+ private void getHMMSearchParams(List<ArgumentI> args)
+ {
+ args.add(new IntegerParameter(
+ MessageManager.getString("label.number_of_results"),
+ MessageManager.getString("label.number_of_results_desc"), true,
+ 100, 0, 100000));
+ String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ if (names != null && !names.isEmpty())
+ {
+ Collection<String> databases = new ArrayList<>();
+ databases.add(MessageManager.getString("label.this_alignment"));
+ Scanner nameScanner = new Scanner(names);
+
+ if (nameScanner.hasNext())
+ {
+ while (nameScanner.hasNext())
+ {
+ String next = nameScanner.next();
+ if (next == "null")
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+ }
+ else
+ {
+ databases.add(next);
+ }
+ }
+ }
+ nameScanner.close();
+ args.add(new Option(MessageManager.getString("label.database"),
+ MessageManager.getString("label.database_for_hmmsearch"),
+ true, MessageManager.getString("label.this_alignment"),
+ MessageManager.getString("label.this_alignment"), databases,
+ null));
+ }
+ args.add(new BooleanOption(
+ MessageManager.getString("label.auto_align_seqs"),
+ MessageManager.getString("label.auto_align_seqs_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_accessions"),
+ MessageManager.getString("label.use_accessions_desc"), false,
+ false, true, null));
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), false,
+ false, true, null));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString("label.seq_e_value"),
+ MessageManager.getString("label.seq_e_value_desc"), false,
+ -9.96578, -126d, 3.3219d, 2d));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.seq_score"),
+ MessageManager.getString("label.seq_score_desc"), false,
+ 0d, 0d, 10000d));
+ */
+ 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));
+ /*
+ args.add(new DoubleParameter(
+ MessageManager.getString("label.dom_score"),
+ MessageManager.getString("label.dom_score_desc"), false, 0d,
+ 0d,
+ 10000d));
+ */
+ }
+
+ private void getHMMAlignParams(List<ArgumentI> args)
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString(
+ "label.trim_termini = Trim Non-Matching Termini_desc"),
+ false, false, true, null));
+ }
+