X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2fd17737892ddbaf6fd867838e7aa4923ea4e88b;hb=436a05e4d6015e30a04bb0234cebd07210137df8;hp=3f3bab166729fadbe2d24a2dac57a79cc8a9ad76;hpb=321d45cdcd1db34cddebdd9ded7c277e84295c1a;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3f3bab1..2fd1773 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;
@@ -403,49 +403,6 @@ public class AlignSeq
         }
     }
 
-    public int [] getExactMapping()
-    {
-        // Print out the matching chars
-        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++)
-        {
-            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;
-    }
-
     /**
      * DOCUMENT ME!
      */