From a8b8b22653a1141befc8705517262a4890bdb1f7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 28 Nov 2005 17:14:49 +0000
Subject: [PATCH 1/1] Mapping now performed in PDBChain

---
 src/jalview/analysis/AlignSeq.java |   20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0e6f1bd..6b40e91 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -69,8 +69,8 @@ public class AlignSeq
     int maxj;
     int[] aseq1;
     int[] aseq2;
-    String astr1 = "";
-    String astr2 = "";
+    public String astr1 = "";
+    public String astr2 = "";
 
     /** DOCUMENT ME!! */
     public int seq1start;
@@ -406,15 +406,15 @@ public class AlignSeq
     public int [] getExactMapping()
     {
         // Print out the matching chars
-        int size = s2.getLength();
+        int size = s2.getLength()+1;
         int [] mapping = new int[size];
         for(int i=0; i<size; i++)
           mapping[i] = -1;
 
-        int pdbpos = seq2start-2;
-        int alignpos = seq1start-2;
-
+        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) != '-')
@@ -432,16 +432,18 @@ public class AlignSeq
               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++)
+        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])+" "+
+                               s1.findIndex(mapping[i]+1)+" "+
                                s1.getCharAt(s1.findIndex(mapping[i])));
           else
             System.out.println(i+" "+"XX"+s2.getCharAt(i));
-        }*/
+        }
 
         return mapping;
     }
-- 
1.7.10.2