From bdcab58436069b690cc613f19961d6cda35d6b97 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 7 May 2007 13:56:30 +0000
Subject: [PATCH] Use PDB id for grouping mappings

---
 src/MCview/PDBChain.java |   16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 33944fd..30712f2 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -126,7 +126,7 @@ public class PDBChain
     SequenceFeature[] features = sequence.getSequenceFeatures();
     for (int i = 0; i < features.length; i++)
     {
-      if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE))
+      if (features[i].getFeatureGroup().equals(pdbid))
       {
         SequenceFeature tx = new SequenceFeature(features[i]);
         tx.setBegin(1 +
@@ -235,7 +235,9 @@ public class PDBChain
                               tmpat.resName + ":" + tmpat.resNumIns + " " +
                               pdbid + id,
                               "", offset + count, offset + count,
-                              MCview.PDBChain.PDBFILEFEATURE);
+                              pdbid);
+
+      //MCview.PDBChain.PDBFILEFEATURE);
       resFeatures.addElement(sf);
       resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
@@ -277,7 +279,7 @@ public class PDBChain
         max = annots[i].value;
       resAnnotation.setElementAt(null, i);
     }
-    AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(), 
+    AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(),
             annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
     tfactorann.setSequenceRef(sequence);
     sequence.addAlignmentAnnotation(tfactorann);
@@ -379,9 +381,9 @@ public class PDBChain
   public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, String status)
   {
     AlignmentAnnotation[] transferred = null;
-    
+
     return transferred;
-    
+
   }
 
   /**
@@ -395,7 +397,7 @@ public class PDBChain
     {
       if (sequence!=null && sequence.getAnnotation()!=null)
       {
-        
+
       }
       float min=-1,max=0;
       Annotation[] an=new Annotation[sq.getEnd()-sq.getStart()+1];
@@ -412,7 +414,7 @@ public class PDBChain
           if (min>k)
           {
             min=k;
-          } else 
+          } else
             if (max<k)
             {
               max=k;
-- 
1.7.10.2