/*\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
\r
import jalview.datamodel.*;\r
\r
-import java.util.Vector;\r
-\r
\r
/**\r
* DOCUMENT ME!\r
*/\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
*\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
jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
}\r
\r
- afile.setSeqs(s);\r
+ afile.setSeqs(seqs);\r
\r
return afile.print();\r
}\r