+ * Answers default parameters for jackhmmer, taking into account any configured
+ * as user preferences
+ *
+ * @param args
+ */
+ private void getJackhmmerParams(List<ArgumentI> args)
+ {
+
+ /*
+ * '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));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
+ MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
+ 1000d));
+ }
+
+ /**
+ * Constructs a choice parameter for database to search; always includes 'this
+ * alignment', and also includes any databases held under user preferences key
+ * "HMMSEARCH_DBS" as a comma-delimited list
+ *
+ * @param args
+ */
+ protected void addChoiceOfDatabase(List<ArgumentI> args)
+ {
+ String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+ if (names == null || names.isEmpty())
+ {
+ return;
+ }
+
+ List<String> filePaths = new ArrayList<>();
+ List<String> fileNames = new ArrayList<>();
+
+ String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
+ filePaths.add(thisAlignment);
+ fileNames.add(thisAlignment);
+
+ Scanner nameScanner = new Scanner(names);
+ nameScanner.useDelimiter(Preferences.COMMA);
+
+ while (nameScanner.hasNext())
+ {
+ String next = nameScanner.next();
+ if ("null".equals(next))
+ {
+ Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+ }
+ else
+ {
+ filePaths.add(next);
+ int pos = next.lastIndexOf(File.separator);
+ String fileName = next.substring(pos + 1);
+ fileNames.add(fileName);
+ }
+ }
+ nameScanner.close();
+ ArgumentI databasesOption = new StringParameter(
+ MessageManager.getString(HMMSearch.DATABASE_KEY),
+ MessageManager.getString("label.database_for_hmmsearch"), true,
+ thisAlignment,
+ thisAlignment,
+ filePaths, fileNames);
+ args.add(databasesOption);
+ }
+
+ /**