clarified help documentation for annotation file format and tweaked reader code to...

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

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