From 436a05e4d6015e30a04bb0234cebd07210137df8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 29 Nov 2005 17:58:40 +0000
Subject: [PATCH] ExactMapping is in pdbchain

---
 src/jalview/analysis/AlignSeq.java |   45 ------------------------------------
 1 file changed, 45 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 6b40e91..2fd1773 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -403,51 +403,6 @@ public class AlignSeq
         }
     }
 
-    public int [] getExactMapping()
-    {
-        // Print out the matching chars
-        int size = s2.getLength()+1;
-        int [] mapping = new int[size];
-        for(int i=0; i<size; i++)
-          mapping[i] = -1;
-
-        int pdbpos = s2.getStart() + seq2start-3;
-        int alignpos = s1.getStart() + seq1start-3;
-
-System.out.println(pdbpos+" "+alignpos);
-        for(int i=0; i<astr1.length(); i++)
-        {
-            if (astr1.charAt(i) != '-')
-            {
-              alignpos++;
-            }
-
-            if (astr2.charAt(i) != '-')
-            {
-              pdbpos++;
-            }
-
-            if (astr1.charAt(i) == astr2.charAt(i))
-            {
-              mapping[pdbpos] = alignpos;
-            }
-        }
-System.out.println(s1.getStart()+" "+s2.getStart()+" "+seq1start+" "+seq2start+"\n"+
-                           s1.getSequence()+"\n"+s2.getSequence()+"\n"+astr1+"\n"+astr2);
-
-        for(int i=0; i<mapping.length; i++)
-        {
-          if(mapping[i]!=-1)
-            System.out.println(i+" "+s2.getCharAt(i) + " " + mapping[i] + " " +
-                               s1.findIndex(mapping[i]+1)+" "+
-                               s1.getCharAt(s1.findIndex(mapping[i])));
-          else
-            System.out.println(i+" "+"XX"+s2.getCharAt(i));
-        }
-
-        return mapping;
-    }
-
     /**
      * DOCUMENT ME!
      */
-- 
1.7.10.2