Uniprot retrieves features from XML

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1b7351b..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
@@ -403,37 +403,6 @@ public class AlignSeq
         }\r
     }\r
 \r
-    public int [] getExactMapping()\r
-    {\r
-        // Print out the matching chars\r
-        int [] mapping = new int[astr1.length()];\r
-        int agap=0, bgap=0;\r
-        boolean gap;\r
-        for(int i=0; i<astr1.length(); i++)\r
-        {\r
-          mapping[i] = -1;\r
-          gap = false;\r
-\r
-          if(astr1.charAt(i)=='-')\r
-          {\r
-            agap++;gap = true;\r
-          }\r
-          if(astr2.charAt(i)=='-')\r
-          {\r
-            bgap++;gap = true;\r
-          }\r
-\r
-          if(!gap && astr1.charAt(i)==astr2.charAt(i))\r
-          {\r
-            mapping[i-agap] = i - bgap;\r
-          }\r
-\r
-          System.out.println(astr1.charAt(i)+" "+i + " "+mapping[i-agap]+" "+astr2.charAt(i));\r
-        }\r
-\r
-        return mapping;\r
-    }\r
-\r
     /**\r
      * DOCUMENT ME!\r
      */\r