+ MessageManager.getString("label.trim_termini_desc"),
+ false, false, def, null));
+ }
+
+ /**
+ * Adds an argument representing the choice of HMM sequences (profiles)
+ * against which to perform align or search, provided at least one is found
+ *
+ * @param args
+ */
+ protected void addChoiceOfHmm(List<ArgumentI> args)
+ {
+ List<SequenceI> hmms = viewport.getAlignment().getHmmSequences();
+ if (!hmms.isEmpty())
+ {
+ List<String> options = new ArrayList<>();
+ for (SequenceI hmmSeq : hmms)
+ {
+ options.add(hmmSeq.getName());
+ }
+ String defseq = options.get(0);
+ ArgumentI arg = new StringParameter(
+ MessageManager.getString("label.use_hmm"), null, true, defseq,
+ defseq, options, null);
+ args.add(arg);
+ }
+ }
+
+ /**
+ * Adds an argument representing the choice of sequence against which to perform
+ * jackhmmer
+ *
+ * @param args
+ */
+ protected void addChoiceOfSequence(List<ArgumentI> args)
+ {
+ List<SequenceI> sequences = viewport.getAlignment().getSequences();
+
+ List<String> options = new ArrayList<>();
+
+ for (SequenceI seq : sequences)
+ {
+ options.add(seq.getName());
+ }
+
+ String defseq = options.get(0);
+ ArgumentI arg = new StringParameter(
+ MessageManager.getString("label.use_sequence"), null, true,
+ defseq,
+ defseq, options, null);
+ args.add(arg);
+ }
+
+ /**
+ * Answers default parameters for hmmbuild, taking into account any configured
+ * as user preferences
+ *
+ * @param args
+ */
+ private void getHMMBuildParams(List<ArgumentI> args)
+ {
+ /*
+ * name to give the computed alignment HMM consensus sequence
+ * (Jalview constructs group HMM consensus sequence names)
+ */
+ String defValue = "Alignment_HMM";
+ StringParameter nameParam = new StringParameter(MessageManager.getString("label.hmm_name"),
+ MessageManager.getString("label.hmm_name_desc"), true, defValue,
+ defValue);
+ args.add(nameParam);
+
+ /*
+ * only enable Use Reference Annotation if RF is present
+ */
+ if (viewport.hasReferenceAnnotation())
+ {
+ args.add(new BooleanOption(
+ MessageManager.getString("label.use_reference"),
+ MessageManager.getString("label.use_reference_desc"), true,
+ true, true, null));
+ }
+
+ /*
+ * choice of whether to compute HMM for alignment and/or group(s)
+ * - only if there are any groups
+ */
+ if (!viewport.getAlignment().getGroups().isEmpty())
+ {
+ List<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));
+ }