+ * 'Parameters'
+ */
+ addChoiceOfSequence(args);
+
+ // addChoiceOfDatabase(args);
+
+ String thisAlignment = MessageManager
+ .getString(JackHMMER.THIS_ALIGNMENT_KEY);
+ String database = MessageManager.getString("label.database");
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString("action.search"), null,
+ Arrays.asList(thisAlignment, database), thisAlignment));
+ args.add(new FileParameter(database, "", false, "", ""));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
+ Arrays.asList(JackHMMER.CUTOFF_NONE, JackHMMER.CUTOFF_EVALUE,
+ JackHMMER.CUTOFF_SCORE),
+ JackHMMER.CUTOFF_EVALUE));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
+ MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+ 1E-38, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
+ MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+ 1E-38, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
+ MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
+ 1000d));