X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2fd17737892ddbaf6fd867838e7aa4923ea4e88b;hb=75d17bc3d8444203906499e651df6a69f6c2f518;hp=1b7351bc37a5ce54c2cb7aec2f2408a4f28896a6;hpb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1b7351b..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;
@@ -403,37 +403,6 @@ public class AlignSeq
         }
     }
 
-    public int [] getExactMapping()
-    {
-        // Print out the matching chars
-        int [] mapping = new int[astr1.length()];
-        int agap=0, bgap=0;
-        boolean gap;
-        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));
-        }
-
-        return mapping;
-    }
-
     /**
      * DOCUMENT ME!
      */