 +1384,23 @@ public class PopupMenu
       new TextColourChooser().chooseColour(ap, sg);
     }
   }
+
+  public void colourByStructure(String pdbid)
+  {
+    Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+        .colourSequenceFromStructure(sequence, pdbid);
+
+    AlignmentAnnotation an = new AlignmentAnnotation(
+      "Structure", "Coloured by "+pdbid, anots);
+
+    ap.av.alignment.addAnnotation(an);
+    an.createSequenceMapping(sequence, 0, true);
+    //an.adjustForAlignment();
+    ap.av.alignment.setAnnotationIndex(an,0);
+
+    ap.adjustAnnotationHeight();
+
+    sequence.addAlignmentAnnotation(an);
+
+    }
 }
-- 
1.7.10.2