X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=a23bbba3b665a4a6685fabef14588b76315d06b4;hb=811f68c1dc1e4c409751b785203ed0a7289529b3;hp=0c8554af6ece5dc20c7aa59d3fdf9254fcc7b9be;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0c8554a..a23bbba 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -20,8 +20,6 @@ package jalview.io;
 
 import jalview.datamodel.*;
 
-import java.util.Vector;
-
 
 /**
  * DOCUMENT ME!
@@ -31,6 +29,26 @@ import java.util.Vector;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
+
+    public String formatSequences(String format,
+                                  SequenceI [] seqs,
+                                  String [] omitHiddenColumns)
+    {
+      if(omitHiddenColumns!=null)
+      {
+        SequenceI [] tmp = new SequenceI[seqs.length];
+        for(int i=0; i<seqs.length; i++)
+          tmp [i] = new Sequence(
+              seqs[i].getName(), omitHiddenColumns[i],
+              seqs[i].getStart(), seqs[i].getEnd());
+
+        seqs = tmp;
+      }
+
+      return formatSequences(format, seqs);
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -39,12 +57,9 @@ public class FormatAdapter extends AppletFormatAdapter
      *
      * @return DOCUMENT ME!
      */
-    public String formatSequences(String format, Vector seqs)
+    public String formatSequences(String format,
+                                  SequenceI [] seqs)
     {
-        SequenceI[] s = new SequenceI[seqs.size()];
-
-        for (int i = 0; i < seqs.size(); i++)
-            s[i] = (SequenceI) seqs.elementAt(i);
 
         try
         {
@@ -93,7 +108,7 @@ public class FormatAdapter extends AppletFormatAdapter
                     jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
             }
 
-            afile.setSeqs(s);
+            afile.setSeqs(seqs);
 
             return afile.print();
         }