ExactMapping is in pdbchain

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