package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.Option;
PrintWriter pw = new PrintWriter(
new OutputStreamWriter(new BufferedOutputStream(
new FileOutputStream(fa)), "UTF-8"));
- pw.append(new jalview.io.FormatAdapter().formatSequences(format,
+ pw.append(new FormatAdapter().formatSequences(format,
alignment, jvsuffix));
pw.close();
return new FileBody(fa, "text/plain");
}
else
{
- jalview.io.FormatAdapter fa = new jalview.io.FormatAdapter();
+ FormatAdapter fa = new FormatAdapter();
fa.setNewlineString("\r\n");
return new StringBody(
(fa.formatSequences(format, alignment, jvsuffix)));
if (tok.startsWith("format"))
{
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (String fmt : FormatAdapter.WRITEABLE_FORMATS)
{
if (val.equalsIgnoreCase(fmt))
{
}
warnings.append("Invalid alignment format '" + val
+ "'. Must be one of (");
- for (String fmt : jalview.io.FormatAdapter.WRITEABLE_FORMATS)
+ for (String fmt : FormatAdapter.WRITEABLE_FORMATS)
{
warnings.append(" " + fmt);
}
lst.add(new Option("format", "Alignment upload format", true, "FASTA",
format, Arrays
- .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+ .asList(FormatAdapter.WRITEABLE_FORMATS),
null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));