+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+ null,
+ Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+ MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+ MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_seq_e_value_desc"),
+ false, 1D,
+ 1E-100, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_dom_e_value_desc"),
+ false, 1D,
+ 1E-100, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+ MessageManager.getString("label.inclusion_seq_score_desc"),
+ false, 0d, 0d,
+ 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+ MessageManager.getString("label.inclusion_dom_score_desc"),
+ false, 0d, 0d,
+ 1000d));
+ }
+
+ /**
+ * 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 database = MessageManager.getString("label.database");
+ args.add(new FileParameter(database, "", false, "", ""));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
+ Arrays.asList(MessageManager.getString(JackHMMER.CUTOFF_NONE),
+ MessageManager.getString(JackHMMER.CUTOFF_EVALUE),
+ MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
+ MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.reporting_seq_e_value_desc"),
+ false, 1D,
+ 1E-38, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
+ MessageManager.getString(
+ "label.reporting_seq_dom_e_value_desc"),
+ false, 1D,
+ 1E-38, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
+ MessageManager.getString("label.reporting_seq_seq_score_desc"),
+ false, 0d, 0d,
+ 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
+ MessageManager.getString("label.reporting_seq_dom_score_desc"),
+ false, 0d, 0d,
+ 1000d));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+ null,
+ Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+ MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+ MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_seq_e_value_desc"),
+ false, 1D, 1E-100, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_dom_e_value_desc"),
+ false, 1D, 1E-100, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+ MessageManager.getString("label.inclusion_seq_score_desc"),
+ false, 0d, 0d, 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+ MessageManager.getString("label.inclusion_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);