X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=bd4cc223152a38191ca5fccff936147c4f68744e;hb=bc98852ff1a926cf7b11a92db96ff8fe308ceae0;hp=ba7e520e4be08450e63f262e892dbb8a41cfb007;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index ba7e520..bd4cc22 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -804,19 +804,23 @@ public class AlignSeq
   }
 
   /**
-   * DOCUMENT ME!
+   * Returns the given sequence with all of the given gap characters removed.
    * 
-   * @param gapChar
-   *          DOCUMENT ME!
+   * @param gapChars
+   *          a string of characters to be treated as gaps
    * @param seq
-   *          DOCUMENT ME!
+   *          the input sequence
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  public static String extractGaps(String gapChar, String seq)
+  public static String extractGaps(String gapChars, String seq)
   {
-    StringTokenizer str = new StringTokenizer(seq, gapChar);
-    StringBuffer newString = new StringBuffer();
+    if (gapChars == null || seq == null)
+    {
+      return null;
+    }
+    StringTokenizer str = new StringTokenizer(seq, gapChars);
+    StringBuilder newString = new StringBuilder(seq.length());
 
     while (str.hasMoreTokens())
     {
@@ -1155,7 +1159,8 @@ public class AlignSeq
           }
           if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+            annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+                    Arrays.asList(sq.getAnnotation()));
           }
         }
       }