/** DOCUMENT ME!! */
public static final String[] READABLE_FORMATS = new String[]
{
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile"
};
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";
-
+ // TODO: make these messages dynamic
public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
{
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);