\r
import jalview.datamodel.*;\r
\r
- import java.util.Vector;\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
};\r
\r
public static final String [] WRITEABLE_FORMATS = new String[]\r
- {\r
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"\r
+ {\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"\r
};\r
\r
\r
* @return DOCUMENT ME!\r
*/\r
public String formatSequences(String format,\r
- Vector seqs,\r
+ AlignmentI alignment,\r
boolean jvsuffix)\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
AlignFile afile = null;\r
{\r
afile = new StockholmFile();\r
}\r
-\r
+ else if (format.equals("AMSA"))\r
+ {\r
+ afile = new AMSAFile(alignment);\r
+ }\r
\r
afile.addJVSuffix(jvsuffix);\r
\r
- afile.setSeqs(s);\r
+ afile.setSeqs( alignment.getSequencesArray() );\r
\r
return afile.print();\r
}\r