X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=a71d6450449f74bd06bb5dbbce7ae687bfc91e39;hb=f7c96b0eada06e354b66a186f272aeb3ff872a90;hp=79a9190a4b997365c522ee8e81e535fbeff2086a;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 79a9190..a71d645 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -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
@@ -194,7 +194,8 @@ public class FormatAdapter extends AppletFormatAdapter
   {
     if (omitHidden != null)
     {
-      //
+      // 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();