From 321d45cdcd1db34cddebdd9ded7c277e84295c1a Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 25 Nov 2005 16:08:06 +0000
Subject: [PATCH] Correct mapping for pdb file

---
 src/jalview/analysis/AlignSeq.java |   54 ++++++++++++++++++++++--------------
 1 file changed, 33 insertions(+), 21 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1b7351b..3f3bab1 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -406,31 +406,43 @@ public class AlignSeq
     public int [] getExactMapping()
     {
         // Print out the matching chars
-        int [] mapping = new int[astr1.length()];
-        int agap=0, bgap=0;
-        boolean gap;
+        int size = s2.getLength();
+        int [] mapping = new int[size];
+        for(int i=0; i<size; i++)
+          mapping[i] = -1;
+
+        int pdbpos = seq2start-2;
+        int alignpos = seq1start-2;
+
+
         for(int i=0; i<astr1.length(); i++)
         {
-          mapping[i] = -1;
-          gap = false;
-
-          if(astr1.charAt(i)=='-')
-          {
-            agap++;gap = true;
-          }
-          if(astr2.charAt(i)=='-')
-          {
-            bgap++;gap = true;
-          }
-
-          if(!gap && astr1.charAt(i)==astr2.charAt(i))
-          {
-            mapping[i-agap] = i - bgap;
-          }
-
-          System.out.println(astr1.charAt(i)+" "+i + " "+mapping[i-agap]+" "+astr2.charAt(i));
+            if (astr1.charAt(i) != '-')
+            {
+              alignpos++;
+            }
+
+            if (astr2.charAt(i) != '-')
+            {
+              pdbpos++;
+            }
+
+            if (astr1.charAt(i) == astr2.charAt(i))
+            {
+              mapping[pdbpos] = alignpos;
+            }
         }
 
+       /* 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.getCharAt(s1.findIndex(mapping[i])-1));
+          else
+            System.out.println(i+" "+"XX"+s2.getCharAt(i));
+        }*/
+
         return mapping;
     }
 
-- 
1.7.10.2