+ return printId(seq, true);
+ }
+
+ /**
+ * vector of String[] treeName, newickString pairs
+ */
+ Vector<String[]> newickStrings = null;
+
+ protected void addNewickTree(String treeName, String newickString)
+ {
+ if (newickStrings == null)
+ {
+ newickStrings = new Vector<>();
+ }
+ newickStrings.addElement(new String[] { treeName, newickString });
+ }
+
+ protected int getTreeCount()
+ {
+ return newickStrings == null ? 0 : newickStrings.size();
+ }
+
+ @Override
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
+
+ /**
+ * Used only for hmmer statistics, so should probably be removed at some
+ * point. TODO remove this
+ *
+ * @return
+ */
+ public Vector<AlignmentAnnotation> getAnnotations()
+ {
+ return annotations;