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 092928f..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
@@ -655,14 +655,14 @@ public class AlignSeq
     public static String extractGaps(String gapChar, String seq)\r
     {\r
         StringTokenizer str = new StringTokenizer(seq, gapChar);\r
-        String newString = new String();\r
+        StringBuffer newString = new StringBuffer();\r
 \r
         while (str.hasMoreTokens())\r
         {\r
-            newString = newString + str.nextToken();\r
+            newString.append( str.nextToken() );\r
         }\r
 \r
-        return newString;\r
+        return newString.toString();\r
     }\r
 \r
     /**\r