ExactMapping is in pdbchain

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3f3bab1..2fd1773 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -69,8 +69,8 @@ public class AlignSeq
     int maxj;\r
     int[] aseq1;\r
     int[] aseq2;\r
-    String astr1 = "";\r
-    String astr2 = "";\r
+    public String astr1 = "";\r
+    public String astr2 = "";\r
 \r
     /** DOCUMENT ME!! */\r
     public int seq1start;\r
@@ -403,49 +403,6 @@ public class AlignSeq
         }\r
     }\r
 \r
-    public int [] getExactMapping()\r
-    {\r
-        // Print out the matching chars\r
-        int size = s2.getLength();\r
-        int [] mapping = new int[size];\r
-        for(int i=0; i<size; i++)\r
-          mapping[i] = -1;\r
-\r
-        int pdbpos = seq2start-2;\r
-        int alignpos = seq1start-2;\r
-\r
-\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
-\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])+" "+\r
-                               s1.getCharAt(s1.findIndex(mapping[i])-1));\r
-          else\r
-            System.out.println(i+" "+"XX"+s2.getCharAt(i));\r
-        }*/\r
-\r
-        return mapping;\r
-    }\r
-\r
     /**\r
      * DOCUMENT ME!\r
      */\r