if (tok.startsWith("format"))
{
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (FileFormatI fmt : FileFormat.values())
{
- if (val.equalsIgnoreCase(fmt))
+ if (fmt.isWritable() && val.equalsIgnoreCase(fmt.toString()))
{
format = fmt;
return true;
}
warnings.append("Invalid alignment format '" + val
+ "'. Must be one of (");
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (FileFormatI fmt : FileFormat.values())
{
- warnings.append(" " + fmt);
+ if (fmt.isWritable())
+ {
+ warnings.append(" " + fmt).toString();
+ }
}
warnings.append(")\n");
}
"Append jalview style /start-end suffix to ID", false, false,
writeAsFile, null));
- lst.add(new Option("format", "Alignment upload format", true, "FASTA",
- format, Arrays
+ lst.add(new Option("format", "Alignment upload format", true,
+ FileFormat.Fasta.toString(),
+ format.toString(), Arrays
.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));