From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 18 Jan 2007 16:46:10 +0000 (+0000)
Subject: 1.1 enabled
X-Git-Tag: Release_2_3~481
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6af1258218f8fdbb2d9d6794e72db4c41ec8bf48;p=jalview.git

1.1 enabled
---

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 75915c1..d5a6a66 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -80,9 +80,10 @@ public class FastaFile extends AlignFile
                     if (annotation)
                     {
                       Annotation[] anots = new Annotation[sb.length()];
+                      String anotString = sb.toString();
                       for (int i = 0; i < sb.length(); i++)
                       {
-                        anots[i] = new Annotation(sb.substring(i, i+1),
+                        anots[i] = new Annotation(anotString.substring(i, i+1),
                                                   null,
                                                   ' ', 0);
                       }
@@ -90,7 +91,7 @@ public class FastaFile extends AlignFile
                           seq.getName().substring(2), seq.getDescription(),
                           anots);
 
-                      annotations.add(aa);
+                      annotations.addElement(aa);
                     }
                     annotation = true;
                   }
@@ -127,9 +128,10 @@ public class FastaFile extends AlignFile
         if (annotation)
         {
           Annotation[] anots = new Annotation[sb.length()];
+          String anotString = sb.toString();
           for (int i = 0; i < sb.length(); i++)
           {
-            anots[i] = new Annotation(sb.substring(i, i + 1),
+            anots[i] = new Annotation(anotString.substring(i, i + 1),
                                       null,
                                       ' ', 0);
           }
@@ -137,7 +139,7 @@ public class FastaFile extends AlignFile
               seq.getName().substring(2), seq.getDescription(),
               anots);
 
-          annotations.add(aa);
+          annotations.addElement(aa);
         }
 
         else if (!firstLine)