package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.BooleanOption;
import jalview.ws.params.simple.Option;
import java.io.PrintWriter;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
super(new Class[] { AlignmentI.class });
}
- String format = "FASTA";
+ FileFormatI format = FileFormat.Fasta;
molType type;
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)));
{
prms.add("jvsuffix");
}
- ;
if (writeAsFile)
{
prms.add("writeasfile");
}
- ;
return prms;
}
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
- .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+ lst.add(new Option("format", "Alignment upload format", true,
+ FileFormat.Fasta.toString(), format.toString(), getWritableFormats(),
null));
lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
return lst;
}
+ /**
+ * @return
+ */
+ protected List<String> getWritableFormats()
+ {
+ List<String> formats = new ArrayList<String>();
+ for (FileFormatI ff : FileFormat.values())
+ {
+ if (ff.isWritable())
+ {
+ formats.add(ff.toString());
+ }
+ }
+ return formats;
+ }
+
}