+ /**
+ * Creates a new Sequence object.
+ *
+ * @param name
+ * DOCUMENT ME!
+ * @param sequence
+ * DOCUMENT ME!
+ */
+ public Sequence(String name, String sequence)
+ {
+ this(name, sequence, 1, -1);
+ }
+
+ /**
+ * Creates a new Sequence object with new AlignmentAnnotations but inherits
+ * any existing dataset sequence reference. If non exists, everything is
+ * copied.
+ *
+ * @param seq
+ * if seq is a dataset sequence, behaves like a plain old copy
+ * constructor
+ */
+ public Sequence(SequenceI seq)
+ {
+ this(seq, seq.getAnnotation());
+ }
+
+ /**
+ * Create a new sequence object with new features, DBRefEntries, and PDBIds
+ * but inherits any existing dataset sequence reference, and duplicate of any
+ * annotation that is present in the given annotation array.
+ *
+ * @param seq
+ * the sequence to be copied
+ * @param alAnnotation
+ * an array of annotation including some associated with seq
+ */
+ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+ {
+ initSeqFrom(seq, alAnnotation);
+
+ }
+
+ /**
+ * does the heavy lifting when cloning a dataset sequence, or coping data from
+ * dataset to a new derived sequence.
+ *
+ * @param seq
+ * - source of attributes.
+ * @param alAnnotation
+ * - alignment annotation present on seq that should be copied onto
+ * this sequence
+ */
+ protected void initSeqFrom(SequenceI seq,
+ AlignmentAnnotation[] alAnnotation)
+ {