From fc188c9e23935ae5cf9008ba173076e1d743ce61 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 14:40:59 +0000
Subject: [PATCH] ColourByStructure not ready yet

---
 .../structure/StructureSelectionManager.java       |   29 ++++++--------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 550fce0..10f99a4 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -184,7 +184,7 @@ public class StructureSelectionManager
 
       if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
         pdbFile = "INLINE"+pdb.id;
-      
+
       mappings[mappings.length - 1]
           = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,
                                  mapping, mappingDetails.toString());
@@ -242,6 +242,7 @@ public class StructureSelectionManager
 
         for (int j = 0; j < mappings.length; j++)
         {
+
           if (mappings[j].pdbfile.equals(pdbfile) &&
               mappings[j].pdbchain.equals(chain))
           {
@@ -286,7 +287,10 @@ public class StructureSelectionManager
 
   public Annotation[] colourSequenceFromStructure(SequenceI seq, String pdbid)
   {
-    Annotation [] annotations = new Annotation[seq.getLength()];
+    return null;
+    //THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
+    //UNTIL THE COLOUR BY ANNOTATION IS REWORKED
+   /* Annotation [] annotations = new Annotation[seq.getLength()];
 
     StructureListener sl;
     int atomNo = 0;
@@ -320,9 +324,6 @@ public class StructureSelectionManager
                                  mappings[j].getPDBResNum(index),
                                  mappings[j].pdbchain,
                                  mappings[j].pdbfile);
-
-            //    System.out.println(atomNo+" "+mappings[j].getPDBResNum(index)
-            //                     +" "+index+" "+col);
               }
 
               annotations[index] = new Annotation("X",null,' ',0,col);
@@ -333,27 +334,15 @@ public class StructureSelectionManager
       }
     }
 
-    return annotations;
+    return annotations;*/
   }
 
 
   public void structureSelectionChanged()
-  {
-    StructureListener svl;
-    for (int i = 0; i < listeners.size(); i++)
-    {
-      svl = (StructureListener) listeners.elementAt(i);
-    }
-  }
+  {  }
 
   public void sequenceSelectionChanged()
-  {
-    StructureListener svl;
-    for (int i = 0; i < listeners.size(); i++)
-    {
-      svl = (StructureListener) listeners.elementAt(i);
-    }
-  }
+  {  }
 
   public void sequenceColoursChanged(Object source)
   {
-- 
1.7.10.2