public static final String[] WRITEABLE_FORMATS = new String[]
{
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" , "AMSA"
};
public static String INVALID_CHARACTERS = "Contains invalid characters";
{
afile = new StockholmFile();
}
- else if (format.equals("AMSA"))
+ else if (format.equalsIgnoreCase("AMSA"))
{
afile = new AMSAFile(alignment);
+ } else {
+ throw new Exception("Implementation error: Unknown file format string");
}
afile.addJVSuffix(jvsuffix);