From 99792d48de35bb2d0e2017871fa44da1c3be38a2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 18 Jul 2006 15:31:51 +0000
Subject: [PATCH] omitHiddenColumns

---
 src/jalview/io/FormatAdapter.java |   28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 0c8554a..84940a8 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -20,8 +20,6 @@ package jalview.io;
 
 import jalview.datamodel.*;
 
-import java.util.Vector;
-
 
 /**
  * DOCUMENT ME!
@@ -31,6 +29,23 @@ import java.util.Vector;
  */
 public class FormatAdapter extends AppletFormatAdapter
 {
+
+    public String formatSequences(String format,
+                                  SequenceI [] seqs,
+                                  String [] omitHiddenColumns)
+    {
+      if(omitHiddenColumns!=null)
+      {
+        for(int i=0; i<seqs.length; i++)
+          seqs [i] = new Sequence(
+              seqs[i].getName(), omitHiddenColumns[i],
+              seqs[i].getStart(), seqs[i].getEnd());
+      }
+
+      return formatSequences(format, seqs);
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -39,12 +54,9 @@ 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 +105,7 @@ public class FormatAdapter extends AppletFormatAdapter
                     jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
             }
 
-            afile.setSeqs(s);
+            afile.setSeqs(seqs);
 
             return afile.print();
         }
-- 
1.7.10.2