apply version 2.7 copyright

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 3c741f4..643e971 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -36,7 +36,7 @@ public class FormatAdapter extends AppletFormatAdapter
   }
 
   /**
-   * create sequences with each seuqence string replaced with the one given in
+   * create sequences with each sequence string replaced with the one given in
    * omitHiddenCOlumns
    * 
    * @param seqs
@@ -194,9 +194,10 @@ public class FormatAdapter extends AppletFormatAdapter
   {
     if (omitHidden != null)
     {
-      // 
-      Alignment alv = new Alignment(replaceStrings(alignment
-              .getSequencesArray(), omitHidden));
+      // TODO consider using AlignmentView to prune to visible region
+      // TODO prune sequence annotation and groups to visible region
+      Alignment alv = new Alignment(replaceStrings(
+              alignment.getSequencesArray(), omitHidden));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
       if (ala != null)
       {
@@ -205,8 +206,8 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
-                    .getEndRes(), na);
+            colSel.makeVisibleAnnotation(selgp.getStartRes(),
+                    selgp.getEndRes(), na);
           }
           else
           {