import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.LogarithmicParameter;
import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
import java.io.IOException;
import java.util.ArrayList;
}
if ("hmmbuild".equals(name))
{
-
+ getHMMBuildParams(args);
}
return args;
args.add(new LogarithmicParameter(
MessageManager.getString("label.seq_e_value"),
MessageManager.getString("label.seq_e_value_desc"), false,
- -9.96578, -126d, 3.3219d, 2d));
+ -3d, -37.92977945, 1d, 10d));
/*
args.add(new DoubleParameter(
MessageManager.getString("label.seq_score"),
args.add(new LogarithmicParameter(
MessageManager.getString("label.dom_e_value_desc"),
MessageManager.getString("label.dom_e_value_desc"), false,
- -9.96578, -126d, 3.3219d, 2d));
+ -3d, -37.92977945, 1d, 10d));
/*
args.add(new DoubleParameter(
MessageManager.getString("label.dom_score"),
*/
}
+
private void getHMMAlignParams(List<ArgumentI> args)
{
args.add(new BooleanOption(
false, false, true, null));
}
+ private void getHMMBuildParams(List<ArgumentI> args)
+ {
+ args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
+ MessageManager.getString("label.hmm_name_desc"), true, ""));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_reference"),
+ MessageManager.getString("label.use_reference_desc"), true,
+ true, true, null));
+
+ Collection<String> options = new ArrayList<>();
+ options.add(MessageManager.getString("label.alignment"));
+ options.add(MessageManager.getString("label.groups_and_alignment"));
+ options.add(MessageManager.getString("label.groups"));
+ options.add(MessageManager.getString("label.selected_group"));
+
+ args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+ MessageManager.getString("label.hmmbuild_for_desc"), true,
+ MessageManager.getString("label.alignment"),
+ MessageManager.getString("label.alignment"), options, null));
+ }
+
@Override
public boolean presetExists(String name)
{