+
+ if (tok.startsWith("format"))
+ {
+ for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ {
+ if (val.equalsIgnoreCase(fmt))
+ {
+ format = fmt;
+ return true;
+ }
+ }
+ warnings.append("Invalid alignment format '" + val
+ + "'. Must be one of (");
+ for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ {
+ warnings.append(" " + fmt);
+ }
+ warnings.append(")\n");
+ }
+ if (tok.startsWith("type"))
+ {
+ try
+ {
+ type = molType.valueOf(val);
+ return true;
+ } catch (Exception x)
+ {
+ warnings.append("Invalid molecule type '" + val
+ + "'. Must be one of (");
+ for (molType v : molType.values())
+ {
+ warnings.append(" " + v);
+ }
+ warnings.append(")\n");
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new BooleanOption("jvsuffix",
+ "Append jalview style /start-end suffix to ID", false, false,
+ jvsuffix, null));
+ lst.add(new BooleanOption("writeasfile",
+ "Append jalview style /start-end suffix to ID", false, false,
+ writeAsFile, null));
+
+ lst.add(new Option("format", "Alignment upload format", true, "FASTA",
+ format, Arrays
+ .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+ null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
+
+ return lst;