Watch out for - symbol lin jnet files

[jalview.git] / src / jalview / io / BLCFile.java

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 56d40f9..4a9e777 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -42,15 +42,6 @@ public class BLCFile extends AlignFile
     {\r
     }\r
 \r
-    /**\r
-     * Creates a new BLCFile object.\r
-     *\r
-     * @param inStr DOCUMENT ME!\r
-     */\r
-    public BLCFile(String inStr)\r
-    {\r
-        super(inStr);\r
-    }\r
 \r
     /**\r
      * Creates a new BLCFile object.\r
@@ -197,9 +188,9 @@ public class BLCFile extends AlignFile
         {\r
             out.append(">" + printId(s[i]) +"\n");\r
 \r
-            if (s[i].getSequence().length() > max)\r
+            if (s[i].getSequence().length > max)\r
             {\r
-                max = s[i].getSequence().length();\r
+                max = s[i].getSequence().length;\r
             }\r
 \r
             i++;\r
@@ -213,9 +204,9 @@ public class BLCFile extends AlignFile
 \r
             while ((i < s.length) && (s[i] != null))\r
             {\r
-                if (s[i].getSequence().length() > j)\r
+                if (s[i].getSequence().length > j)\r
                 {\r
-                    out.append(s[i].getSequence().substring(j, j + 1));\r
+                    out.append(s[i].getSequenceAsString(j, j + 1));\r
                 }\r
                 else\r
                 {\r